You are viewing a plain text version of this content. The canonical link for it is here.
Posted to users@jena.apache.org by Markus Neumann <mn...@meteomatics.com> on 2018/09/17 08:13:57 UTC

Building a spatial index with jena/fuseki

Hi, 
(sorry for the long post)

I've been struggling with the spatial index for a while now.
I've read https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> and skipped through about every spatial related thread here on the list.
I managed to get an in-memory version up and running at some point following this
https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
and this
https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>

But that was on a small dataset that I uploaded via the web-interface of Fuseki.

Now the story is a bit different. I'm building the database using tdbloader2 and would like to create the spatial index upfront.

java -cp jena-spatial.jar jena.spatialindexer --desc=assembler_file
I could not figure out, how to get this line to work. I have the following possible scenarios:

1. I download the jena-spatial-3.8.0.jar and specify that in the classpath:
$ java -cp jena-spatial-3.8.0.jar jena.spatialindexer --desc=../fuseki-server/run/configuration/mm.ttl 
Error: Could not find or load main class jena.spatialindexer

2. I use the fuseki-server jar:
$ java -cp fuseki-server.jar jena.spatialindexer --desc=./run/configuration/mm.ttl
WARN  Custom SpatialContextFactory lib is not ready in classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
org.apache.jena.dboe.transaction.txn.TransactionException: Not in a transaction

I managed to eliminate the warning about jts by including that in the classpath, but the error remains the same (with full trace):
java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer --desc=./run/configuration/mm.ttl
org.apache.jena.dboe.transaction.txn.TransactionException: Not in a transaction
	at org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
	at org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
	at org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
	at org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
	at org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
	at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
	at org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
	at org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
	at org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
	at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
	at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
	at jena.spatialindexer.exec(spatialindexer.java:110)
	at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
	at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
	at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
	at jena.spatialindexer.main(spatialindexer.java:53)

My configuration is the following:
@prefix :      <http://base/#> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
@prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix fuseki: <http://jena.apache.org/fuseki#> .
@prefix spatial: <http://jena.apache.org/spatial#> .
@prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
@prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
# Spatial
[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .

:service_tdb_all  a                   fuseki:Service ;
        rdfs:label                    "TDB2 mm" ;
        fuseki:dataset                :spatial_dataset ;
        fuseki:name                   "mm" ;
        fuseki:serviceQuery           "query" , "sparql" ;
        fuseki:serviceReadGraphStore  "get" ;
        fuseki:serviceReadWriteGraphStore
                "data" ;
        fuseki:serviceUpdate          "update" ;
        fuseki:serviceUpload          "upload" .

:spatial_dataset a spatial:SpatialDataset ;
    spatial:dataset   :tdb_dataset_readwrite ;
    spatial:index     <#indexLucene> ;
    .

<#indexLucene> a spatial:SpatialIndexLucene ;
    spatial:directory <file:Lucene> ;
    #spatial:directory "mem" ;
    spatial:definition <#definition> ;
    .

<#definition> a spatial:EntityDefinition ;
    spatial:entityField      "uri" ;
    spatial:geoField     "geo" ;
    # custom geo predicates for 1) Latitude/Longitude Format
    spatial:hasSpatialPredicatePairs (
         [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
         ) ;
    # custom geo predicates for 2) Well Known Text (WKT) Literal
    spatial:hasWKTPredicates (geosparql:asWKT) ;
    # custom SpatialContextFactory for 2) Well Known Text (WKT) Literal
    spatial:spatialContextFactory
#         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
	"org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
    .

:tdb_dataset_readwrite
        a              tdb2:DatasetTDB2 ;
        tdb2:location  "/srv/linked_data_store/fuseki-server/run/databases/mm" .

And I've changed the fuseki script to include the jts jar:
FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar

I see no errors or warnings in the server log, when starting with that configuration, the Lucene folder is created and populated with something:
$ ll run/configuration/Lucene/
total 4
-rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
-rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock

But any spatial query does not return any results.
Any help on how to tackle this would be highly appreciated.

Best
Markus Neumann

Re: Building a spatial index with jena/fuseki

Posted by Marco Neumann <ma...@gmail.com>.
Adam--

as per conversation about tdbloader2 with Andy when indexed correctly
with tdb2.tdbloader the spatial predicate pairs are now picked up correctly
during indexing with the patch.

On Wed, Sep 19, 2018 at 11:19 AM Marco Neumann <ma...@gmail.com>
wrote:

>
> again thank you for the quick edit. as discussed I did run a test this
> morning with the new code in place and it still works fine with the tdb
> configuration in place. but once you switch to a tdb2 setup it will pass
> invocation of the spatialindexer (no transaction exception) but does not
> pick up spatial predicate pairs during indexing.
>
> I have noticed that the transaction lock in tdb seems to crash
> out ungracefully (no error report) without releasing the lock . this
> requires me to manually remove the lock to allow access.
>
> On Tue, Sep 18, 2018 at 7:16 PM Marco Neumann <ma...@gmail.com>
> wrote:
>
>> Oh I see Adam, great. yes well in that case the order should not be too
>> tall. I will take a look at it in the morning.
>>
>> On Tue, Sep 18, 2018 at 5:40 PM ajs6f <aj...@apache.org> wrote:
>>
>>> Marco--
>>>
>>> I think I didn't express myself well. I'm not asking you to do any code
>>> updates of any kind-- I'm asking you to take a look at the updates _I've_
>>> made available in that PR, try them out, and see if they fix your problem.
>>> Again, if that seems like a bit too tall an order, that's okay-- we'll find
>>> some other way to confirm this fix. I can set up a duplication of your
>>> problem, but it will take a few days for me to get around to it.
>>>
>>> ajs6f
>>>
>>> > On Sep 18, 2018, at 12:37 PM, Marco Neumann <ma...@gmail.com>
>>> wrote:
>>> >
>>> > I will take a look at it over the weekend, haven't done code updates
>>> to the
>>> > new jena repo. not sure if I can submit changes in my current setup,
>>> but
>>> > am happy to learn about it.
>>> >
>>> > On Tue, Sep 18, 2018 at 4:47 PM ajs6f <aj...@apache.org> wrote:
>>> >
>>> >> Marco--
>>> >>
>>> >> I've got a PR at https://github.com/apache/jena/pull/471. Until we
>>> hear
>>> >> from Andy, could you perhaps try cloning that PR/branch and trying
>>> the new
>>> >> code out? If that is not a reasonable piece of work for you, no
>>> problem,
>>> >> but it would help greatly in validating that we've found and fixed the
>>> >> problem.
>>> >>
>>> >> ajs6f
>>> >>
>>> >>> On Sep 18, 2018, at 4:51 AM, Marco Neumann <ma...@gmail.com>
>>> >> wrote:
>>> >>>
>>> >>> well spotted Adam, I think that nails it. I guess I was lucky with my
>>> >> setup
>>> >>> to avoid this glitch so far. Don't want to anticipates Andy's call
>>> here
>>> >> but
>>> >>> what's your plan? wrap the call into a transaction to fix it? If so
>>> I'd
>>> >>> like to see it as an option in the code to work with tdb2 access
>>> methods
>>> >> if
>>> >>> required in addition the current tdb support.
>>> >>>
>>> >>>
>>> >>> On Mon, Sep 17, 2018 at 3:26 PM ajs6f <aj...@apache.org> wrote:
>>> >>>
>>> >>>> Okay, I think we've got it. Nice debugging, Markus!
>>> >>>>
>>> >>>> If you look at the line of the spatial indexer code that is
>>> throwing an
>>> >>>> exception:
>>> >>>>
>>> >>>>
>>> >>>>
>>> >>
>>> https://github.com/apache/jena/blob/master/jena-spatial/src/main/java/jena/spatialindexer.java#L110
>>> >>>>
>>> >>>> indeed, it does not start a transaction against the dataset before
>>> >>>> starting to read quads to index them. Now, in TDB1 this isn't
>>> >> inherently a
>>> >>>> problem-- it's possible to work against a dataset without
>>> transactions.
>>> >>>> (Although it's generally not a good idea at all.) But IIRC, TDB2
>>> >> requires
>>> >>>> transactions. If that's true (and Andy can verify that for us) then
>>> >> this is
>>> >>>> a bug and we can fix it in a straightforward way.
>>> >>>>
>>> >>>> Andy, can you confirm that diagnosis? If so, I'll open a ticket and
>>> >> write
>>> >>>> a PR to use a Txn method to fix this.
>>> >>>>
>>> >>>> ajs6f
>>> >>>>
>>> >>>>> On Sep 17, 2018, at 10:14 AM, Markus Neumann <
>>> mneumann@meteomatics.com
>>> >>>
>>> >>>> wrote:
>>> >>>>>
>>> >>>>> It seems I made a mess with absolute and relative paths all
>>> together.
>>> >> So
>>> >>>> I created a minimal setup for testing:
>>> >>>>> (I include the file-contents at the bottom)
>>> >>>>>
>>> >>>>> $ export JENA_HOME=/srv/linked_data_store/apache-jena-3.8.0
>>> >>>>> $ export PATH=$PATH:$JENA_HOME/bin
>>> >>>>> $ tdb2.tdbloader
>>> >>>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>>> >>>>
>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
>>> >>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl
>>> >>>>> 13:50:54 INFO  loader               :: Loader = LoaderPhased
>>> >>>>> 13:50:54 INFO  loader               :: Data:
>>> >>>>
>>> >>
>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl:
>>> >>>> 13 mm-loc-mini.ttl 0.06s (Avg: 232)
>>> >>>>> 13:50:54 INFO  loader               :: Data:
>>> >>>>
>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl: 50
>>> >>>> mm-rdf.ttl 0.01s (Avg: 6,250)
>>> >>>>> 13:50:55 INFO  loader               :: Finish - index SPO
>>> >>>>> 13:50:55 INFO  loader               :: Start replay index SPO
>>> >>>>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
>>> >>>> SPO->OSP
>>> >>>>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
>>> >>>> SPO->OSP [63 items, 0.0 seconds]
>>> >>>>> 13:50:55 INFO  loader               :: Finish - index POS
>>> >>>>> 13:50:55 INFO  loader               :: Finish - index OSP
>>> >>>>> $ java -cp
>>> >>>>
>>> >>
>>> /srv/linked_data_store/fuseki-server/fuseki-server.jar:/srv/linked_data_store/apache-jena-3.8.0/lib/*
>>> >>>> jena.spatialindexer
>>> >>>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>>> >>>>> SLF4J: Class path contains multiple SLF4J bindings.
>>> >>>>> SLF4J: Found binding in
>>> >>>>
>>> >>
>>> [jar:file:/srv/linked_data_store/fuseki-server/fuseki-server.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>>> >>>>> SLF4J: Found binding in
>>> >>>>
>>> >>
>>> [jar:file:/srv/linked_data_store/apache-jena-3.8.0/lib/slf4j-log4j12-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>>> >>>>> SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for
>>> an
>>> >>>> explanation.
>>> >>>>> SLF4J: Actual binding is of type
>>> [org.slf4j.impl.Log4jLoggerFactory]
>>> >>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>> >>>> transaction
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>> >>>>>     at
>>> >> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>> >>>>>     at jena.spatialindexer.exec(spatialindexer.java:110)
>>> >>>>>     at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>> >>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>> >>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>> >>>>>     at jena.spatialindexer.main(spatialindexer.java:53)
>>> >>>>>
>>> >>>>> I can get rid of the SLF4J warnings:
>>> >>>>> $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar
>>> >>>> jena.spatialindexer
>>> >>>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>>> >>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>> >>>> transaction
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>> >>>>>     at
>>> >> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>> >>>>>     at
>>> >>>>
>>> >>
>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>> >>>>>     at jena.spatialindexer.exec(spatialindexer.java:110)
>>> >>>>>     at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>> >>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>> >>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>> >>>>>     at jena.spatialindexer.main(spatialindexer.java:53)
>>> >>>>>
>>> >>>>> There is no other java instance running at the time when I run
>>> those
>>> >>>> commands.
>>> >>>>> All paths are fully qualified and double checked. The destination
>>> >>>> directory and the Lucene directory were cleared just before.
>>> >>>>>
>>> >>>>> The server does start and serve the data without errors or
>>> warnings in
>>> >>>> the log, but spatial queries do not work.
>>> >>>>>
>>> >>>>> Does anyone see a reason for the TransactionException?
>>> >>>>> Thanks and best regards
>>> >>>>> Markus
>>> >>>>>
>>> >>>>> Attachments:
>>> >>>>>
>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
>>> >>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>> >>>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>> >>>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
>>> >>>>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
>>> >>>>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
>>> >>>>> @prefix dcterms: <http://purl.org/dc/terms/> .
>>> >>>>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#>
>>> >>>>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
>>> >>>>>
>>> >>>>> <http://rdf.meteomatics.com/mm/>
>>> >>>>>  dcterms:publisher <http://api.meteomatics.com/Imprint.html> ;
>>> >>>>>  dcterms:title "Meteomatics RDF Vocabulary"@en .
>>> >>>>>
>>> >>>>> mm:location a rdf:Property ;
>>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>> >>>>>  rdfs:label "location" ;
>>> >>>>>  dcterms:description "Location of a measurement"@en .
>>> >>>>>
>>> >>>>> mm:elevation a rdf:Property ;
>>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>> >>>>>  rdfs:label "elevation" ;
>>> >>>>>  dcterms:description "Elevation of a location"@en .
>>> >>>>>
>>> >>>>> mm:validdate a rdf:Property ;
>>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>> >>>>>  rdfs:label "validdate" ;
>>> >>>>>  dcterms:description "Temporal information describing when a
>>> >>>> Measurement is/was valid"@en .
>>> >>>>>
>>> >>>>> mm:value a rdf:Property ;
>>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>> >>>>>  rdfs:label "value" ;
>>> >>>>>  dcterms:description "The (observed or predicted) value of a
>>> >>>> Measurement"@en .
>>> >>>>>
>>> >>>>> mm:parameter a rdf:Property ;
>>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>> >>>>>  rdfs:label "parameter" ;
>>> >>>>>  dcterms:description "what was measured"@en .
>>> >>>>>
>>> >>>>> mm:station_name a rdf:Property ;
>>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>> >>>>>  rdfs:label "station_name" ;
>>> >>>>>  dcterms:description "Name of a station"@en .
>>> >>>>>
>>> >>>>> mm:abbreviation a rdf:Property ;
>>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>> >>>>>  rdfs:label "abbreviation" ;
>>> >>>>>  dcterms:description "Abbreviation of a station name"@en .
>>> >>>>>
>>> >>>>> mm:didok_id a rdf:Property ;
>>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>> >>>>>  rdfs:label "didok_id" ;
>>> >>>>>  dcterms:description "didok id of a station"@en .
>>> >>>>>
>>> >>>>> mm:unit_symbol a rdf:Property ;
>>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>> >>>>>  rdfs:label "unit symbol" ;
>>> >>>>>  dcterms:description "unit symbol of a parameter"@en .
>>> >>>>>
>>> >>>>> mm:Measurement a rdf:Class ;
>>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>> >>>>>  rdfs:label "Measurement" ;
>>> >>>>>  dcterms:description "Measurement of a specific weather parameter
>>> at
>>> >>>> specific location at a specific date (both future or past)" .
>>> >>>>>
>>> >>>>> mm:Location a rdf:Class ;
>>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>> >>>>>  rdfs:label "Location" ;
>>> >>>>>  dcterms:description "A Point on the globe where we observe
>>> >>>> weather"@en .
>>> >>>>>
>>> >>>>> mm:Parameter a rdf:Class ;
>>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>> >>>>>  rdfs:label "Parameter" ;
>>> >>>>>  dcterms:description "A parameter describing an observable aspect
>>> of
>>> >>>> the weather"@en .
>>> >>>>>
>>> >>>>>
>>> >>
>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
>>> >>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>> >>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>> >>>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>> >>>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
>>> >>>>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
>>> >>>>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
>>> >>>>> @prefix dcterms: <http://purl.org/dc/terms/> .
>>> >>>>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
>>> >>>>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
>>> >>>>> @prefix mm-measurements: <
>>> http://rdf.meteomatics.com/mm/measurements/>
>>> >> .
>>> >>>>> @prefix mm-locations: <http://rdf.meteomatics.com/mm/locations/> .
>>> >>>>>
>>> >>>>>
>>> >>>>> mm-locations:8500015 a mm:Location ;
>>> >>>>>  a geosparql:Geometry ;
>>> >>>>>  mm:didok_id 8500015 ;
>>> >>>>>  geo:lat 47.54259 ;
>>> >>>>>  geo:long 7.61574 ;
>>> >>>>>  mm:elevation 273 .
>>> >>>>>
>>> >>>>>
>>> >>>>> mm-locations:8504238 a mm:Location ;
>>> >>>>>  a geosparql:Geometry ;
>>> >>>>>  geosparql:asWKT "POINT(6.86466645231
>>> >>>> 47.0840196485)"^^geosparql:wktLiteral ;
>>> >>>>>  mm:didok_id 8504238 ;
>>> >>>>>  geo:lat 47.08402 ;
>>> >>>>>  geo:long 6.86467 ;
>>> >>>>>  mm:elevation 1086 .
>>> >>>>>
>>> >>>>> /srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>>> >>>>> @prefix :      <http://base/#> .
>>> >>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>> >>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>> >>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>>> >>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>> >>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>> >>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>> >>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>> >>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>> >>>>> # Spatial
>>> >>>>> #[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>>> >>>>> #spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>> >>>>> #spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>>> >>>>>
>>> >>>>> :service_tdb_all  a                   fuseki:Service ;
>>> >>>>>      rdfs:label                    "TDB2 mm" ;
>>> >>>>>      fuseki:dataset                :spatial_dataset ;
>>> >>>>>      fuseki:name                   "mm" ;
>>> >>>>>      fuseki:serviceQuery           "query" , "sparql" ;
>>> >>>>>      fuseki:serviceReadGraphStore  "get" ;
>>> >>>>>      fuseki:serviceReadWriteGraphStore
>>> >>>>>              "data" ;
>>> >>>>>      fuseki:serviceUpdate          "update" ;
>>> >>>>>      fuseki:serviceUpload          "upload" .
>>> >>>>>
>>> >>>>> :spatial_dataset a spatial:SpatialDataset ;
>>> >>>>>  spatial:dataset   :tdb_dataset_readwrite ;
>>> >>>>>  spatial:index     <#indexLucene> ;
>>> >>>>>  .
>>> >>>>>
>>> >>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>> >>>>>  spatial:directory <file:Lucene> ;
>>> >>>>>  #spatial:directory "mem" ;
>>> >>>>>  spatial:definition <#definition> ;
>>> >>>>>  .
>>> >>>>>
>>> >>>>> <#definition> a spatial:EntityDefinition ;
>>> >>>>>  spatial:entityField      "uri" ;
>>> >>>>>  spatial:geoField     "geo" ;
>>> >>>>>  # custom geo predicates for 1) Latitude/Longitude Format
>>> >>>>>  spatial:hasSpatialPredicatePairs (
>>> >>>>>       [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>> >>>>>       ) ;
>>> >>>>>  # custom geo predicates for 2) Well Known Text (WKT) Literal
>>> >>>>>  spatial:hasWKTPredicates (geosparql:asWKT) ;
>>> >>>>>  #spatial:spatialContextFactory
>>> >>>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>> >>>>> #
>>>  "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>> >>>>>  .
>>> >>>>>
>>> >>>>> :tdb_dataset_readwrite
>>> >>>>>      a              tdb2:DatasetTDB2 ;
>>> >>>>>      tdb2:location
>>> >>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>> >>>>>
>>> >>>>>
>>> >>>>>> Am 17.09.2018 um 15:15 schrieb ajs6f <aj...@apache.org>:
>>> >>>>>>
>>> >>>>>> I think you might have misunderstood the use of $JENA_HOME, or
>>> perhaps
>>> >>>> the Java classpath. $JENA_HOME, which should generally be an
>>> absolute
>>> >>>> filepath, allows the Jena scripts to find their libraries at
>>> runtime.
>>> >>>> Internally, the scripts use $JENA_HOME to set up the classpaths with
>>> >> which
>>> >>>> to start running Java code. But in this case, you're not using the
>>> >> scripts.
>>> >>>> You're calling a Java class directly, which means you have to give
>>> it
>>> >> all
>>> >>>> the libraries directly, using the classpath flag directly. For
>>> example,
>>> >>>> your second attempt:
>>> >>>>>>
>>> >>>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
>>> >>>> --desc=fuseki-server/run/configuration/mm.ttl
>>> >>>>>> Error: Could not find or load main class
>>> >>>> apache-jena-3.8.0.lib.commons-cli-1.4.jar
>>> >>>>>>
>>> >>>>>> may have failed because whatever directory you are in probably
>>> doesn't
>>> >>>> happen to have a Jena distribution in it called "apache-jena-3.8.0".
>>> >>>> Perhaps try:
>>> >>>>>>
>>> >>>>>> java -cp $JENA_HOME/lib/* jena.spatialindexer
>>> >>>> --desc=fuseki-server/run/configuration/mm.ttl
>>> >>>>>>
>>> >>>>>> Your first example looks like it might be misusing the -cp flag
>>> [1].
>>> >>>> You probably don't want the *.jar, just *, like
>>> >>>>>>
>>> >>>>>> java -cp lib/* jena.spatialindexer
>>> >>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>> >>>>>>
>>> >>>>>> especially if you happen to be using Windows. [2] That might not
>>> be
>>> >> the
>>> >>>> entire story, but you can at least try those invocations and see if
>>> you
>>> >> get
>>> >>>> anything different/better.
>>> >>>>>>
>>> >>>>>> ajs6f
>>> >>>>>>
>>> >>>>>> [1]
>>> >>>>
>>> >>
>>> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
>>> >>>> <
>>> >>>>
>>> >>
>>> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
>>> >>>>>
>>> >>>>>> [2]
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
>>> >>>>>
>>> >>>>>>
>>> >>>>>>
>>> >>>>>>> On Sep 17, 2018, at 7:07 AM, Markus Neumann <
>>> >> mneumann@meteomatics.com
>>> >>>> <ma...@meteomatics.com>> wrote:
>>> >>>>>>>
>>> >>>>>>> Ok, that's exactly what I did here:
>>> >>>>>>> $ java -cp lib/*.jar jena.spatialindexer
>>> >>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>> >>>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>>> >>>>>>>
>>> >>>>>>> Or from outside JENA_HOME:
>>> >>>>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
>>> >>>> --desc=fuseki-server/run/configuration/mm.ttl
>>> >>>>>>> Error: Could not find or load main class
>>> >>>> apache-jena-3.8.0.lib.commons-cli-1.4.jar
>>> >>>>>>>
>>> >>>>>>> Or did I missunderstand something?
>>> >>>>>>>
>>> >>>>>>>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <
>>> >> marco.neumann@gmail.com
>>> >>>>> :
>>> >>>>>>>>
>>> >>>>>>>> don't worry it's a common problem and frequent source of
>>> confusion
>>> >>>> not only
>>> >>>>>>>> with jena but java projects. try to simply inlcude all the jars.
>>> >>>>>>>>
>>> >>>>>>>> I presume you run this on a linux box with OpenJDK 8. correct?
>>> >>>>>>>>
>>> >>>>>>>> now once you have set up jena just add the following
>>> >>>>>>>> {replace_with_your_path}/apache-jena-3.8.0/lib/*
>>> >>>>>>>>
>>> >>>>>>>>
>>> >>>>>>>>
>>> >>>>>>>>
>>> >>>>>>>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <
>>> >>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
>>> >>>> mneumann@meteomatics.com <ma...@meteomatics.com>>>
>>> >>>>>>>> wrote:
>>> >>>>>>>>
>>> >>>>>>>>> This is embarrassing but I don't get it.
>>> >>>>>>>>>
>>> >>>>>>>>> I've configured $JENA_HOME and adjusted the PATH.
>>> >>>>>>>>>
>>> >>>>>>>>> Now what classpath should I include when invoking the indexer?
>>> >>>>>>>>> What I've tried so far:
>>> >>>>>>>>>
>>> >>>>>>>>> $ cd $JENA_HOME
>>> >>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>> >>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>> >>>>>>>>> Error: Could not find or load main class jena.spatialindexer
>>> >>>>>>>>> $ java -cp lib/*.jar jena.spatialindexer
>>> >>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>> >>>>>>>>> Error: Could not find or load main class
>>> lib.commons-cli-1.4.jar
>>> >>>>>>>>>
>>> >>>>>>>>> Thanks for your patience
>>> >>>>>>>>>
>>> >>>>>>>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <
>>> >>>> marco.neumann@gmail.com <ma...@gmail.com>>:
>>> >>>>>>>>>>
>>> >>>>>>>>>> yes correct, this looks good. now include the classpath during
>>> >>>> invocation
>>> >>>>>>>>>> of the spatialindexer
>>> >>>>>>>>>>
>>> >>>>>>>>>> in addition it's always a good idea to properly configure jena
>>> >>>> along your
>>> >>>>>>>>>> java runtime environment settings to avoid jdk / lib conflicts
>>> >>>> during
>>> >>>>>>>>>> execution.
>>> >>>>>>>>>>
>>> >>>>>>>>>> https://jena.apache.org/documentation/tools/index.html <
>>> >>>> https://jena.apache.org/documentation/tools/index.html> <
>>> >>>>>>>>> https://jena.apache.org/documentation/tools/index.html <
>>> >>>> https://jena.apache.org/documentation/tools/index.html> <
>>> >>>> https://jena.apache.org/documentation/tools/index.html <
>>> >>>> https://jena.apache.org/documentation/tools/index.html>>>
>>> >>>>>>>>>>
>>> >>>>>>>>>>
>>> >>>>>>>>>>
>>> >>>>>>>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
>>> >>>>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com>
>>> >> <mailto:
>>> >>>> mneumann@meteomatics.com <ma...@meteomatics.com>>
>>> <mailto:
>>> >>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
>>> >>>> mneumann@meteomatics.com <ma...@meteomatics.com>>>>
>>> >>>>>>>>>> wrote:
>>> >>>>>>>>>>
>>> >>>>>>>>>>> 1.: what do you mean by indexer?
>>> >>>>>>>>>>> Probably my biggest problem is, that I have no clue how to
>>> find
>>> >>>> out,
>>> >>>>>>>>> where
>>> >>>>>>>>>>> the jena.spatialindexer could be located except for asking
>>> here.
>>> >>>>>>>>>>>
>>> >>>>>>>>>>> Here is the content of the apache jena I downloaded:
>>> >>>>>>>>>>> $ ls -lh ../apache-jena-3.8.0/lib
>>> >>>>>>>>>>> total 17M
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 162K Oct 26  2017
>>> collection-0.7.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process  53K Oct 26  2017
>>> >> commons-cli-1.4.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 328K Mar  5  2018
>>> >>>> commons-codec-1.11.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59
>>> >>>> commons-compress-1.17.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process  41K Mar  5  2018
>>> >> commons-csv-1.5.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 210K Mar  5  2018
>>> commons-io-2.6.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 425K Oct 26  2017
>>> >>>> commons-lang3-3.4.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01
>>> >> httpclient-4.5.5.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
>>> >>>>>>>>> httpclient-cache-4.5.5.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01
>>> httpcore-4.4.9.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
>>> >>>>>>>>>>> jackson-annotations-2.9.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01
>>> >>>> jackson-core-2.9.5.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
>>> >>>>>>>>> jackson-databind-2.9.5.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process  17K Oct 26  2017
>>> >>>> jcl-over-slf4j-1.7.25.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03
>>> jena-arq-3.8.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01
>>> >> jena-base-3.8.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07
>>> >> jena-cmds-3.8.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02
>>> >> jena-core-3.8.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05
>>> >>>> jena-dboe-base-3.8.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05
>>> >>>> jena-dboe-index-3.8.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
>>> >>>>>>>>>>> jena-dboe-transaction-3.8.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
>>> >>>>>>>>>>> jena-dboe-trans-data-3.8.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01
>>> jena-iri-3.8.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
>>> >>>>>>>>> jena-rdfconnection-3.8.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
>>> >>>>>>>>> jena-shaded-guava-3.8.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06
>>> >> jena-tdb2-3.8.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04
>>> jena-tdb-3.8.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01
>>> >>>> jsonld-java-0.12.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 232K Mar  5  2018
>>> >> libthrift-0.10.0.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process 479K Oct 26  2017
>>> log4j-1.2.17.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process  41K Oct 26  2017
>>> >> slf4j-api-1.7.25.jar
>>> >>>>>>>>>>> -rw-r--r-- 1 process process  12K Oct 26  2017
>>> >>>> slf4j-log4j12-1.7.25.jar
>>> >>>>>>>>>>>
>>> >>>>>>>>>>> 2.: Turns out, I don't need the jts. after commenting out the
>>> >>>> affected
>>> >>>>>>>>>>> lines, the server still runs fine. (But still without spatial
>>> >>>> index)
>>> >>>>>>>>>>>
>>> >>>>>>>>>>> Best Markus
>>> >>>>>>>>>>>
>>> >>>>>>>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <
>>> >>>> marco.neumann@gmail.com <ma...@gmail.com> <mailto:
>>> >>>> marco.neumann@gmail.com <ma...@gmail.com>>
>>> >>>>>>>>>> :
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> Ok let's take a look at this.
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> 1. please include in the indexer in the classpath. It's
>>> part of
>>> >>>> the
>>> >>>>>>>>>>> current
>>> >>>>>>>>>>>> jena distribution.
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> 2. do you need jts? it's a package that allows you to index
>>> >> multi
>>> >>>> point
>>> >>>>>>>>>>>> geometries. here a sample query would be helpful. If single
>>> >> point
>>> >>>>>>>>>>>> geometries are indexed and used in conjunction with MBR
>>> range
>>> >>>> queries.
>>> >>>>>>>>>>>> there is no need for jts.
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
>>> >>>>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com>
>>> >> <mailto:
>>> >>>> mneumann@meteomatics.com <ma...@meteomatics.com>>
>>> >>>>>>>>>>> <mailto:mneumann@meteomatics.com <mailto:
>>> >> mneumann@meteomatics.com>
>>> >>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>
>>> >>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>
>>> >>>> <mailto:mneumann@meteomatics.com <mailto:mneumann@meteomatics.com
>>> >>>>>
>>> >>>>>>>>>>>> wrote:
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>>> Hi,
>>> >>>>>>>>>>>>> (sorry for the long post)
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> I've been struggling with the spatial index for a while
>>> now.
>>> >>>>>>>>>>>>> I've read
>>> >>>>>>>>>>>
>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
>>> <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>> >>>>>>>>>>>
>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
>>> <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>>>>
>>> <
>>> >>>>>>>>>>>>>
>>> https://jena.apache.org/documentation/query/spatial-query.html
>>> >> <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
>>> <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>> >>>>>>>>>>>
>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
>>> <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>>>>>
>>> and
>>> >>>>>>>>>>>>> skipped through about every spatial related thread here on
>>> the
>>> >>>> list.
>>> >>>>>>>>>>>>> I managed to get an in-memory version up and running at
>>> some
>>> >>>> point
>>> >>>>>>>>>>>>> following this
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>>>
>>> >>>>>>>>> <
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>>>
>>> >>>>>>>>>>
>>> >>>>>>>>>>> <
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>>>
>>> >>>>>>>>> <
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>>>
>>> >>>>>>>>>>
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>>> <
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>>>
>>> >>>>>>>>> <
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>>>
>>> >>>>>>>>>>
>>> >>>>>>>>>>> <
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>>>
>>> >>>>>>>>> <
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>> <
>>> >>>>
>>> >>
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> >>>>>>
>>> >>>>>>>>>>
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>>>>
>>> >>>>>>>>>>>>> and this
>>> >>>>>>>>>>>>>
>>> >>>>
>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
>>> >>>>
>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>> >>>>
>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
>>> >>>>
>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>>
>>> >>>>>>>>> <
>>> >>>>
>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>> >>>>>>>>>>>
>>> >>>>
>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>> >>>>>>>>>>>>>
>>> >>>>
>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> But that was on a small dataset that I uploaded via the
>>> >>>> web-interface
>>> >>>>>>>>> of
>>> >>>>>>>>>>>>> Fuseki.
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> Now the story is a bit different. I'm building the database
>>> >> using
>>> >>>>>>>>>>>>> tdbloader2 and would like to create the spatial index
>>> upfront.
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> java -cp jena-spatial.jar jena.spatialindexer
>>> >>>> --desc=assembler_file
>>> >>>>>>>>>>>>> I could not figure out, how to get this line to work. I
>>> have
>>> >> the
>>> >>>>>>>>>>> following
>>> >>>>>>>>>>>>> possible scenarios:
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that
>>> in
>>> >> the
>>> >>>>>>>>>>> classpath:
>>> >>>>>>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>> >>>>>>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>> >>>>>>>>>>>>> Error: Could not find or load main class
>>> jena.spatialindexer
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> 2. I use the fuseki-server jar:
>>> >>>>>>>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
>>> >>>>>>>>>>>>> --desc=./run/configuration/mm.ttl
>>> >>>>>>>>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
>>> >>>>>>>>>>>>>
>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
>>> >>>>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException:
>>> Not
>>> >>>> in a
>>> >>>>>>>>>>>>> transaction
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> I managed to eliminate the warning about jts by including
>>> that
>>> >>>> in the
>>> >>>>>>>>>>>>> classpath, but the error remains the same (with full
>>> trace):
>>> >>>>>>>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
>>> >>>>>>>>>>>>> --desc=./run/configuration/mm.ttl
>>> >>>>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException:
>>> Not
>>> >>>> in a
>>> >>>>>>>>>>>>> transaction
>>> >>>>>>>>>>>>> at
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>> >>>>>>>>>>>>> at
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>> >>>>>>>>>>>>> at
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>> >>>>>>>>>>>>> at
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>> >>>>>>>>>>>>> at
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>> >>>>>>>>>>>>> at
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>> >>>>>>>>>>>>> at
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>> >>>>>>>>>>>>> at
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>> >>>>>>>>>>>>> at
>>> >>>>>>>>>>>
>>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>> >>>>>>>>>>>>> at
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>> >>>>>>>>>>>>> at
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>> >>>>>>>>>>>>> at
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>> >>>>>>>>>>>>> at
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>> >>>>>>>>>>>>> at
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>
>>> >>>>
>>> >>
>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>> >>>>>>>>>>>>> at jena.spatialindexer.exec(spatialindexer.java:110)
>>> >>>>>>>>>>>>> at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>> >>>>>>>>>>>>> at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>> >>>>>>>>>>>>> at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>> >>>>>>>>>>>>> at jena.spatialindexer.main(spatialindexer.java:53)
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> My configuration is the following:
>>> >>>>>>>>>>>>> @prefix :      <http://base/#> .
>>> >>>>>>>>>>>>> @prefix rdf:   <
>>> http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>> >>>>>>>>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>> >>>>>>>>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#>
>>> .
>>> >>>>>>>>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>> >>>>>>>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>> >>>>>>>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>> >>>>>>>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>> >>>>>>>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#>
>>> .
>>> >>>>>>>>>>>>> # Spatial
>>> >>>>>>>>>>>>> [] ja:loadClass
>>> "org.apache.jena.query.spatial.SpatialQuery" .
>>> >>>>>>>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>> >>>>>>>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf
>>> >> spatial:SpatialIndex .
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> :service_tdb_all  a                   fuseki:Service ;
>>> >>>>>>>>>>>>> rdfs:label                    "TDB2 mm" ;
>>> >>>>>>>>>>>>> fuseki:dataset                :spatial_dataset ;
>>> >>>>>>>>>>>>> fuseki:name                   "mm" ;
>>> >>>>>>>>>>>>> fuseki:serviceQuery           "query" , "sparql" ;
>>> >>>>>>>>>>>>> fuseki:serviceReadGraphStore  "get" ;
>>> >>>>>>>>>>>>> fuseki:serviceReadWriteGraphStore
>>> >>>>>>>>>>>>>         "data" ;
>>> >>>>>>>>>>>>> fuseki:serviceUpdate          "update" ;
>>> >>>>>>>>>>>>> fuseki:serviceUpload          "upload" .
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> :spatial_dataset a spatial:SpatialDataset ;
>>> >>>>>>>>>>>>> spatial:dataset   :tdb_dataset_readwrite ;
>>> >>>>>>>>>>>>> spatial:index     <#indexLucene> ;
>>> >>>>>>>>>>>>> .
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>> >>>>>>>>>>>>> spatial:directory <file:Lucene> ;
>>> >>>>>>>>>>>>> #spatial:directory "mem" ;
>>> >>>>>>>>>>>>> spatial:definition <#definition> ;
>>> >>>>>>>>>>>>> .
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> <#definition> a spatial:EntityDefinition ;
>>> >>>>>>>>>>>>> spatial:entityField      "uri" ;
>>> >>>>>>>>>>>>> spatial:geoField     "geo" ;
>>> >>>>>>>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format
>>> >>>>>>>>>>>>> spatial:hasSpatialPredicatePairs (
>>> >>>>>>>>>>>>>  [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>> >>>>>>>>>>>>>  ) ;
>>> >>>>>>>>>>>>> # custom geo predicates for 2) Well Known Text (WKT)
>>> Literal
>>> >>>>>>>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ;
>>> >>>>>>>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT)
>>> >>>> Literal
>>> >>>>>>>>>>>>> spatial:spatialContextFactory
>>> >>>>>>>>>>>>> #
>>> >>>> "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>
>>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>> >>>>>>>>>>>>> .
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> :tdb_dataset_readwrite
>>> >>>>>>>>>>>>> a              tdb2:DatasetTDB2 ;
>>> >>>>>>>>>>>>> tdb2:location
>>> >>>>>>>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> And I've changed the fuseki script to include the jts jar:
>>> >>>>>>>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> I see no errors or warnings in the server log, when
>>> starting
>>> >>>> with that
>>> >>>>>>>>>>>>> configuration, the Lucene folder is created and populated
>>> with
>>> >>>>>>>>>>> something:
>>> >>>>>>>>>>>>> $ ll run/configuration/Lucene/
>>> >>>>>>>>>>>>> total 4
>>> >>>>>>>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
>>> >>>>>>>>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> But any spatial query does not return any results.
>>> >>>>>>>>>>>>> Any help on how to tackle this would be highly appreciated.
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> Best
>>> >>>>>>>>>>>>> Markus Neumann
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> --
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> ---
>>> >>>>>>>>>>>> Marco Neumann
>>> >>>>>>>>>>>> KONA
>>> >>>>>>>>>>>
>>> >>>>>>>>>>>
>>> >>>>>>>>>>
>>> >>>>>>>>>> --
>>> >>>>>>>>>>
>>> >>>>>>>>>>
>>> >>>>>>>>>> ---
>>> >>>>>>>>>> Marco Neumann
>>> >>>>>>>>>> KONA
>>> >>>>>>>>>
>>> >>>>>>>>>
>>> >>>>>>>>
>>> >>>>>>>> --
>>> >>>>>>>>
>>> >>>>>>>>
>>> >>>>>>>> ---
>>> >>>>>>>> Marco Neumann
>>> >>>>>>>> KONA
>>> >>>>>
>>> >>>>
>>> >>>>
>>> >>>>
>>> >>>
>>> >>> --
>>> >>>
>>> >>>
>>> >>> ---
>>> >>> Marco Neumann
>>> >>> KONA
>>> >>
>>> >>
>>> >>
>>> >
>>> > --
>>> >
>>> >
>>> > ---
>>> > Marco Neumann
>>> > KONA
>>>
>>>
>>>
>>
>> --
>>
>>
>> ---
>> Marco Neumann
>> KONA
>>
>>
>
> --
>
>
> ---
> Marco Neumann
> KONA
>
>

-- 


---
Marco Neumann
KONA

Re: Building a spatial index with jena/fuseki

Posted by Marco Neumann <ma...@gmail.com>.
again thank you for the quick edit. as discussed I did run a test this
morning with the new code in place and it still works fine with the tdb
configuration in place. but once you switch to a tdb2 setup it will pass
invocation of the spatialindexer (no transaction exception) but does not
pick up spatial predicate pairs during indexing.

I have noticed that the transaction lock in tdb seems to crash
out ungracefully (no error report) without releasing the lock . this
requires me to manually remove the lock to allow access.

On Tue, Sep 18, 2018 at 7:16 PM Marco Neumann <ma...@gmail.com>
wrote:

> Oh I see Adam, great. yes well in that case the order should not be too
> tall. I will take a look at it in the morning.
>
> On Tue, Sep 18, 2018 at 5:40 PM ajs6f <aj...@apache.org> wrote:
>
>> Marco--
>>
>> I think I didn't express myself well. I'm not asking you to do any code
>> updates of any kind-- I'm asking you to take a look at the updates _I've_
>> made available in that PR, try them out, and see if they fix your problem.
>> Again, if that seems like a bit too tall an order, that's okay-- we'll find
>> some other way to confirm this fix. I can set up a duplication of your
>> problem, but it will take a few days for me to get around to it.
>>
>> ajs6f
>>
>> > On Sep 18, 2018, at 12:37 PM, Marco Neumann <ma...@gmail.com>
>> wrote:
>> >
>> > I will take a look at it over the weekend, haven't done code updates to
>> the
>> > new jena repo. not sure if I can submit changes in my current setup,
>> but
>> > am happy to learn about it.
>> >
>> > On Tue, Sep 18, 2018 at 4:47 PM ajs6f <aj...@apache.org> wrote:
>> >
>> >> Marco--
>> >>
>> >> I've got a PR at https://github.com/apache/jena/pull/471. Until we
>> hear
>> >> from Andy, could you perhaps try cloning that PR/branch and trying the
>> new
>> >> code out? If that is not a reasonable piece of work for you, no
>> problem,
>> >> but it would help greatly in validating that we've found and fixed the
>> >> problem.
>> >>
>> >> ajs6f
>> >>
>> >>> On Sep 18, 2018, at 4:51 AM, Marco Neumann <ma...@gmail.com>
>> >> wrote:
>> >>>
>> >>> well spotted Adam, I think that nails it. I guess I was lucky with my
>> >> setup
>> >>> to avoid this glitch so far. Don't want to anticipates Andy's call
>> here
>> >> but
>> >>> what's your plan? wrap the call into a transaction to fix it? If so
>> I'd
>> >>> like to see it as an option in the code to work with tdb2 access
>> methods
>> >> if
>> >>> required in addition the current tdb support.
>> >>>
>> >>>
>> >>> On Mon, Sep 17, 2018 at 3:26 PM ajs6f <aj...@apache.org> wrote:
>> >>>
>> >>>> Okay, I think we've got it. Nice debugging, Markus!
>> >>>>
>> >>>> If you look at the line of the spatial indexer code that is throwing
>> an
>> >>>> exception:
>> >>>>
>> >>>>
>> >>>>
>> >>
>> https://github.com/apache/jena/blob/master/jena-spatial/src/main/java/jena/spatialindexer.java#L110
>> >>>>
>> >>>> indeed, it does not start a transaction against the dataset before
>> >>>> starting to read quads to index them. Now, in TDB1 this isn't
>> >> inherently a
>> >>>> problem-- it's possible to work against a dataset without
>> transactions.
>> >>>> (Although it's generally not a good idea at all.) But IIRC, TDB2
>> >> requires
>> >>>> transactions. If that's true (and Andy can verify that for us) then
>> >> this is
>> >>>> a bug and we can fix it in a straightforward way.
>> >>>>
>> >>>> Andy, can you confirm that diagnosis? If so, I'll open a ticket and
>> >> write
>> >>>> a PR to use a Txn method to fix this.
>> >>>>
>> >>>> ajs6f
>> >>>>
>> >>>>> On Sep 17, 2018, at 10:14 AM, Markus Neumann <
>> mneumann@meteomatics.com
>> >>>
>> >>>> wrote:
>> >>>>>
>> >>>>> It seems I made a mess with absolute and relative paths all
>> together.
>> >> So
>> >>>> I created a minimal setup for testing:
>> >>>>> (I include the file-contents at the bottom)
>> >>>>>
>> >>>>> $ export JENA_HOME=/srv/linked_data_store/apache-jena-3.8.0
>> >>>>> $ export PATH=$PATH:$JENA_HOME/bin
>> >>>>> $ tdb2.tdbloader
>> >>>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>> >>>>
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
>> >>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl
>> >>>>> 13:50:54 INFO  loader               :: Loader = LoaderPhased
>> >>>>> 13:50:54 INFO  loader               :: Data:
>> >>>>
>> >>
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl:
>> >>>> 13 mm-loc-mini.ttl 0.06s (Avg: 232)
>> >>>>> 13:50:54 INFO  loader               :: Data:
>> >>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
>> 50
>> >>>> mm-rdf.ttl 0.01s (Avg: 6,250)
>> >>>>> 13:50:55 INFO  loader               :: Finish - index SPO
>> >>>>> 13:50:55 INFO  loader               :: Start replay index SPO
>> >>>>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
>> >>>> SPO->OSP
>> >>>>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
>> >>>> SPO->OSP [63 items, 0.0 seconds]
>> >>>>> 13:50:55 INFO  loader               :: Finish - index POS
>> >>>>> 13:50:55 INFO  loader               :: Finish - index OSP
>> >>>>> $ java -cp
>> >>>>
>> >>
>> /srv/linked_data_store/fuseki-server/fuseki-server.jar:/srv/linked_data_store/apache-jena-3.8.0/lib/*
>> >>>> jena.spatialindexer
>> >>>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>> >>>>> SLF4J: Class path contains multiple SLF4J bindings.
>> >>>>> SLF4J: Found binding in
>> >>>>
>> >>
>> [jar:file:/srv/linked_data_store/fuseki-server/fuseki-server.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>> >>>>> SLF4J: Found binding in
>> >>>>
>> >>
>> [jar:file:/srv/linked_data_store/apache-jena-3.8.0/lib/slf4j-log4j12-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>> >>>>> SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
>> >>>> explanation.
>> >>>>> SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
>> >>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>> >>>> transaction
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>> >>>>>     at
>> >> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>> >>>>>     at jena.spatialindexer.exec(spatialindexer.java:110)
>> >>>>>     at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>> >>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>> >>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>> >>>>>     at jena.spatialindexer.main(spatialindexer.java:53)
>> >>>>>
>> >>>>> I can get rid of the SLF4J warnings:
>> >>>>> $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar
>> >>>> jena.spatialindexer
>> >>>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>> >>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>> >>>> transaction
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>> >>>>>     at
>> >> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>> >>>>>     at
>> >>>>
>> >>
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>> >>>>>     at jena.spatialindexer.exec(spatialindexer.java:110)
>> >>>>>     at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>> >>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>> >>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>> >>>>>     at jena.spatialindexer.main(spatialindexer.java:53)
>> >>>>>
>> >>>>> There is no other java instance running at the time when I run those
>> >>>> commands.
>> >>>>> All paths are fully qualified and double checked. The destination
>> >>>> directory and the Lucene directory were cleared just before.
>> >>>>>
>> >>>>> The server does start and serve the data without errors or warnings
>> in
>> >>>> the log, but spatial queries do not work.
>> >>>>>
>> >>>>> Does anyone see a reason for the TransactionException?
>> >>>>> Thanks and best regards
>> >>>>> Markus
>> >>>>>
>> >>>>> Attachments:
>> >>>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
>> >>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>> >>>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>> >>>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
>> >>>>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
>> >>>>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
>> >>>>> @prefix dcterms: <http://purl.org/dc/terms/> .
>> >>>>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#>
>> >>>>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
>> >>>>>
>> >>>>> <http://rdf.meteomatics.com/mm/>
>> >>>>>  dcterms:publisher <http://api.meteomatics.com/Imprint.html> ;
>> >>>>>  dcterms:title "Meteomatics RDF Vocabulary"@en .
>> >>>>>
>> >>>>> mm:location a rdf:Property ;
>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>> >>>>>  rdfs:label "location" ;
>> >>>>>  dcterms:description "Location of a measurement"@en .
>> >>>>>
>> >>>>> mm:elevation a rdf:Property ;
>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>> >>>>>  rdfs:label "elevation" ;
>> >>>>>  dcterms:description "Elevation of a location"@en .
>> >>>>>
>> >>>>> mm:validdate a rdf:Property ;
>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>> >>>>>  rdfs:label "validdate" ;
>> >>>>>  dcterms:description "Temporal information describing when a
>> >>>> Measurement is/was valid"@en .
>> >>>>>
>> >>>>> mm:value a rdf:Property ;
>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>> >>>>>  rdfs:label "value" ;
>> >>>>>  dcterms:description "The (observed or predicted) value of a
>> >>>> Measurement"@en .
>> >>>>>
>> >>>>> mm:parameter a rdf:Property ;
>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>> >>>>>  rdfs:label "parameter" ;
>> >>>>>  dcterms:description "what was measured"@en .
>> >>>>>
>> >>>>> mm:station_name a rdf:Property ;
>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>> >>>>>  rdfs:label "station_name" ;
>> >>>>>  dcterms:description "Name of a station"@en .
>> >>>>>
>> >>>>> mm:abbreviation a rdf:Property ;
>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>> >>>>>  rdfs:label "abbreviation" ;
>> >>>>>  dcterms:description "Abbreviation of a station name"@en .
>> >>>>>
>> >>>>> mm:didok_id a rdf:Property ;
>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>> >>>>>  rdfs:label "didok_id" ;
>> >>>>>  dcterms:description "didok id of a station"@en .
>> >>>>>
>> >>>>> mm:unit_symbol a rdf:Property ;
>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>> >>>>>  rdfs:label "unit symbol" ;
>> >>>>>  dcterms:description "unit symbol of a parameter"@en .
>> >>>>>
>> >>>>> mm:Measurement a rdf:Class ;
>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>> >>>>>  rdfs:label "Measurement" ;
>> >>>>>  dcterms:description "Measurement of a specific weather parameter at
>> >>>> specific location at a specific date (both future or past)" .
>> >>>>>
>> >>>>> mm:Location a rdf:Class ;
>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>> >>>>>  rdfs:label "Location" ;
>> >>>>>  dcterms:description "A Point on the globe where we observe
>> >>>> weather"@en .
>> >>>>>
>> >>>>> mm:Parameter a rdf:Class ;
>> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>> >>>>>  rdfs:label "Parameter" ;
>> >>>>>  dcterms:description "A parameter describing an observable aspect of
>> >>>> the weather"@en .
>> >>>>>
>> >>>>>
>> >>
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
>> >>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>> >>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>> >>>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>> >>>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
>> >>>>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
>> >>>>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
>> >>>>> @prefix dcterms: <http://purl.org/dc/terms/> .
>> >>>>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
>> >>>>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
>> >>>>> @prefix mm-measurements: <
>> http://rdf.meteomatics.com/mm/measurements/>
>> >> .
>> >>>>> @prefix mm-locations: <http://rdf.meteomatics.com/mm/locations/> .
>> >>>>>
>> >>>>>
>> >>>>> mm-locations:8500015 a mm:Location ;
>> >>>>>  a geosparql:Geometry ;
>> >>>>>  mm:didok_id 8500015 ;
>> >>>>>  geo:lat 47.54259 ;
>> >>>>>  geo:long 7.61574 ;
>> >>>>>  mm:elevation 273 .
>> >>>>>
>> >>>>>
>> >>>>> mm-locations:8504238 a mm:Location ;
>> >>>>>  a geosparql:Geometry ;
>> >>>>>  geosparql:asWKT "POINT(6.86466645231
>> >>>> 47.0840196485)"^^geosparql:wktLiteral ;
>> >>>>>  mm:didok_id 8504238 ;
>> >>>>>  geo:lat 47.08402 ;
>> >>>>>  geo:long 6.86467 ;
>> >>>>>  mm:elevation 1086 .
>> >>>>>
>> >>>>> /srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>> >>>>> @prefix :      <http://base/#> .
>> >>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>> >>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>> >>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>> >>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>> >>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>> >>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>> >>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>> >>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>> >>>>> # Spatial
>> >>>>> #[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>> >>>>> #spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>> >>>>> #spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>> >>>>>
>> >>>>> :service_tdb_all  a                   fuseki:Service ;
>> >>>>>      rdfs:label                    "TDB2 mm" ;
>> >>>>>      fuseki:dataset                :spatial_dataset ;
>> >>>>>      fuseki:name                   "mm" ;
>> >>>>>      fuseki:serviceQuery           "query" , "sparql" ;
>> >>>>>      fuseki:serviceReadGraphStore  "get" ;
>> >>>>>      fuseki:serviceReadWriteGraphStore
>> >>>>>              "data" ;
>> >>>>>      fuseki:serviceUpdate          "update" ;
>> >>>>>      fuseki:serviceUpload          "upload" .
>> >>>>>
>> >>>>> :spatial_dataset a spatial:SpatialDataset ;
>> >>>>>  spatial:dataset   :tdb_dataset_readwrite ;
>> >>>>>  spatial:index     <#indexLucene> ;
>> >>>>>  .
>> >>>>>
>> >>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>> >>>>>  spatial:directory <file:Lucene> ;
>> >>>>>  #spatial:directory "mem" ;
>> >>>>>  spatial:definition <#definition> ;
>> >>>>>  .
>> >>>>>
>> >>>>> <#definition> a spatial:EntityDefinition ;
>> >>>>>  spatial:entityField      "uri" ;
>> >>>>>  spatial:geoField     "geo" ;
>> >>>>>  # custom geo predicates for 1) Latitude/Longitude Format
>> >>>>>  spatial:hasSpatialPredicatePairs (
>> >>>>>       [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>> >>>>>       ) ;
>> >>>>>  # custom geo predicates for 2) Well Known Text (WKT) Literal
>> >>>>>  spatial:hasWKTPredicates (geosparql:asWKT) ;
>> >>>>>  #spatial:spatialContextFactory
>> >>>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>> >>>>> #
>>  "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>> >>>>>  .
>> >>>>>
>> >>>>> :tdb_dataset_readwrite
>> >>>>>      a              tdb2:DatasetTDB2 ;
>> >>>>>      tdb2:location
>> >>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>> >>>>>
>> >>>>>
>> >>>>>> Am 17.09.2018 um 15:15 schrieb ajs6f <aj...@apache.org>:
>> >>>>>>
>> >>>>>> I think you might have misunderstood the use of $JENA_HOME, or
>> perhaps
>> >>>> the Java classpath. $JENA_HOME, which should generally be an absolute
>> >>>> filepath, allows the Jena scripts to find their libraries at runtime.
>> >>>> Internally, the scripts use $JENA_HOME to set up the classpaths with
>> >> which
>> >>>> to start running Java code. But in this case, you're not using the
>> >> scripts.
>> >>>> You're calling a Java class directly, which means you have to give it
>> >> all
>> >>>> the libraries directly, using the classpath flag directly. For
>> example,
>> >>>> your second attempt:
>> >>>>>>
>> >>>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
>> >>>> --desc=fuseki-server/run/configuration/mm.ttl
>> >>>>>> Error: Could not find or load main class
>> >>>> apache-jena-3.8.0.lib.commons-cli-1.4.jar
>> >>>>>>
>> >>>>>> may have failed because whatever directory you are in probably
>> doesn't
>> >>>> happen to have a Jena distribution in it called "apache-jena-3.8.0".
>> >>>> Perhaps try:
>> >>>>>>
>> >>>>>> java -cp $JENA_HOME/lib/* jena.spatialindexer
>> >>>> --desc=fuseki-server/run/configuration/mm.ttl
>> >>>>>>
>> >>>>>> Your first example looks like it might be misusing the -cp flag
>> [1].
>> >>>> You probably don't want the *.jar, just *, like
>> >>>>>>
>> >>>>>> java -cp lib/* jena.spatialindexer
>> >>>> --desc=../fuseki-server/run/configuration/mm.ttl
>> >>>>>>
>> >>>>>> especially if you happen to be using Windows. [2] That might not be
>> >> the
>> >>>> entire story, but you can at least try those invocations and see if
>> you
>> >> get
>> >>>> anything different/better.
>> >>>>>>
>> >>>>>> ajs6f
>> >>>>>>
>> >>>>>> [1]
>> >>>>
>> >>
>> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
>> >>>> <
>> >>>>
>> >>
>> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
>> >>>>>
>> >>>>>> [2]
>> >>>>
>> >>
>> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
>> >>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>>> On Sep 17, 2018, at 7:07 AM, Markus Neumann <
>> >> mneumann@meteomatics.com
>> >>>> <ma...@meteomatics.com>> wrote:
>> >>>>>>>
>> >>>>>>> Ok, that's exactly what I did here:
>> >>>>>>> $ java -cp lib/*.jar jena.spatialindexer
>> >>>> --desc=../fuseki-server/run/configuration/mm.ttl
>> >>>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>> >>>>>>>
>> >>>>>>> Or from outside JENA_HOME:
>> >>>>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
>> >>>> --desc=fuseki-server/run/configuration/mm.ttl
>> >>>>>>> Error: Could not find or load main class
>> >>>> apache-jena-3.8.0.lib.commons-cli-1.4.jar
>> >>>>>>>
>> >>>>>>> Or did I missunderstand something?
>> >>>>>>>
>> >>>>>>>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <
>> >> marco.neumann@gmail.com
>> >>>>> :
>> >>>>>>>>
>> >>>>>>>> don't worry it's a common problem and frequent source of
>> confusion
>> >>>> not only
>> >>>>>>>> with jena but java projects. try to simply inlcude all the jars.
>> >>>>>>>>
>> >>>>>>>> I presume you run this on a linux box with OpenJDK 8. correct?
>> >>>>>>>>
>> >>>>>>>> now once you have set up jena just add the following
>> >>>>>>>> {replace_with_your_path}/apache-jena-3.8.0/lib/*
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <
>> >>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
>> >>>> mneumann@meteomatics.com <ma...@meteomatics.com>>>
>> >>>>>>>> wrote:
>> >>>>>>>>
>> >>>>>>>>> This is embarrassing but I don't get it.
>> >>>>>>>>>
>> >>>>>>>>> I've configured $JENA_HOME and adjusted the PATH.
>> >>>>>>>>>
>> >>>>>>>>> Now what classpath should I include when invoking the indexer?
>> >>>>>>>>> What I've tried so far:
>> >>>>>>>>>
>> >>>>>>>>> $ cd $JENA_HOME
>> >>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>> >>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>> >>>>>>>>> Error: Could not find or load main class jena.spatialindexer
>> >>>>>>>>> $ java -cp lib/*.jar jena.spatialindexer
>> >>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>> >>>>>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>> >>>>>>>>>
>> >>>>>>>>> Thanks for your patience
>> >>>>>>>>>
>> >>>>>>>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <
>> >>>> marco.neumann@gmail.com <ma...@gmail.com>>:
>> >>>>>>>>>>
>> >>>>>>>>>> yes correct, this looks good. now include the classpath during
>> >>>> invocation
>> >>>>>>>>>> of the spatialindexer
>> >>>>>>>>>>
>> >>>>>>>>>> in addition it's always a good idea to properly configure jena
>> >>>> along your
>> >>>>>>>>>> java runtime environment settings to avoid jdk / lib conflicts
>> >>>> during
>> >>>>>>>>>> execution.
>> >>>>>>>>>>
>> >>>>>>>>>> https://jena.apache.org/documentation/tools/index.html <
>> >>>> https://jena.apache.org/documentation/tools/index.html> <
>> >>>>>>>>> https://jena.apache.org/documentation/tools/index.html <
>> >>>> https://jena.apache.org/documentation/tools/index.html> <
>> >>>> https://jena.apache.org/documentation/tools/index.html <
>> >>>> https://jena.apache.org/documentation/tools/index.html>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
>> >>>>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com>
>> >> <mailto:
>> >>>> mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:
>> >>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
>> >>>> mneumann@meteomatics.com <ma...@meteomatics.com>>>>
>> >>>>>>>>>> wrote:
>> >>>>>>>>>>
>> >>>>>>>>>>> 1.: what do you mean by indexer?
>> >>>>>>>>>>> Probably my biggest problem is, that I have no clue how to
>> find
>> >>>> out,
>> >>>>>>>>> where
>> >>>>>>>>>>> the jena.spatialindexer could be located except for asking
>> here.
>> >>>>>>>>>>>
>> >>>>>>>>>>> Here is the content of the apache jena I downloaded:
>> >>>>>>>>>>> $ ls -lh ../apache-jena-3.8.0/lib
>> >>>>>>>>>>> total 17M
>> >>>>>>>>>>> -rw-r--r-- 1 process process 162K Oct 26  2017
>> collection-0.7.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process  53K Oct 26  2017
>> >> commons-cli-1.4.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 328K Mar  5  2018
>> >>>> commons-codec-1.11.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59
>> >>>> commons-compress-1.17.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process  41K Mar  5  2018
>> >> commons-csv-1.5.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 210K Mar  5  2018
>> commons-io-2.6.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 425K Oct 26  2017
>> >>>> commons-lang3-3.4.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01
>> >> httpclient-4.5.5.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
>> >>>>>>>>> httpclient-cache-4.5.5.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01
>> httpcore-4.4.9.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
>> >>>>>>>>>>> jackson-annotations-2.9.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01
>> >>>> jackson-core-2.9.5.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
>> >>>>>>>>> jackson-databind-2.9.5.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process  17K Oct 26  2017
>> >>>> jcl-over-slf4j-1.7.25.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03
>> jena-arq-3.8.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01
>> >> jena-base-3.8.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07
>> >> jena-cmds-3.8.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02
>> >> jena-core-3.8.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05
>> >>>> jena-dboe-base-3.8.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05
>> >>>> jena-dboe-index-3.8.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
>> >>>>>>>>>>> jena-dboe-transaction-3.8.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
>> >>>>>>>>>>> jena-dboe-trans-data-3.8.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01
>> jena-iri-3.8.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
>> >>>>>>>>> jena-rdfconnection-3.8.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
>> >>>>>>>>> jena-shaded-guava-3.8.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06
>> >> jena-tdb2-3.8.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04
>> jena-tdb-3.8.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01
>> >>>> jsonld-java-0.12.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 232K Mar  5  2018
>> >> libthrift-0.10.0.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process 479K Oct 26  2017
>> log4j-1.2.17.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process  41K Oct 26  2017
>> >> slf4j-api-1.7.25.jar
>> >>>>>>>>>>> -rw-r--r-- 1 process process  12K Oct 26  2017
>> >>>> slf4j-log4j12-1.7.25.jar
>> >>>>>>>>>>>
>> >>>>>>>>>>> 2.: Turns out, I don't need the jts. after commenting out the
>> >>>> affected
>> >>>>>>>>>>> lines, the server still runs fine. (But still without spatial
>> >>>> index)
>> >>>>>>>>>>>
>> >>>>>>>>>>> Best Markus
>> >>>>>>>>>>>
>> >>>>>>>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <
>> >>>> marco.neumann@gmail.com <ma...@gmail.com> <mailto:
>> >>>> marco.neumann@gmail.com <ma...@gmail.com>>
>> >>>>>>>>>> :
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> Ok let's take a look at this.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> 1. please include in the indexer in the classpath. It's part
>> of
>> >>>> the
>> >>>>>>>>>>> current
>> >>>>>>>>>>>> jena distribution.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> 2. do you need jts? it's a package that allows you to index
>> >> multi
>> >>>> point
>> >>>>>>>>>>>> geometries. here a sample query would be helpful. If single
>> >> point
>> >>>>>>>>>>>> geometries are indexed and used in conjunction with MBR range
>> >>>> queries.
>> >>>>>>>>>>>> there is no need for jts.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
>> >>>>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com>
>> >> <mailto:
>> >>>> mneumann@meteomatics.com <ma...@meteomatics.com>>
>> >>>>>>>>>>> <mailto:mneumann@meteomatics.com <mailto:
>> >> mneumann@meteomatics.com>
>> >>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>
>> >>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>
>> >>>> <mailto:mneumann@meteomatics.com <mailto:mneumann@meteomatics.com
>> >>>>>
>> >>>>>>>>>>>> wrote:
>> >>>>>>>>>>>>
>> >>>>>>>>>>>>> Hi,
>> >>>>>>>>>>>>> (sorry for the long post)
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> I've been struggling with the spatial index for a while now.
>> >>>>>>>>>>>>> I've read
>> >>>>>>>>>>>
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
>> <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>>> <
>> >>>>>>>>>>>
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
>> <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>>>> <
>> >>>>>>>>>>>>>
>> https://jena.apache.org/documentation/query/spatial-query.html
>> >> <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
>> <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>>> <
>> >>>>>>>>>>>
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
>> <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> >>>> https://jena.apache.org/documentation/query/spatial-query.html>>>>>
>> and
>> >>>>>>>>>>>>> skipped through about every spatial related thread here on
>> the
>> >>>> list.
>> >>>>>>>>>>>>> I managed to get an in-memory version up and running at some
>> >>>> point
>> >>>>>>>>>>>>> following this
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>>>
>> >>>>>>>>> <
>> >>>>>>>>>
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>> <
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>>>
>> >>>>>>>>> <
>> >>>>>>>>>
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>>>
>> >>>>>>>>>>>>> <
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>>>
>> >>>>>>>>> <
>> >>>>>>>>>
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>> <
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>>>
>> >>>>>>>>> <
>> >>>>>>>>>
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>> <
>> >>>>
>> >>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> >>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>>>
>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>> and this
>> >>>>>>>>>>>>>
>> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/
>> <
>> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>> <
>> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/
>> <
>> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/
>> >>
>> >>>>>>>>> <
>> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>> <
>> >>>>>>>>>>>
>> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>> <
>> >>>>>>>>>>>>>
>> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/
>> >
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> But that was on a small dataset that I uploaded via the
>> >>>> web-interface
>> >>>>>>>>> of
>> >>>>>>>>>>>>> Fuseki.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Now the story is a bit different. I'm building the database
>> >> using
>> >>>>>>>>>>>>> tdbloader2 and would like to create the spatial index
>> upfront.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> java -cp jena-spatial.jar jena.spatialindexer
>> >>>> --desc=assembler_file
>> >>>>>>>>>>>>> I could not figure out, how to get this line to work. I have
>> >> the
>> >>>>>>>>>>> following
>> >>>>>>>>>>>>> possible scenarios:
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in
>> >> the
>> >>>>>>>>>>> classpath:
>> >>>>>>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>> >>>>>>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>> >>>>>>>>>>>>> Error: Could not find or load main class jena.spatialindexer
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> 2. I use the fuseki-server jar:
>> >>>>>>>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
>> >>>>>>>>>>>>> --desc=./run/configuration/mm.ttl
>> >>>>>>>>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
>> >>>>>>>>>>>>>
>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
>> >>>>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException:
>> Not
>> >>>> in a
>> >>>>>>>>>>>>> transaction
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> I managed to eliminate the warning about jts by including
>> that
>> >>>> in the
>> >>>>>>>>>>>>> classpath, but the error remains the same (with full trace):
>> >>>>>>>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
>> >>>>>>>>>>>>> --desc=./run/configuration/mm.ttl
>> >>>>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException:
>> Not
>> >>>> in a
>> >>>>>>>>>>>>> transaction
>> >>>>>>>>>>>>> at
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>> >>>>>>>>>>>>> at
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>> >>>>>>>>>>>>> at
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>> >>>>>>>>>>>>> at
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>> >>>>>>>>>>>>> at
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>> >>>>>>>>>>>>> at
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>> >>>>>>>>>>>>> at
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>> >>>>>>>>>>>>> at
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>> >>>>>>>>>>>>> at
>> >>>>>>>>>>>
>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>> >>>>>>>>>>>>> at
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>> >>>>>>>>>>>>> at
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>> >>>>>>>>>>>>> at
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>> >>>>>>>>>>>>> at
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>> >>>>>>>>>>>>> at
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>
>> >>>>
>> >>
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>> >>>>>>>>>>>>> at jena.spatialindexer.exec(spatialindexer.java:110)
>> >>>>>>>>>>>>> at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>> >>>>>>>>>>>>> at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>> >>>>>>>>>>>>> at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>> >>>>>>>>>>>>> at jena.spatialindexer.main(spatialindexer.java:53)
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> My configuration is the following:
>> >>>>>>>>>>>>> @prefix :      <http://base/#> .
>> >>>>>>>>>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
>> .
>> >>>>>>>>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>> >>>>>>>>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#>
>> .
>> >>>>>>>>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>> >>>>>>>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>> >>>>>>>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>> >>>>>>>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>> >>>>>>>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#>
>> .
>> >>>>>>>>>>>>> # Spatial
>> >>>>>>>>>>>>> [] ja:loadClass
>> "org.apache.jena.query.spatial.SpatialQuery" .
>> >>>>>>>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>> >>>>>>>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf
>> >> spatial:SpatialIndex .
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> :service_tdb_all  a                   fuseki:Service ;
>> >>>>>>>>>>>>> rdfs:label                    "TDB2 mm" ;
>> >>>>>>>>>>>>> fuseki:dataset                :spatial_dataset ;
>> >>>>>>>>>>>>> fuseki:name                   "mm" ;
>> >>>>>>>>>>>>> fuseki:serviceQuery           "query" , "sparql" ;
>> >>>>>>>>>>>>> fuseki:serviceReadGraphStore  "get" ;
>> >>>>>>>>>>>>> fuseki:serviceReadWriteGraphStore
>> >>>>>>>>>>>>>         "data" ;
>> >>>>>>>>>>>>> fuseki:serviceUpdate          "update" ;
>> >>>>>>>>>>>>> fuseki:serviceUpload          "upload" .
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> :spatial_dataset a spatial:SpatialDataset ;
>> >>>>>>>>>>>>> spatial:dataset   :tdb_dataset_readwrite ;
>> >>>>>>>>>>>>> spatial:index     <#indexLucene> ;
>> >>>>>>>>>>>>> .
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>> >>>>>>>>>>>>> spatial:directory <file:Lucene> ;
>> >>>>>>>>>>>>> #spatial:directory "mem" ;
>> >>>>>>>>>>>>> spatial:definition <#definition> ;
>> >>>>>>>>>>>>> .
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> <#definition> a spatial:EntityDefinition ;
>> >>>>>>>>>>>>> spatial:entityField      "uri" ;
>> >>>>>>>>>>>>> spatial:geoField     "geo" ;
>> >>>>>>>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format
>> >>>>>>>>>>>>> spatial:hasSpatialPredicatePairs (
>> >>>>>>>>>>>>>  [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>> >>>>>>>>>>>>>  ) ;
>> >>>>>>>>>>>>> # custom geo predicates for 2) Well Known Text (WKT) Literal
>> >>>>>>>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ;
>> >>>>>>>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT)
>> >>>> Literal
>> >>>>>>>>>>>>> spatial:spatialContextFactory
>> >>>>>>>>>>>>> #
>> >>>> "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>> >>>>>>>>>>>>>
>> >>>>>>>>>
>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>> >>>>>>>>>>>>> .
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> :tdb_dataset_readwrite
>> >>>>>>>>>>>>> a              tdb2:DatasetTDB2 ;
>> >>>>>>>>>>>>> tdb2:location
>> >>>>>>>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> And I've changed the fuseki script to include the jts jar:
>> >>>>>>>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> I see no errors or warnings in the server log, when starting
>> >>>> with that
>> >>>>>>>>>>>>> configuration, the Lucene folder is created and populated
>> with
>> >>>>>>>>>>> something:
>> >>>>>>>>>>>>> $ ll run/configuration/Lucene/
>> >>>>>>>>>>>>> total 4
>> >>>>>>>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
>> >>>>>>>>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> But any spatial query does not return any results.
>> >>>>>>>>>>>>> Any help on how to tackle this would be highly appreciated.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Best
>> >>>>>>>>>>>>> Markus Neumann
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> --
>> >>>>>>>>>>>>
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> ---
>> >>>>>>>>>>>> Marco Neumann
>> >>>>>>>>>>>> KONA
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> --
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> ---
>> >>>>>>>>>> Marco Neumann
>> >>>>>>>>>> KONA
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>
>> >>>>>>>> --
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>> ---
>> >>>>>>>> Marco Neumann
>> >>>>>>>> KONA
>> >>>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>
>> >>> --
>> >>>
>> >>>
>> >>> ---
>> >>> Marco Neumann
>> >>> KONA
>> >>
>> >>
>> >>
>> >
>> > --
>> >
>> >
>> > ---
>> > Marco Neumann
>> > KONA
>>
>>
>>
>
> --
>
>
> ---
> Marco Neumann
> KONA
>
>

-- 


---
Marco Neumann
KONA

Re: Building a spatial index with jena/fuseki

Posted by Marco Neumann <ma...@gmail.com>.
Oh I see Adam, great. yes well in that case the order should not be too
tall. I will take a look at it in the morning.

On Tue, Sep 18, 2018 at 5:40 PM ajs6f <aj...@apache.org> wrote:

> Marco--
>
> I think I didn't express myself well. I'm not asking you to do any code
> updates of any kind-- I'm asking you to take a look at the updates _I've_
> made available in that PR, try them out, and see if they fix your problem.
> Again, if that seems like a bit too tall an order, that's okay-- we'll find
> some other way to confirm this fix. I can set up a duplication of your
> problem, but it will take a few days for me to get around to it.
>
> ajs6f
>
> > On Sep 18, 2018, at 12:37 PM, Marco Neumann <ma...@gmail.com>
> wrote:
> >
> > I will take a look at it over the weekend, haven't done code updates to
> the
> > new jena repo. not sure if I can submit changes in my current setup,  but
> > am happy to learn about it.
> >
> > On Tue, Sep 18, 2018 at 4:47 PM ajs6f <aj...@apache.org> wrote:
> >
> >> Marco--
> >>
> >> I've got a PR at https://github.com/apache/jena/pull/471. Until we hear
> >> from Andy, could you perhaps try cloning that PR/branch and trying the
> new
> >> code out? If that is not a reasonable piece of work for you, no problem,
> >> but it would help greatly in validating that we've found and fixed the
> >> problem.
> >>
> >> ajs6f
> >>
> >>> On Sep 18, 2018, at 4:51 AM, Marco Neumann <ma...@gmail.com>
> >> wrote:
> >>>
> >>> well spotted Adam, I think that nails it. I guess I was lucky with my
> >> setup
> >>> to avoid this glitch so far. Don't want to anticipates Andy's call here
> >> but
> >>> what's your plan? wrap the call into a transaction to fix it? If so I'd
> >>> like to see it as an option in the code to work with tdb2 access
> methods
> >> if
> >>> required in addition the current tdb support.
> >>>
> >>>
> >>> On Mon, Sep 17, 2018 at 3:26 PM ajs6f <aj...@apache.org> wrote:
> >>>
> >>>> Okay, I think we've got it. Nice debugging, Markus!
> >>>>
> >>>> If you look at the line of the spatial indexer code that is throwing
> an
> >>>> exception:
> >>>>
> >>>>
> >>>>
> >>
> https://github.com/apache/jena/blob/master/jena-spatial/src/main/java/jena/spatialindexer.java#L110
> >>>>
> >>>> indeed, it does not start a transaction against the dataset before
> >>>> starting to read quads to index them. Now, in TDB1 this isn't
> >> inherently a
> >>>> problem-- it's possible to work against a dataset without
> transactions.
> >>>> (Although it's generally not a good idea at all.) But IIRC, TDB2
> >> requires
> >>>> transactions. If that's true (and Andy can verify that for us) then
> >> this is
> >>>> a bug and we can fix it in a straightforward way.
> >>>>
> >>>> Andy, can you confirm that diagnosis? If so, I'll open a ticket and
> >> write
> >>>> a PR to use a Txn method to fix this.
> >>>>
> >>>> ajs6f
> >>>>
> >>>>> On Sep 17, 2018, at 10:14 AM, Markus Neumann <
> mneumann@meteomatics.com
> >>>
> >>>> wrote:
> >>>>>
> >>>>> It seems I made a mess with absolute and relative paths all together.
> >> So
> >>>> I created a minimal setup for testing:
> >>>>> (I include the file-contents at the bottom)
> >>>>>
> >>>>> $ export JENA_HOME=/srv/linked_data_store/apache-jena-3.8.0
> >>>>> $ export PATH=$PATH:$JENA_HOME/bin
> >>>>> $ tdb2.tdbloader
> >>>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >>>>
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
> >>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl
> >>>>> 13:50:54 INFO  loader               :: Loader = LoaderPhased
> >>>>> 13:50:54 INFO  loader               :: Data:
> >>>>
> >>
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl:
> >>>> 13 mm-loc-mini.ttl 0.06s (Avg: 232)
> >>>>> 13:50:54 INFO  loader               :: Data:
> >>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
> 50
> >>>> mm-rdf.ttl 0.01s (Avg: 6,250)
> >>>>> 13:50:55 INFO  loader               :: Finish - index SPO
> >>>>> 13:50:55 INFO  loader               :: Start replay index SPO
> >>>>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
> >>>> SPO->OSP
> >>>>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
> >>>> SPO->OSP [63 items, 0.0 seconds]
> >>>>> 13:50:55 INFO  loader               :: Finish - index POS
> >>>>> 13:50:55 INFO  loader               :: Finish - index OSP
> >>>>> $ java -cp
> >>>>
> >>
> /srv/linked_data_store/fuseki-server/fuseki-server.jar:/srv/linked_data_store/apache-jena-3.8.0/lib/*
> >>>> jena.spatialindexer
> >>>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >>>>> SLF4J: Class path contains multiple SLF4J bindings.
> >>>>> SLF4J: Found binding in
> >>>>
> >>
> [jar:file:/srv/linked_data_store/fuseki-server/fuseki-server.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> >>>>> SLF4J: Found binding in
> >>>>
> >>
> [jar:file:/srv/linked_data_store/apache-jena-3.8.0/lib/slf4j-log4j12-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> >>>>> SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
> >>>> explanation.
> >>>>> SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
> >>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> >>>> transaction
> >>>>>     at
> >>>>
> >>
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>>>>     at
> >> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>>     at jena.spatialindexer.exec(spatialindexer.java:110)
> >>>>>     at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>>>>     at jena.spatialindexer.main(spatialindexer.java:53)
> >>>>>
> >>>>> I can get rid of the SLF4J warnings:
> >>>>> $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar
> >>>> jena.spatialindexer
> >>>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> >>>> transaction
> >>>>>     at
> >>>>
> >>
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>>>>     at
> >> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>>     at
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>>     at jena.spatialindexer.exec(spatialindexer.java:110)
> >>>>>     at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>>>>     at jena.spatialindexer.main(spatialindexer.java:53)
> >>>>>
> >>>>> There is no other java instance running at the time when I run those
> >>>> commands.
> >>>>> All paths are fully qualified and double checked. The destination
> >>>> directory and the Lucene directory were cleared just before.
> >>>>>
> >>>>> The server does start and serve the data without errors or warnings
> in
> >>>> the log, but spatial queries do not work.
> >>>>>
> >>>>> Does anyone see a reason for the TransactionException?
> >>>>> Thanks and best regards
> >>>>> Markus
> >>>>>
> >>>>> Attachments:
> >>>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
> >>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >>>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> >>>>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
> >>>>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
> >>>>> @prefix dcterms: <http://purl.org/dc/terms/> .
> >>>>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#>
> >>>>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
> >>>>>
> >>>>> <http://rdf.meteomatics.com/mm/>
> >>>>>  dcterms:publisher <http://api.meteomatics.com/Imprint.html> ;
> >>>>>  dcterms:title "Meteomatics RDF Vocabulary"@en .
> >>>>>
> >>>>> mm:location a rdf:Property ;
> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>>  rdfs:label "location" ;
> >>>>>  dcterms:description "Location of a measurement"@en .
> >>>>>
> >>>>> mm:elevation a rdf:Property ;
> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>>  rdfs:label "elevation" ;
> >>>>>  dcterms:description "Elevation of a location"@en .
> >>>>>
> >>>>> mm:validdate a rdf:Property ;
> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>>  rdfs:label "validdate" ;
> >>>>>  dcterms:description "Temporal information describing when a
> >>>> Measurement is/was valid"@en .
> >>>>>
> >>>>> mm:value a rdf:Property ;
> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>>  rdfs:label "value" ;
> >>>>>  dcterms:description "The (observed or predicted) value of a
> >>>> Measurement"@en .
> >>>>>
> >>>>> mm:parameter a rdf:Property ;
> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>>  rdfs:label "parameter" ;
> >>>>>  dcterms:description "what was measured"@en .
> >>>>>
> >>>>> mm:station_name a rdf:Property ;
> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>>  rdfs:label "station_name" ;
> >>>>>  dcterms:description "Name of a station"@en .
> >>>>>
> >>>>> mm:abbreviation a rdf:Property ;
> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>>  rdfs:label "abbreviation" ;
> >>>>>  dcterms:description "Abbreviation of a station name"@en .
> >>>>>
> >>>>> mm:didok_id a rdf:Property ;
> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>>  rdfs:label "didok_id" ;
> >>>>>  dcterms:description "didok id of a station"@en .
> >>>>>
> >>>>> mm:unit_symbol a rdf:Property ;
> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>>  rdfs:label "unit symbol" ;
> >>>>>  dcterms:description "unit symbol of a parameter"@en .
> >>>>>
> >>>>> mm:Measurement a rdf:Class ;
> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>>  rdfs:label "Measurement" ;
> >>>>>  dcterms:description "Measurement of a specific weather parameter at
> >>>> specific location at a specific date (both future or past)" .
> >>>>>
> >>>>> mm:Location a rdf:Class ;
> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>>  rdfs:label "Location" ;
> >>>>>  dcterms:description "A Point on the globe where we observe
> >>>> weather"@en .
> >>>>>
> >>>>> mm:Parameter a rdf:Class ;
> >>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>>  rdfs:label "Parameter" ;
> >>>>>  dcterms:description "A parameter describing an observable aspect of
> >>>> the weather"@en .
> >>>>>
> >>>>>
> >> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
> >>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >>>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >>>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> >>>>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
> >>>>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
> >>>>> @prefix dcterms: <http://purl.org/dc/terms/> .
> >>>>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
> >>>>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
> >>>>> @prefix mm-measurements: <
> http://rdf.meteomatics.com/mm/measurements/>
> >> .
> >>>>> @prefix mm-locations: <http://rdf.meteomatics.com/mm/locations/> .
> >>>>>
> >>>>>
> >>>>> mm-locations:8500015 a mm:Location ;
> >>>>>  a geosparql:Geometry ;
> >>>>>  mm:didok_id 8500015 ;
> >>>>>  geo:lat 47.54259 ;
> >>>>>  geo:long 7.61574 ;
> >>>>>  mm:elevation 273 .
> >>>>>
> >>>>>
> >>>>> mm-locations:8504238 a mm:Location ;
> >>>>>  a geosparql:Geometry ;
> >>>>>  geosparql:asWKT "POINT(6.86466645231
> >>>> 47.0840196485)"^^geosparql:wktLiteral ;
> >>>>>  mm:didok_id 8504238 ;
> >>>>>  geo:lat 47.08402 ;
> >>>>>  geo:long 6.86467 ;
> >>>>>  mm:elevation 1086 .
> >>>>>
> >>>>> /srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >>>>> @prefix :      <http://base/#> .
> >>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> >>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> >>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> >>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
> >>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
> >>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >>>>> # Spatial
> >>>>> #[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
> >>>>> #spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> >>>>> #spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
> >>>>>
> >>>>> :service_tdb_all  a                   fuseki:Service ;
> >>>>>      rdfs:label                    "TDB2 mm" ;
> >>>>>      fuseki:dataset                :spatial_dataset ;
> >>>>>      fuseki:name                   "mm" ;
> >>>>>      fuseki:serviceQuery           "query" , "sparql" ;
> >>>>>      fuseki:serviceReadGraphStore  "get" ;
> >>>>>      fuseki:serviceReadWriteGraphStore
> >>>>>              "data" ;
> >>>>>      fuseki:serviceUpdate          "update" ;
> >>>>>      fuseki:serviceUpload          "upload" .
> >>>>>
> >>>>> :spatial_dataset a spatial:SpatialDataset ;
> >>>>>  spatial:dataset   :tdb_dataset_readwrite ;
> >>>>>  spatial:index     <#indexLucene> ;
> >>>>>  .
> >>>>>
> >>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
> >>>>>  spatial:directory <file:Lucene> ;
> >>>>>  #spatial:directory "mem" ;
> >>>>>  spatial:definition <#definition> ;
> >>>>>  .
> >>>>>
> >>>>> <#definition> a spatial:EntityDefinition ;
> >>>>>  spatial:entityField      "uri" ;
> >>>>>  spatial:geoField     "geo" ;
> >>>>>  # custom geo predicates for 1) Latitude/Longitude Format
> >>>>>  spatial:hasSpatialPredicatePairs (
> >>>>>       [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
> >>>>>       ) ;
> >>>>>  # custom geo predicates for 2) Well Known Text (WKT) Literal
> >>>>>  spatial:hasWKTPredicates (geosparql:asWKT) ;
> >>>>>  #spatial:spatialContextFactory
> >>>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
> >>>>> #
>  "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
> >>>>>  .
> >>>>>
> >>>>> :tdb_dataset_readwrite
> >>>>>      a              tdb2:DatasetTDB2 ;
> >>>>>      tdb2:location
> >>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
> >>>>>
> >>>>>
> >>>>>> Am 17.09.2018 um 15:15 schrieb ajs6f <aj...@apache.org>:
> >>>>>>
> >>>>>> I think you might have misunderstood the use of $JENA_HOME, or
> perhaps
> >>>> the Java classpath. $JENA_HOME, which should generally be an absolute
> >>>> filepath, allows the Jena scripts to find their libraries at runtime.
> >>>> Internally, the scripts use $JENA_HOME to set up the classpaths with
> >> which
> >>>> to start running Java code. But in this case, you're not using the
> >> scripts.
> >>>> You're calling a Java class directly, which means you have to give it
> >> all
> >>>> the libraries directly, using the classpath flag directly. For
> example,
> >>>> your second attempt:
> >>>>>>
> >>>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
> >>>> --desc=fuseki-server/run/configuration/mm.ttl
> >>>>>> Error: Could not find or load main class
> >>>> apache-jena-3.8.0.lib.commons-cli-1.4.jar
> >>>>>>
> >>>>>> may have failed because whatever directory you are in probably
> doesn't
> >>>> happen to have a Jena distribution in it called "apache-jena-3.8.0".
> >>>> Perhaps try:
> >>>>>>
> >>>>>> java -cp $JENA_HOME/lib/* jena.spatialindexer
> >>>> --desc=fuseki-server/run/configuration/mm.ttl
> >>>>>>
> >>>>>> Your first example looks like it might be misusing the -cp flag [1].
> >>>> You probably don't want the *.jar, just *, like
> >>>>>>
> >>>>>> java -cp lib/* jena.spatialindexer
> >>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>>
> >>>>>> especially if you happen to be using Windows. [2] That might not be
> >> the
> >>>> entire story, but you can at least try those invocations and see if
> you
> >> get
> >>>> anything different/better.
> >>>>>>
> >>>>>> ajs6f
> >>>>>>
> >>>>>> [1]
> >>>>
> >>
> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
> >>>> <
> >>>>
> >>
> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
> >>>>>
> >>>>>> [2]
> >>>>
> >>
> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
> >>>>>
> >>>>>>
> >>>>>>
> >>>>>>> On Sep 17, 2018, at 7:07 AM, Markus Neumann <
> >> mneumann@meteomatics.com
> >>>> <ma...@meteomatics.com>> wrote:
> >>>>>>>
> >>>>>>> Ok, that's exactly what I did here:
> >>>>>>> $ java -cp lib/*.jar jena.spatialindexer
> >>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
> >>>>>>>
> >>>>>>> Or from outside JENA_HOME:
> >>>>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
> >>>> --desc=fuseki-server/run/configuration/mm.ttl
> >>>>>>> Error: Could not find or load main class
> >>>> apache-jena-3.8.0.lib.commons-cli-1.4.jar
> >>>>>>>
> >>>>>>> Or did I missunderstand something?
> >>>>>>>
> >>>>>>>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <
> >> marco.neumann@gmail.com
> >>>>> :
> >>>>>>>>
> >>>>>>>> don't worry it's a common problem and frequent source of confusion
> >>>> not only
> >>>>>>>> with jena but java projects. try to simply inlcude all the jars.
> >>>>>>>>
> >>>>>>>> I presume you run this on a linux box with OpenJDK 8. correct?
> >>>>>>>>
> >>>>>>>> now once you have set up jena just add the following
> >>>>>>>> {replace_with_your_path}/apache-jena-3.8.0/lib/*
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <
> >>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
> >>>> mneumann@meteomatics.com <ma...@meteomatics.com>>>
> >>>>>>>> wrote:
> >>>>>>>>
> >>>>>>>>> This is embarrassing but I don't get it.
> >>>>>>>>>
> >>>>>>>>> I've configured $JENA_HOME and adjusted the PATH.
> >>>>>>>>>
> >>>>>>>>> Now what classpath should I include when invoking the indexer?
> >>>>>>>>> What I've tried so far:
> >>>>>>>>>
> >>>>>>>>> $ cd $JENA_HOME
> >>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> >>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>>>>> Error: Could not find or load main class jena.spatialindexer
> >>>>>>>>> $ java -cp lib/*.jar jena.spatialindexer
> >>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
> >>>>>>>>>
> >>>>>>>>> Thanks for your patience
> >>>>>>>>>
> >>>>>>>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <
> >>>> marco.neumann@gmail.com <ma...@gmail.com>>:
> >>>>>>>>>>
> >>>>>>>>>> yes correct, this looks good. now include the classpath during
> >>>> invocation
> >>>>>>>>>> of the spatialindexer
> >>>>>>>>>>
> >>>>>>>>>> in addition it's always a good idea to properly configure jena
> >>>> along your
> >>>>>>>>>> java runtime environment settings to avoid jdk / lib conflicts
> >>>> during
> >>>>>>>>>> execution.
> >>>>>>>>>>
> >>>>>>>>>> https://jena.apache.org/documentation/tools/index.html <
> >>>> https://jena.apache.org/documentation/tools/index.html> <
> >>>>>>>>> https://jena.apache.org/documentation/tools/index.html <
> >>>> https://jena.apache.org/documentation/tools/index.html> <
> >>>> https://jena.apache.org/documentation/tools/index.html <
> >>>> https://jena.apache.org/documentation/tools/index.html>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
> >>>>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com>
> >> <mailto:
> >>>> mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:
> >>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
> >>>> mneumann@meteomatics.com <ma...@meteomatics.com>>>>
> >>>>>>>>>> wrote:
> >>>>>>>>>>
> >>>>>>>>>>> 1.: what do you mean by indexer?
> >>>>>>>>>>> Probably my biggest problem is, that I have no clue how to find
> >>>> out,
> >>>>>>>>> where
> >>>>>>>>>>> the jena.spatialindexer could be located except for asking
> here.
> >>>>>>>>>>>
> >>>>>>>>>>> Here is the content of the apache jena I downloaded:
> >>>>>>>>>>> $ ls -lh ../apache-jena-3.8.0/lib
> >>>>>>>>>>> total 17M
> >>>>>>>>>>> -rw-r--r-- 1 process process 162K Oct 26  2017
> collection-0.7.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process  53K Oct 26  2017
> >> commons-cli-1.4.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 328K Mar  5  2018
> >>>> commons-codec-1.11.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59
> >>>> commons-compress-1.17.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process  41K Mar  5  2018
> >> commons-csv-1.5.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 210K Mar  5  2018
> commons-io-2.6.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 425K Oct 26  2017
> >>>> commons-lang3-3.4.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01
> >> httpclient-4.5.5.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
> >>>>>>>>> httpclient-cache-4.5.5.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01
> httpcore-4.4.9.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
> >>>>>>>>>>> jackson-annotations-2.9.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01
> >>>> jackson-core-2.9.5.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
> >>>>>>>>> jackson-databind-2.9.5.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process  17K Oct 26  2017
> >>>> jcl-over-slf4j-1.7.25.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03
> jena-arq-3.8.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01
> >> jena-base-3.8.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07
> >> jena-cmds-3.8.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02
> >> jena-core-3.8.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05
> >>>> jena-dboe-base-3.8.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05
> >>>> jena-dboe-index-3.8.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
> >>>>>>>>>>> jena-dboe-transaction-3.8.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
> >>>>>>>>>>> jena-dboe-trans-data-3.8.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01
> jena-iri-3.8.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
> >>>>>>>>> jena-rdfconnection-3.8.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
> >>>>>>>>> jena-shaded-guava-3.8.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06
> >> jena-tdb2-3.8.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04
> jena-tdb-3.8.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01
> >>>> jsonld-java-0.12.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 232K Mar  5  2018
> >> libthrift-0.10.0.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process  41K Oct 26  2017
> >> slf4j-api-1.7.25.jar
> >>>>>>>>>>> -rw-r--r-- 1 process process  12K Oct 26  2017
> >>>> slf4j-log4j12-1.7.25.jar
> >>>>>>>>>>>
> >>>>>>>>>>> 2.: Turns out, I don't need the jts. after commenting out the
> >>>> affected
> >>>>>>>>>>> lines, the server still runs fine. (But still without spatial
> >>>> index)
> >>>>>>>>>>>
> >>>>>>>>>>> Best Markus
> >>>>>>>>>>>
> >>>>>>>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <
> >>>> marco.neumann@gmail.com <ma...@gmail.com> <mailto:
> >>>> marco.neumann@gmail.com <ma...@gmail.com>>
> >>>>>>>>>> :
> >>>>>>>>>>>>
> >>>>>>>>>>>> Ok let's take a look at this.
> >>>>>>>>>>>>
> >>>>>>>>>>>> 1. please include in the indexer in the classpath. It's part
> of
> >>>> the
> >>>>>>>>>>> current
> >>>>>>>>>>>> jena distribution.
> >>>>>>>>>>>>
> >>>>>>>>>>>> 2. do you need jts? it's a package that allows you to index
> >> multi
> >>>> point
> >>>>>>>>>>>> geometries. here a sample query would be helpful. If single
> >> point
> >>>>>>>>>>>> geometries are indexed and used in conjunction with MBR range
> >>>> queries.
> >>>>>>>>>>>> there is no need for jts.
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
> >>>>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com>
> >> <mailto:
> >>>> mneumann@meteomatics.com <ma...@meteomatics.com>>
> >>>>>>>>>>> <mailto:mneumann@meteomatics.com <mailto:
> >> mneumann@meteomatics.com>
> >>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>
> >>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>
> >>>> <mailto:mneumann@meteomatics.com <mailto:mneumann@meteomatics.com
> >>>>>
> >>>>>>>>>>>> wrote:
> >>>>>>>>>>>>
> >>>>>>>>>>>>> Hi,
> >>>>>>>>>>>>> (sorry for the long post)
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> I've been struggling with the spatial index for a while now.
> >>>>>>>>>>>>> I've read
> >>>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
> <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html>>> <
> >>>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
> <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html>>>> <
> >>>>>>>>>>>>>
> https://jena.apache.org/documentation/query/spatial-query.html
> >> <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html>>> <
> >>>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
> <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html> <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html>>>>>
> and
> >>>>>>>>>>>>> skipped through about every spatial related thread here on
> the
> >>>> list.
> >>>>>>>>>>>>> I managed to get an in-memory version up and running at some
> >>>> point
> >>>>>>>>>>>>> following this
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>>>
> >>>>>>>>> <
> >>>>>>>>>
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>>>
> >>>>>>>>>>
> >>>>>>>>>>> <
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>>>
> >>>>>>>>> <
> >>>>>>>>>
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>>>
> >>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>> <
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>>>
> >>>>>>>>> <
> >>>>>>>>>
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>>>
> >>>>>>>>>>
> >>>>>>>>>>> <
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>>>
> >>>>>>>>> <
> >>>>>>>>>
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>>>
> >>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>> and this
> >>>>>>>>>>>>>
> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/
> <
> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
> <
> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/
> <
> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/
> >>
> >>>>>>>>> <
> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
> <
> >>>>>>>>>>>
> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
> <
> >>>>>>>>>>>>>
> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> But that was on a small dataset that I uploaded via the
> >>>> web-interface
> >>>>>>>>> of
> >>>>>>>>>>>>> Fuseki.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Now the story is a bit different. I'm building the database
> >> using
> >>>>>>>>>>>>> tdbloader2 and would like to create the spatial index
> upfront.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> java -cp jena-spatial.jar jena.spatialindexer
> >>>> --desc=assembler_file
> >>>>>>>>>>>>> I could not figure out, how to get this line to work. I have
> >> the
> >>>>>>>>>>> following
> >>>>>>>>>>>>> possible scenarios:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in
> >> the
> >>>>>>>>>>> classpath:
> >>>>>>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> >>>>>>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>>>>>>>>> Error: Could not find or load main class jena.spatialindexer
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> 2. I use the fuseki-server jar:
> >>>>>>>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
> >>>>>>>>>>>>> --desc=./run/configuration/mm.ttl
> >>>>>>>>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
> >>>>>>>>>>>>>
> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
> >>>>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException:
> Not
> >>>> in a
> >>>>>>>>>>>>> transaction
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> I managed to eliminate the warning about jts by including
> that
> >>>> in the
> >>>>>>>>>>>>> classpath, but the error remains the same (with full trace):
> >>>>>>>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
> >>>>>>>>>>>>> --desc=./run/configuration/mm.ttl
> >>>>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException:
> Not
> >>>> in a
> >>>>>>>>>>>>> transaction
> >>>>>>>>>>>>> at
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>>>>>>>>>>>> at
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>>>>>>>>>>>> at
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>>>>>>>>>>>> at
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>>>>>>>>>>>> at
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>>>>>>>>>>>> at
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>>>>>>>>>>>> at
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>>>>>>>>>>>> at
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>>>>>>>>>>>> at
> >>>>>>>>>>>
> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>>>>>>>>>>>> at
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>>>>>>>>>>>> at
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>>>>>>>>>>>> at
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>>>>>>>>>>>> at
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>>>>>>>>>> at
> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>>>>>>>>>> at jena.spatialindexer.exec(spatialindexer.java:110)
> >>>>>>>>>>>>> at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>>>>>>>>>>>> at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>>>>>>>>>>>> at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>>>>>>>>>>>> at jena.spatialindexer.main(spatialindexer.java:53)
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> My configuration is the following:
> >>>>>>>>>>>>> @prefix :      <http://base/#> .
> >>>>>>>>>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
> .
> >>>>>>>>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> >>>>>>>>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> >>>>>>>>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> >>>>>>>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
> >>>>>>>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
> >>>>>>>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>>>>>>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >>>>>>>>>>>>> # Spatial
> >>>>>>>>>>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery"
> .
> >>>>>>>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> >>>>>>>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf
> >> spatial:SpatialIndex .
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> :service_tdb_all  a                   fuseki:Service ;
> >>>>>>>>>>>>> rdfs:label                    "TDB2 mm" ;
> >>>>>>>>>>>>> fuseki:dataset                :spatial_dataset ;
> >>>>>>>>>>>>> fuseki:name                   "mm" ;
> >>>>>>>>>>>>> fuseki:serviceQuery           "query" , "sparql" ;
> >>>>>>>>>>>>> fuseki:serviceReadGraphStore  "get" ;
> >>>>>>>>>>>>> fuseki:serviceReadWriteGraphStore
> >>>>>>>>>>>>>         "data" ;
> >>>>>>>>>>>>> fuseki:serviceUpdate          "update" ;
> >>>>>>>>>>>>> fuseki:serviceUpload          "upload" .
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> :spatial_dataset a spatial:SpatialDataset ;
> >>>>>>>>>>>>> spatial:dataset   :tdb_dataset_readwrite ;
> >>>>>>>>>>>>> spatial:index     <#indexLucene> ;
> >>>>>>>>>>>>> .
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
> >>>>>>>>>>>>> spatial:directory <file:Lucene> ;
> >>>>>>>>>>>>> #spatial:directory "mem" ;
> >>>>>>>>>>>>> spatial:definition <#definition> ;
> >>>>>>>>>>>>> .
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> <#definition> a spatial:EntityDefinition ;
> >>>>>>>>>>>>> spatial:entityField      "uri" ;
> >>>>>>>>>>>>> spatial:geoField     "geo" ;
> >>>>>>>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format
> >>>>>>>>>>>>> spatial:hasSpatialPredicatePairs (
> >>>>>>>>>>>>>  [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
> >>>>>>>>>>>>>  ) ;
> >>>>>>>>>>>>> # custom geo predicates for 2) Well Known Text (WKT) Literal
> >>>>>>>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ;
> >>>>>>>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT)
> >>>> Literal
> >>>>>>>>>>>>> spatial:spatialContextFactory
> >>>>>>>>>>>>> #
> >>>> "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
> >>>>>>>>>>>>>
> >>>>>>>>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
> >>>>>>>>>>>>> .
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> :tdb_dataset_readwrite
> >>>>>>>>>>>>> a              tdb2:DatasetTDB2 ;
> >>>>>>>>>>>>> tdb2:location
> >>>>>>>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> And I've changed the fuseki script to include the jts jar:
> >>>>>>>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> I see no errors or warnings in the server log, when starting
> >>>> with that
> >>>>>>>>>>>>> configuration, the Lucene folder is created and populated
> with
> >>>>>>>>>>> something:
> >>>>>>>>>>>>> $ ll run/configuration/Lucene/
> >>>>>>>>>>>>> total 4
> >>>>>>>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
> >>>>>>>>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> But any spatial query does not return any results.
> >>>>>>>>>>>>> Any help on how to tackle this would be highly appreciated.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Best
> >>>>>>>>>>>>> Markus Neumann
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> --
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> ---
> >>>>>>>>>>>> Marco Neumann
> >>>>>>>>>>>> KONA
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> --
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> ---
> >>>>>>>>>> Marco Neumann
> >>>>>>>>>> KONA
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>> --
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> ---
> >>>>>>>> Marco Neumann
> >>>>>>>> KONA
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>> --
> >>>
> >>>
> >>> ---
> >>> Marco Neumann
> >>> KONA
> >>
> >>
> >>
> >
> > --
> >
> >
> > ---
> > Marco Neumann
> > KONA
>
>
>

-- 


---
Marco Neumann
KONA

Re: Building a spatial index with jena/fuseki

Posted by ajs6f <aj...@apache.org>.
Marco--

I think I didn't express myself well. I'm not asking you to do any code updates of any kind-- I'm asking you to take a look at the updates _I've_ made available in that PR, try them out, and see if they fix your problem. Again, if that seems like a bit too tall an order, that's okay-- we'll find some other way to confirm this fix. I can set up a duplication of your problem, but it will take a few days for me to get around to it.

ajs6f

> On Sep 18, 2018, at 12:37 PM, Marco Neumann <ma...@gmail.com> wrote:
> 
> I will take a look at it over the weekend, haven't done code updates to the
> new jena repo. not sure if I can submit changes in my current setup,  but
> am happy to learn about it.
> 
> On Tue, Sep 18, 2018 at 4:47 PM ajs6f <aj...@apache.org> wrote:
> 
>> Marco--
>> 
>> I've got a PR at https://github.com/apache/jena/pull/471. Until we hear
>> from Andy, could you perhaps try cloning that PR/branch and trying the new
>> code out? If that is not a reasonable piece of work for you, no problem,
>> but it would help greatly in validating that we've found and fixed the
>> problem.
>> 
>> ajs6f
>> 
>>> On Sep 18, 2018, at 4:51 AM, Marco Neumann <ma...@gmail.com>
>> wrote:
>>> 
>>> well spotted Adam, I think that nails it. I guess I was lucky with my
>> setup
>>> to avoid this glitch so far. Don't want to anticipates Andy's call here
>> but
>>> what's your plan? wrap the call into a transaction to fix it? If so I'd
>>> like to see it as an option in the code to work with tdb2 access methods
>> if
>>> required in addition the current tdb support.
>>> 
>>> 
>>> On Mon, Sep 17, 2018 at 3:26 PM ajs6f <aj...@apache.org> wrote:
>>> 
>>>> Okay, I think we've got it. Nice debugging, Markus!
>>>> 
>>>> If you look at the line of the spatial indexer code that is throwing an
>>>> exception:
>>>> 
>>>> 
>>>> 
>> https://github.com/apache/jena/blob/master/jena-spatial/src/main/java/jena/spatialindexer.java#L110
>>>> 
>>>> indeed, it does not start a transaction against the dataset before
>>>> starting to read quads to index them. Now, in TDB1 this isn't
>> inherently a
>>>> problem-- it's possible to work against a dataset without transactions.
>>>> (Although it's generally not a good idea at all.) But IIRC, TDB2
>> requires
>>>> transactions. If that's true (and Andy can verify that for us) then
>> this is
>>>> a bug and we can fix it in a straightforward way.
>>>> 
>>>> Andy, can you confirm that diagnosis? If so, I'll open a ticket and
>> write
>>>> a PR to use a Txn method to fix this.
>>>> 
>>>> ajs6f
>>>> 
>>>>> On Sep 17, 2018, at 10:14 AM, Markus Neumann <mneumann@meteomatics.com
>>> 
>>>> wrote:
>>>>> 
>>>>> It seems I made a mess with absolute and relative paths all together.
>> So
>>>> I created a minimal setup for testing:
>>>>> (I include the file-contents at the bottom)
>>>>> 
>>>>> $ export JENA_HOME=/srv/linked_data_store/apache-jena-3.8.0
>>>>> $ export PATH=$PATH:$JENA_HOME/bin
>>>>> $ tdb2.tdbloader
>>>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
>>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl
>>>>> 13:50:54 INFO  loader               :: Loader = LoaderPhased
>>>>> 13:50:54 INFO  loader               :: Data:
>>>> 
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl:
>>>> 13 mm-loc-mini.ttl 0.06s (Avg: 232)
>>>>> 13:50:54 INFO  loader               :: Data:
>>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl: 50
>>>> mm-rdf.ttl 0.01s (Avg: 6,250)
>>>>> 13:50:55 INFO  loader               :: Finish - index SPO
>>>>> 13:50:55 INFO  loader               :: Start replay index SPO
>>>>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
>>>> SPO->OSP
>>>>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
>>>> SPO->OSP [63 items, 0.0 seconds]
>>>>> 13:50:55 INFO  loader               :: Finish - index POS
>>>>> 13:50:55 INFO  loader               :: Finish - index OSP
>>>>> $ java -cp
>>>> 
>> /srv/linked_data_store/fuseki-server/fuseki-server.jar:/srv/linked_data_store/apache-jena-3.8.0/lib/*
>>>> jena.spatialindexer
>>>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>>>>> SLF4J: Class path contains multiple SLF4J bindings.
>>>>> SLF4J: Found binding in
>>>> 
>> [jar:file:/srv/linked_data_store/fuseki-server/fuseki-server.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>>>>> SLF4J: Found binding in
>>>> 
>> [jar:file:/srv/linked_data_store/apache-jena-3.8.0/lib/slf4j-log4j12-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>>>>> SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
>>>> explanation.
>>>>> SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>>> transaction
>>>>>     at
>>>> 
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>>>     at
>>>> 
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>>>     at
>>>> 
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>>>     at
>>>> 
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>>>     at
>>>> 
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>>>     at
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>>>     at
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>>>     at
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>>>     at
>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>>>     at
>>>> 
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>>>     at
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>>>     at
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>>>     at
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>     at
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>     at jena.spatialindexer.exec(spatialindexer.java:110)
>>>>>     at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>>>     at jena.spatialindexer.main(spatialindexer.java:53)
>>>>> 
>>>>> I can get rid of the SLF4J warnings:
>>>>> $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar
>>>> jena.spatialindexer
>>>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>>> transaction
>>>>>     at
>>>> 
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>>>     at
>>>> 
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>>>     at
>>>> 
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>>>     at
>>>> 
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>>>     at
>>>> 
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>>>     at
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>>>     at
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>>>     at
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>>>     at
>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>>>     at
>>>> 
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>>>     at
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>>>     at
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>>>     at
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>     at
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>     at jena.spatialindexer.exec(spatialindexer.java:110)
>>>>>     at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>>>     at jena.spatialindexer.main(spatialindexer.java:53)
>>>>> 
>>>>> There is no other java instance running at the time when I run those
>>>> commands.
>>>>> All paths are fully qualified and double checked. The destination
>>>> directory and the Lucene directory were cleared just before.
>>>>> 
>>>>> The server does start and serve the data without errors or warnings in
>>>> the log, but spatial queries do not work.
>>>>> 
>>>>> Does anyone see a reason for the TransactionException?
>>>>> Thanks and best regards
>>>>> Markus
>>>>> 
>>>>> Attachments:
>>>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
>>>>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
>>>>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
>>>>> @prefix dcterms: <http://purl.org/dc/terms/> .
>>>>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#>
>>>>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
>>>>> 
>>>>> <http://rdf.meteomatics.com/mm/>
>>>>>  dcterms:publisher <http://api.meteomatics.com/Imprint.html> ;
>>>>>  dcterms:title "Meteomatics RDF Vocabulary"@en .
>>>>> 
>>>>> mm:location a rdf:Property ;
>>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>>  rdfs:label "location" ;
>>>>>  dcterms:description "Location of a measurement"@en .
>>>>> 
>>>>> mm:elevation a rdf:Property ;
>>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>>  rdfs:label "elevation" ;
>>>>>  dcterms:description "Elevation of a location"@en .
>>>>> 
>>>>> mm:validdate a rdf:Property ;
>>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>>  rdfs:label "validdate" ;
>>>>>  dcterms:description "Temporal information describing when a
>>>> Measurement is/was valid"@en .
>>>>> 
>>>>> mm:value a rdf:Property ;
>>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>>  rdfs:label "value" ;
>>>>>  dcterms:description "The (observed or predicted) value of a
>>>> Measurement"@en .
>>>>> 
>>>>> mm:parameter a rdf:Property ;
>>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>>  rdfs:label "parameter" ;
>>>>>  dcterms:description "what was measured"@en .
>>>>> 
>>>>> mm:station_name a rdf:Property ;
>>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>>  rdfs:label "station_name" ;
>>>>>  dcterms:description "Name of a station"@en .
>>>>> 
>>>>> mm:abbreviation a rdf:Property ;
>>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>>  rdfs:label "abbreviation" ;
>>>>>  dcterms:description "Abbreviation of a station name"@en .
>>>>> 
>>>>> mm:didok_id a rdf:Property ;
>>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>>  rdfs:label "didok_id" ;
>>>>>  dcterms:description "didok id of a station"@en .
>>>>> 
>>>>> mm:unit_symbol a rdf:Property ;
>>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>>  rdfs:label "unit symbol" ;
>>>>>  dcterms:description "unit symbol of a parameter"@en .
>>>>> 
>>>>> mm:Measurement a rdf:Class ;
>>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>>  rdfs:label "Measurement" ;
>>>>>  dcterms:description "Measurement of a specific weather parameter at
>>>> specific location at a specific date (both future or past)" .
>>>>> 
>>>>> mm:Location a rdf:Class ;
>>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>>  rdfs:label "Location" ;
>>>>>  dcterms:description "A Point on the globe where we observe
>>>> weather"@en .
>>>>> 
>>>>> mm:Parameter a rdf:Class ;
>>>>>  rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>>  rdfs:label "Parameter" ;
>>>>>  dcterms:description "A parameter describing an observable aspect of
>>>> the weather"@en .
>>>>> 
>>>>> 
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
>>>>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
>>>>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
>>>>> @prefix dcterms: <http://purl.org/dc/terms/> .
>>>>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
>>>>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
>>>>> @prefix mm-measurements: <http://rdf.meteomatics.com/mm/measurements/>
>> .
>>>>> @prefix mm-locations: <http://rdf.meteomatics.com/mm/locations/> .
>>>>> 
>>>>> 
>>>>> mm-locations:8500015 a mm:Location ;
>>>>>  a geosparql:Geometry ;
>>>>>  mm:didok_id 8500015 ;
>>>>>  geo:lat 47.54259 ;
>>>>>  geo:long 7.61574 ;
>>>>>  mm:elevation 273 .
>>>>> 
>>>>> 
>>>>> mm-locations:8504238 a mm:Location ;
>>>>>  a geosparql:Geometry ;
>>>>>  geosparql:asWKT "POINT(6.86466645231
>>>> 47.0840196485)"^^geosparql:wktLiteral ;
>>>>>  mm:didok_id 8504238 ;
>>>>>  geo:lat 47.08402 ;
>>>>>  geo:long 6.86467 ;
>>>>>  mm:elevation 1086 .
>>>>> 
>>>>> /srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>>>>> @prefix :      <http://base/#> .
>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>>>> # Spatial
>>>>> #[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>>>>> #spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>>>> #spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>>>>> 
>>>>> :service_tdb_all  a                   fuseki:Service ;
>>>>>      rdfs:label                    "TDB2 mm" ;
>>>>>      fuseki:dataset                :spatial_dataset ;
>>>>>      fuseki:name                   "mm" ;
>>>>>      fuseki:serviceQuery           "query" , "sparql" ;
>>>>>      fuseki:serviceReadGraphStore  "get" ;
>>>>>      fuseki:serviceReadWriteGraphStore
>>>>>              "data" ;
>>>>>      fuseki:serviceUpdate          "update" ;
>>>>>      fuseki:serviceUpload          "upload" .
>>>>> 
>>>>> :spatial_dataset a spatial:SpatialDataset ;
>>>>>  spatial:dataset   :tdb_dataset_readwrite ;
>>>>>  spatial:index     <#indexLucene> ;
>>>>>  .
>>>>> 
>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>>>>  spatial:directory <file:Lucene> ;
>>>>>  #spatial:directory "mem" ;
>>>>>  spatial:definition <#definition> ;
>>>>>  .
>>>>> 
>>>>> <#definition> a spatial:EntityDefinition ;
>>>>>  spatial:entityField      "uri" ;
>>>>>  spatial:geoField     "geo" ;
>>>>>  # custom geo predicates for 1) Latitude/Longitude Format
>>>>>  spatial:hasSpatialPredicatePairs (
>>>>>       [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>>>>       ) ;
>>>>>  # custom geo predicates for 2) Well Known Text (WKT) Literal
>>>>>  spatial:hasWKTPredicates (geosparql:asWKT) ;
>>>>>  #spatial:spatialContextFactory
>>>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>>>> #     "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>>>>  .
>>>>> 
>>>>> :tdb_dataset_readwrite
>>>>>      a              tdb2:DatasetTDB2 ;
>>>>>      tdb2:location
>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>>>> 
>>>>> 
>>>>>> Am 17.09.2018 um 15:15 schrieb ajs6f <aj...@apache.org>:
>>>>>> 
>>>>>> I think you might have misunderstood the use of $JENA_HOME, or perhaps
>>>> the Java classpath. $JENA_HOME, which should generally be an absolute
>>>> filepath, allows the Jena scripts to find their libraries at runtime.
>>>> Internally, the scripts use $JENA_HOME to set up the classpaths with
>> which
>>>> to start running Java code. But in this case, you're not using the
>> scripts.
>>>> You're calling a Java class directly, which means you have to give it
>> all
>>>> the libraries directly, using the classpath flag directly. For example,
>>>> your second attempt:
>>>>>> 
>>>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
>>>> --desc=fuseki-server/run/configuration/mm.ttl
>>>>>> Error: Could not find or load main class
>>>> apache-jena-3.8.0.lib.commons-cli-1.4.jar
>>>>>> 
>>>>>> may have failed because whatever directory you are in probably doesn't
>>>> happen to have a Jena distribution in it called "apache-jena-3.8.0".
>>>> Perhaps try:
>>>>>> 
>>>>>> java -cp $JENA_HOME/lib/* jena.spatialindexer
>>>> --desc=fuseki-server/run/configuration/mm.ttl
>>>>>> 
>>>>>> Your first example looks like it might be misusing the -cp flag [1].
>>>> You probably don't want the *.jar, just *, like
>>>>>> 
>>>>>> java -cp lib/* jena.spatialindexer
>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>> 
>>>>>> especially if you happen to be using Windows. [2] That might not be
>> the
>>>> entire story, but you can at least try those invocations and see if you
>> get
>>>> anything different/better.
>>>>>> 
>>>>>> ajs6f
>>>>>> 
>>>>>> [1]
>>>> 
>> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
>>>> <
>>>> 
>> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
>>>>> 
>>>>>> [2]
>>>> 
>> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
>>>> <
>>>> 
>> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On Sep 17, 2018, at 7:07 AM, Markus Neumann <
>> mneumann@meteomatics.com
>>>> <ma...@meteomatics.com>> wrote:
>>>>>>> 
>>>>>>> Ok, that's exactly what I did here:
>>>>>>> $ java -cp lib/*.jar jena.spatialindexer
>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>>>>>>> 
>>>>>>> Or from outside JENA_HOME:
>>>>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
>>>> --desc=fuseki-server/run/configuration/mm.ttl
>>>>>>> Error: Could not find or load main class
>>>> apache-jena-3.8.0.lib.commons-cli-1.4.jar
>>>>>>> 
>>>>>>> Or did I missunderstand something?
>>>>>>> 
>>>>>>>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <
>> marco.neumann@gmail.com
>>>>> :
>>>>>>>> 
>>>>>>>> don't worry it's a common problem and frequent source of confusion
>>>> not only
>>>>>>>> with jena but java projects. try to simply inlcude all the jars.
>>>>>>>> 
>>>>>>>> I presume you run this on a linux box with OpenJDK 8. correct?
>>>>>>>> 
>>>>>>>> now once you have set up jena just add the following
>>>>>>>> {replace_with_your_path}/apache-jena-3.8.0/lib/*
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <
>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
>>>> mneumann@meteomatics.com <ma...@meteomatics.com>>>
>>>>>>>> wrote:
>>>>>>>> 
>>>>>>>>> This is embarrassing but I don't get it.
>>>>>>>>> 
>>>>>>>>> I've configured $JENA_HOME and adjusted the PATH.
>>>>>>>>> 
>>>>>>>>> Now what classpath should I include when invoking the indexer?
>>>>>>>>> What I've tried so far:
>>>>>>>>> 
>>>>>>>>> $ cd $JENA_HOME
>>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>>>>> Error: Could not find or load main class jena.spatialindexer
>>>>>>>>> $ java -cp lib/*.jar jena.spatialindexer
>>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>>>>>>>>> 
>>>>>>>>> Thanks for your patience
>>>>>>>>> 
>>>>>>>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <
>>>> marco.neumann@gmail.com <ma...@gmail.com>>:
>>>>>>>>>> 
>>>>>>>>>> yes correct, this looks good. now include the classpath during
>>>> invocation
>>>>>>>>>> of the spatialindexer
>>>>>>>>>> 
>>>>>>>>>> in addition it's always a good idea to properly configure jena
>>>> along your
>>>>>>>>>> java runtime environment settings to avoid jdk / lib conflicts
>>>> during
>>>>>>>>>> execution.
>>>>>>>>>> 
>>>>>>>>>> https://jena.apache.org/documentation/tools/index.html <
>>>> https://jena.apache.org/documentation/tools/index.html> <
>>>>>>>>> https://jena.apache.org/documentation/tools/index.html <
>>>> https://jena.apache.org/documentation/tools/index.html> <
>>>> https://jena.apache.org/documentation/tools/index.html <
>>>> https://jena.apache.org/documentation/tools/index.html>>>
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
>>>>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com>
>> <mailto:
>>>> mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:
>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
>>>> mneumann@meteomatics.com <ma...@meteomatics.com>>>>
>>>>>>>>>> wrote:
>>>>>>>>>> 
>>>>>>>>>>> 1.: what do you mean by indexer?
>>>>>>>>>>> Probably my biggest problem is, that I have no clue how to find
>>>> out,
>>>>>>>>> where
>>>>>>>>>>> the jena.spatialindexer could be located except for asking here.
>>>>>>>>>>> 
>>>>>>>>>>> Here is the content of the apache jena I downloaded:
>>>>>>>>>>> $ ls -lh ../apache-jena-3.8.0/lib
>>>>>>>>>>> total 17M
>>>>>>>>>>> -rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
>>>>>>>>>>> -rw-r--r-- 1 process process  53K Oct 26  2017
>> commons-cli-1.4.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 328K Mar  5  2018
>>>> commons-codec-1.11.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59
>>>> commons-compress-1.17.jar
>>>>>>>>>>> -rw-r--r-- 1 process process  41K Mar  5  2018
>> commons-csv-1.5.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 425K Oct 26  2017
>>>> commons-lang3-3.4.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01
>> httpclient-4.5.5.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
>>>>>>>>> httpclient-cache-4.5.5.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
>>>>>>>>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
>>>>>>>>>>> jackson-annotations-2.9.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01
>>>> jackson-core-2.9.5.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
>>>>>>>>> jackson-databind-2.9.5.jar
>>>>>>>>>>> -rw-r--r-- 1 process process  17K Oct 26  2017
>>>> jcl-over-slf4j-1.7.25.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01
>> jena-base-3.8.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07
>> jena-cmds-3.8.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02
>> jena-core-3.8.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05
>>>> jena-dboe-base-3.8.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05
>>>> jena-dboe-index-3.8.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
>>>>>>>>>>> jena-dboe-transaction-3.8.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
>>>>>>>>>>> jena-dboe-trans-data-3.8.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
>>>>>>>>> jena-rdfconnection-3.8.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
>>>>>>>>> jena-shaded-guava-3.8.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06
>> jena-tdb2-3.8.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01
>>>> jsonld-java-0.12.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 232K Mar  5  2018
>> libthrift-0.10.0.jar
>>>>>>>>>>> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
>>>>>>>>>>> -rw-r--r-- 1 process process  41K Oct 26  2017
>> slf4j-api-1.7.25.jar
>>>>>>>>>>> -rw-r--r-- 1 process process  12K Oct 26  2017
>>>> slf4j-log4j12-1.7.25.jar
>>>>>>>>>>> 
>>>>>>>>>>> 2.: Turns out, I don't need the jts. after commenting out the
>>>> affected
>>>>>>>>>>> lines, the server still runs fine. (But still without spatial
>>>> index)
>>>>>>>>>>> 
>>>>>>>>>>> Best Markus
>>>>>>>>>>> 
>>>>>>>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <
>>>> marco.neumann@gmail.com <ma...@gmail.com> <mailto:
>>>> marco.neumann@gmail.com <ma...@gmail.com>>
>>>>>>>>>> :
>>>>>>>>>>>> 
>>>>>>>>>>>> Ok let's take a look at this.
>>>>>>>>>>>> 
>>>>>>>>>>>> 1. please include in the indexer in the classpath. It's part of
>>>> the
>>>>>>>>>>> current
>>>>>>>>>>>> jena distribution.
>>>>>>>>>>>> 
>>>>>>>>>>>> 2. do you need jts? it's a package that allows you to index
>> multi
>>>> point
>>>>>>>>>>>> geometries. here a sample query would be helpful. If single
>> point
>>>>>>>>>>>> geometries are indexed and used in conjunction with MBR range
>>>> queries.
>>>>>>>>>>>> there is no need for jts.
>>>>>>>>>>>> 
>>>>>>>>>>>> 
>>>>>>>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
>>>>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com>
>> <mailto:
>>>> mneumann@meteomatics.com <ma...@meteomatics.com>>
>>>>>>>>>>> <mailto:mneumann@meteomatics.com <mailto:
>> mneumann@meteomatics.com>
>>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>
>>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>
>>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>> 
>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>> (sorry for the long post)
>>>>>>>>>>>>> 
>>>>>>>>>>>>> I've been struggling with the spatial index for a while now.
>>>>>>>>>>>>> I've read
>>>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html>>>> <
>>>>>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
>> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>>>> https://jena.apache.org/documentation/query/spatial-query.html>>>>> and
>>>>>>>>>>>>> skipped through about every spatial related thread here on the
>>>> list.
>>>>>>>>>>>>> I managed to get an in-memory version up and running at some
>>>> point
>>>>>>>>>>>>> following this
>>>>>>>>>>>>> 
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>>> 
>>>>>>>>> <
>>>>>>>>> 
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>>> 
>>>>>>>>>> 
>>>>>>>>>>> <
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>>> 
>>>>>>>>> <
>>>>>>>>> 
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>>> 
>>>>>>>>>> 
>>>>>>>>>>>> 
>>>>>>>>>>>>> <
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>>> 
>>>>>>>>> <
>>>>>>>>> 
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>>> 
>>>>>>>>>> 
>>>>>>>>>>> <
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>>> 
>>>>>>>>> <
>>>>>>>>> 
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>>> 
>>>>>>>>>> 
>>>>>>>>>>>> 
>>>>>>>>>>>>>> 
>>>>>>>>>>>>> and this
>>>>>>>>>>>>> 
>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>>
>>>>>>>>> <
>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>>>>>>>> 
>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>>>>>>>>>> 
>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>>>>>>>>>>>>> 
>>>>>>>>>>>>> But that was on a small dataset that I uploaded via the
>>>> web-interface
>>>>>>>>> of
>>>>>>>>>>>>> Fuseki.
>>>>>>>>>>>>> 
>>>>>>>>>>>>> Now the story is a bit different. I'm building the database
>> using
>>>>>>>>>>>>> tdbloader2 and would like to create the spatial index upfront.
>>>>>>>>>>>>> 
>>>>>>>>>>>>> java -cp jena-spatial.jar jena.spatialindexer
>>>> --desc=assembler_file
>>>>>>>>>>>>> I could not figure out, how to get this line to work. I have
>> the
>>>>>>>>>>> following
>>>>>>>>>>>>> possible scenarios:
>>>>>>>>>>>>> 
>>>>>>>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in
>> the
>>>>>>>>>>> classpath:
>>>>>>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>>>>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>>>>>>>>> Error: Could not find or load main class jena.spatialindexer
>>>>>>>>>>>>> 
>>>>>>>>>>>>> 2. I use the fuseki-server jar:
>>>>>>>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
>>>>>>>>>>>>> --desc=./run/configuration/mm.ttl
>>>>>>>>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
>>>>>>>>>>>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
>>>>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not
>>>> in a
>>>>>>>>>>>>> transaction
>>>>>>>>>>>>> 
>>>>>>>>>>>>> I managed to eliminate the warning about jts by including that
>>>> in the
>>>>>>>>>>>>> classpath, but the error remains the same (with full trace):
>>>>>>>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
>>>>>>>>>>>>> --desc=./run/configuration/mm.ttl
>>>>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not
>>>> in a
>>>>>>>>>>>>> transaction
>>>>>>>>>>>>> at
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>>>>>>>>>>> at
>>>>>>>>>>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>>>>>>>> at
>>>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>>>>>>>> at jena.spatialindexer.exec(spatialindexer.java:110)
>>>>>>>>>>>>> at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>>>>>>>>>>> at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>>>>>>>>>>> at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>>>>>>>>>>> at jena.spatialindexer.main(spatialindexer.java:53)
>>>>>>>>>>>>> 
>>>>>>>>>>>>> My configuration is the following:
>>>>>>>>>>>>> @prefix :      <http://base/#> .
>>>>>>>>>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>>>>>>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>>>>>>>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>>>>>>>>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>>>>>>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>>>>>>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>>>>>>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>>>>>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>>>>>>>>>>>> # Spatial
>>>>>>>>>>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>>>>>>>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>>>>>>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf
>> spatial:SpatialIndex .
>>>>>>>>>>>>> 
>>>>>>>>>>>>> :service_tdb_all  a                   fuseki:Service ;
>>>>>>>>>>>>> rdfs:label                    "TDB2 mm" ;
>>>>>>>>>>>>> fuseki:dataset                :spatial_dataset ;
>>>>>>>>>>>>> fuseki:name                   "mm" ;
>>>>>>>>>>>>> fuseki:serviceQuery           "query" , "sparql" ;
>>>>>>>>>>>>> fuseki:serviceReadGraphStore  "get" ;
>>>>>>>>>>>>> fuseki:serviceReadWriteGraphStore
>>>>>>>>>>>>>         "data" ;
>>>>>>>>>>>>> fuseki:serviceUpdate          "update" ;
>>>>>>>>>>>>> fuseki:serviceUpload          "upload" .
>>>>>>>>>>>>> 
>>>>>>>>>>>>> :spatial_dataset a spatial:SpatialDataset ;
>>>>>>>>>>>>> spatial:dataset   :tdb_dataset_readwrite ;
>>>>>>>>>>>>> spatial:index     <#indexLucene> ;
>>>>>>>>>>>>> .
>>>>>>>>>>>>> 
>>>>>>>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>>>>>>>>>>>> spatial:directory <file:Lucene> ;
>>>>>>>>>>>>> #spatial:directory "mem" ;
>>>>>>>>>>>>> spatial:definition <#definition> ;
>>>>>>>>>>>>> .
>>>>>>>>>>>>> 
>>>>>>>>>>>>> <#definition> a spatial:EntityDefinition ;
>>>>>>>>>>>>> spatial:entityField      "uri" ;
>>>>>>>>>>>>> spatial:geoField     "geo" ;
>>>>>>>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format
>>>>>>>>>>>>> spatial:hasSpatialPredicatePairs (
>>>>>>>>>>>>>  [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>>>>>>>>>>>>  ) ;
>>>>>>>>>>>>> # custom geo predicates for 2) Well Known Text (WKT) Literal
>>>>>>>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ;
>>>>>>>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT)
>>>> Literal
>>>>>>>>>>>>> spatial:spatialContextFactory
>>>>>>>>>>>>> #
>>>> "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>>>>>>>>>>>> 
>>>>>>>>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>>>>>>>>>>>> .
>>>>>>>>>>>>> 
>>>>>>>>>>>>> :tdb_dataset_readwrite
>>>>>>>>>>>>> a              tdb2:DatasetTDB2 ;
>>>>>>>>>>>>> tdb2:location
>>>>>>>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>>>>>>>>>>>> 
>>>>>>>>>>>>> And I've changed the fuseki script to include the jts jar:
>>>>>>>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
>>>>>>>>>>>>> 
>>>>>>>>>>>>> I see no errors or warnings in the server log, when starting
>>>> with that
>>>>>>>>>>>>> configuration, the Lucene folder is created and populated with
>>>>>>>>>>> something:
>>>>>>>>>>>>> $ ll run/configuration/Lucene/
>>>>>>>>>>>>> total 4
>>>>>>>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
>>>>>>>>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
>>>>>>>>>>>>> 
>>>>>>>>>>>>> But any spatial query does not return any results.
>>>>>>>>>>>>> Any help on how to tackle this would be highly appreciated.
>>>>>>>>>>>>> 
>>>>>>>>>>>>> Best
>>>>>>>>>>>>> Markus Neumann
>>>>>>>>>>>>> 
>>>>>>>>>>>>> 
>>>>>>>>>>>> 
>>>>>>>>>>>> --
>>>>>>>>>>>> 
>>>>>>>>>>>> 
>>>>>>>>>>>> ---
>>>>>>>>>>>> Marco Neumann
>>>>>>>>>>>> KONA
>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> --
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> ---
>>>>>>>>>> Marco Neumann
>>>>>>>>>> KONA
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> 
>>>>>>>> --
>>>>>>>> 
>>>>>>>> 
>>>>>>>> ---
>>>>>>>> Marco Neumann
>>>>>>>> KONA
>>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> --
>>> 
>>> 
>>> ---
>>> Marco Neumann
>>> KONA
>> 
>> 
>> 
> 
> -- 
> 
> 
> ---
> Marco Neumann
> KONA

Re: Building a spatial index with jena/fuseki

Posted by Marco Neumann <ma...@gmail.com>.
I will take a look at it over the weekend, haven't done code updates to the
new jena repo. not sure if I can submit changes in my current setup,  but
am happy to learn about it.

On Tue, Sep 18, 2018 at 4:47 PM ajs6f <aj...@apache.org> wrote:

> Marco--
>
> I've got a PR at https://github.com/apache/jena/pull/471. Until we hear
> from Andy, could you perhaps try cloning that PR/branch and trying the new
> code out? If that is not a reasonable piece of work for you, no problem,
> but it would help greatly in validating that we've found and fixed the
> problem.
>
> ajs6f
>
> > On Sep 18, 2018, at 4:51 AM, Marco Neumann <ma...@gmail.com>
> wrote:
> >
> > well spotted Adam, I think that nails it. I guess I was lucky with my
> setup
> > to avoid this glitch so far. Don't want to anticipates Andy's call here
> but
> > what's your plan? wrap the call into a transaction to fix it? If so I'd
> > like to see it as an option in the code to work with tdb2 access methods
> if
> > required in addition the current tdb support.
> >
> >
> > On Mon, Sep 17, 2018 at 3:26 PM ajs6f <aj...@apache.org> wrote:
> >
> >> Okay, I think we've got it. Nice debugging, Markus!
> >>
> >> If you look at the line of the spatial indexer code that is throwing an
> >> exception:
> >>
> >>
> >>
> https://github.com/apache/jena/blob/master/jena-spatial/src/main/java/jena/spatialindexer.java#L110
> >>
> >> indeed, it does not start a transaction against the dataset before
> >> starting to read quads to index them. Now, in TDB1 this isn't
> inherently a
> >> problem-- it's possible to work against a dataset without transactions.
> >> (Although it's generally not a good idea at all.) But IIRC, TDB2
> requires
> >> transactions. If that's true (and Andy can verify that for us) then
> this is
> >> a bug and we can fix it in a straightforward way.
> >>
> >> Andy, can you confirm that diagnosis? If so, I'll open a ticket and
> write
> >> a PR to use a Txn method to fix this.
> >>
> >> ajs6f
> >>
> >>> On Sep 17, 2018, at 10:14 AM, Markus Neumann <mneumann@meteomatics.com
> >
> >> wrote:
> >>>
> >>> It seems I made a mess with absolute and relative paths all together.
> So
> >> I created a minimal setup for testing:
> >>> (I include the file-contents at the bottom)
> >>>
> >>> $ export JENA_HOME=/srv/linked_data_store/apache-jena-3.8.0
> >>> $ export PATH=$PATH:$JENA_HOME/bin
> >>> $ tdb2.tdbloader
> >> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
> >> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl
> >>> 13:50:54 INFO  loader               :: Loader = LoaderPhased
> >>> 13:50:54 INFO  loader               :: Data:
> >>
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl:
> >> 13 mm-loc-mini.ttl 0.06s (Avg: 232)
> >>> 13:50:54 INFO  loader               :: Data:
> >> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl: 50
> >> mm-rdf.ttl 0.01s (Avg: 6,250)
> >>> 13:50:55 INFO  loader               :: Finish - index SPO
> >>> 13:50:55 INFO  loader               :: Start replay index SPO
> >>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
> >> SPO->OSP
> >>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
> >> SPO->OSP [63 items, 0.0 seconds]
> >>> 13:50:55 INFO  loader               :: Finish - index POS
> >>> 13:50:55 INFO  loader               :: Finish - index OSP
> >>> $ java -cp
> >>
> /srv/linked_data_store/fuseki-server/fuseki-server.jar:/srv/linked_data_store/apache-jena-3.8.0/lib/*
> >> jena.spatialindexer
> >> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >>> SLF4J: Class path contains multiple SLF4J bindings.
> >>> SLF4J: Found binding in
> >>
> [jar:file:/srv/linked_data_store/fuseki-server/fuseki-server.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> >>> SLF4J: Found binding in
> >>
> [jar:file:/srv/linked_data_store/apache-jena-3.8.0/lib/slf4j-log4j12-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> >>> SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
> >> explanation.
> >>> SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
> >>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> >> transaction
> >>>      at
> >>
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>>      at
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>>      at
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>>      at
> >>
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>>      at
> >>
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>>      at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>>      at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>>      at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>>      at
> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>>      at
> >>
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>>      at
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>>      at
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>>      at
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>      at
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>      at jena.spatialindexer.exec(spatialindexer.java:110)
> >>>      at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>>      at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>>      at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>>      at jena.spatialindexer.main(spatialindexer.java:53)
> >>>
> >>> I can get rid of the SLF4J warnings:
> >>> $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar
> >> jena.spatialindexer
> >> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> >> transaction
> >>>      at
> >>
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>>      at
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>>      at
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>>      at
> >>
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>>      at
> >>
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>>      at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>>      at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>>      at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>>      at
> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>>      at
> >>
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>>      at
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>>      at
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>>      at
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>      at
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>      at jena.spatialindexer.exec(spatialindexer.java:110)
> >>>      at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>>      at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>>      at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>>      at jena.spatialindexer.main(spatialindexer.java:53)
> >>>
> >>> There is no other java instance running at the time when I run those
> >> commands.
> >>> All paths are fully qualified and double checked. The destination
> >> directory and the Lucene directory were cleared just before.
> >>>
> >>> The server does start and serve the data without errors or warnings in
> >> the log, but spatial queries do not work.
> >>>
> >>> Does anyone see a reason for the TransactionException?
> >>> Thanks and best regards
> >>> Markus
> >>>
> >>> Attachments:
> >>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
> >>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> >>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
> >>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
> >>> @prefix dcterms: <http://purl.org/dc/terms/> .
> >>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#>
> >>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
> >>>
> >>> <http://rdf.meteomatics.com/mm/>
> >>>   dcterms:publisher <http://api.meteomatics.com/Imprint.html> ;
> >>>   dcterms:title "Meteomatics RDF Vocabulary"@en .
> >>>
> >>> mm:location a rdf:Property ;
> >>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>   rdfs:label "location" ;
> >>>   dcterms:description "Location of a measurement"@en .
> >>>
> >>> mm:elevation a rdf:Property ;
> >>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>   rdfs:label "elevation" ;
> >>>   dcterms:description "Elevation of a location"@en .
> >>>
> >>> mm:validdate a rdf:Property ;
> >>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>   rdfs:label "validdate" ;
> >>>   dcterms:description "Temporal information describing when a
> >> Measurement is/was valid"@en .
> >>>
> >>> mm:value a rdf:Property ;
> >>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>   rdfs:label "value" ;
> >>>   dcterms:description "The (observed or predicted) value of a
> >> Measurement"@en .
> >>>
> >>> mm:parameter a rdf:Property ;
> >>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>   rdfs:label "parameter" ;
> >>>   dcterms:description "what was measured"@en .
> >>>
> >>> mm:station_name a rdf:Property ;
> >>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>   rdfs:label "station_name" ;
> >>>   dcterms:description "Name of a station"@en .
> >>>
> >>> mm:abbreviation a rdf:Property ;
> >>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>   rdfs:label "abbreviation" ;
> >>>   dcterms:description "Abbreviation of a station name"@en .
> >>>
> >>> mm:didok_id a rdf:Property ;
> >>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>   rdfs:label "didok_id" ;
> >>>   dcterms:description "didok id of a station"@en .
> >>>
> >>> mm:unit_symbol a rdf:Property ;
> >>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>   rdfs:label "unit symbol" ;
> >>>   dcterms:description "unit symbol of a parameter"@en .
> >>>
> >>> mm:Measurement a rdf:Class ;
> >>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>   rdfs:label "Measurement" ;
> >>>   dcterms:description "Measurement of a specific weather parameter at
> >> specific location at a specific date (both future or past)" .
> >>>
> >>> mm:Location a rdf:Class ;
> >>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>   rdfs:label "Location" ;
> >>>   dcterms:description "A Point on the globe where we observe
> >> weather"@en .
> >>>
> >>> mm:Parameter a rdf:Class ;
> >>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>   rdfs:label "Parameter" ;
> >>>   dcterms:description "A parameter describing an observable aspect of
> >> the weather"@en .
> >>>
> >>>
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
> >>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> >>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
> >>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
> >>> @prefix dcterms: <http://purl.org/dc/terms/> .
> >>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
> >>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
> >>> @prefix mm-measurements: <http://rdf.meteomatics.com/mm/measurements/>
> .
> >>> @prefix mm-locations: <http://rdf.meteomatics.com/mm/locations/> .
> >>>
> >>>
> >>> mm-locations:8500015 a mm:Location ;
> >>>   a geosparql:Geometry ;
> >>>   mm:didok_id 8500015 ;
> >>>   geo:lat 47.54259 ;
> >>>   geo:long 7.61574 ;
> >>>   mm:elevation 273 .
> >>>
> >>>
> >>> mm-locations:8504238 a mm:Location ;
> >>>   a geosparql:Geometry ;
> >>>   geosparql:asWKT "POINT(6.86466645231
> >> 47.0840196485)"^^geosparql:wktLiteral ;
> >>>   mm:didok_id 8504238 ;
> >>>   geo:lat 47.08402 ;
> >>>   geo:long 6.86467 ;
> >>>   mm:elevation 1086 .
> >>>
> >>> /srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >>> @prefix :      <http://base/#> .
> >>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> >>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> >>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> >>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
> >>> @prefix spatial: <http://jena.apache.org/spatial#> .
> >>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >>> # Spatial
> >>> #[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
> >>> #spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> >>> #spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
> >>>
> >>> :service_tdb_all  a                   fuseki:Service ;
> >>>       rdfs:label                    "TDB2 mm" ;
> >>>       fuseki:dataset                :spatial_dataset ;
> >>>       fuseki:name                   "mm" ;
> >>>       fuseki:serviceQuery           "query" , "sparql" ;
> >>>       fuseki:serviceReadGraphStore  "get" ;
> >>>       fuseki:serviceReadWriteGraphStore
> >>>               "data" ;
> >>>       fuseki:serviceUpdate          "update" ;
> >>>       fuseki:serviceUpload          "upload" .
> >>>
> >>> :spatial_dataset a spatial:SpatialDataset ;
> >>>   spatial:dataset   :tdb_dataset_readwrite ;
> >>>   spatial:index     <#indexLucene> ;
> >>>   .
> >>>
> >>> <#indexLucene> a spatial:SpatialIndexLucene ;
> >>>   spatial:directory <file:Lucene> ;
> >>>   #spatial:directory "mem" ;
> >>>   spatial:definition <#definition> ;
> >>>   .
> >>>
> >>> <#definition> a spatial:EntityDefinition ;
> >>>   spatial:entityField      "uri" ;
> >>>   spatial:geoField     "geo" ;
> >>>   # custom geo predicates for 1) Latitude/Longitude Format
> >>>   spatial:hasSpatialPredicatePairs (
> >>>        [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
> >>>        ) ;
> >>>   # custom geo predicates for 2) Well Known Text (WKT) Literal
> >>>   spatial:hasWKTPredicates (geosparql:asWKT) ;
> >>>   #spatial:spatialContextFactory
> >>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
> >>> #     "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
> >>>   .
> >>>
> >>> :tdb_dataset_readwrite
> >>>       a              tdb2:DatasetTDB2 ;
> >>>       tdb2:location
> >> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
> >>>
> >>>
> >>>> Am 17.09.2018 um 15:15 schrieb ajs6f <aj...@apache.org>:
> >>>>
> >>>> I think you might have misunderstood the use of $JENA_HOME, or perhaps
> >> the Java classpath. $JENA_HOME, which should generally be an absolute
> >> filepath, allows the Jena scripts to find their libraries at runtime.
> >> Internally, the scripts use $JENA_HOME to set up the classpaths with
> which
> >> to start running Java code. But in this case, you're not using the
> scripts.
> >> You're calling a Java class directly, which means you have to give it
> all
> >> the libraries directly, using the classpath flag directly. For example,
> >> your second attempt:
> >>>>
> >>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
> >> --desc=fuseki-server/run/configuration/mm.ttl
> >>>> Error: Could not find or load main class
> >> apache-jena-3.8.0.lib.commons-cli-1.4.jar
> >>>>
> >>>> may have failed because whatever directory you are in probably doesn't
> >> happen to have a Jena distribution in it called "apache-jena-3.8.0".
> >> Perhaps try:
> >>>>
> >>>> java -cp $JENA_HOME/lib/* jena.spatialindexer
> >> --desc=fuseki-server/run/configuration/mm.ttl
> >>>>
> >>>> Your first example looks like it might be misusing the -cp flag [1].
> >> You probably don't want the *.jar, just *, like
> >>>>
> >>>> java -cp lib/* jena.spatialindexer
> >> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>
> >>>> especially if you happen to be using Windows. [2] That might not be
> the
> >> entire story, but you can at least try those invocations and see if you
> get
> >> anything different/better.
> >>>>
> >>>> ajs6f
> >>>>
> >>>> [1]
> >>
> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
> >> <
> >>
> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
> >>>
> >>>> [2]
> >>
> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
> >> <
> >>
> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
> >>>
> >>>>
> >>>>
> >>>>> On Sep 17, 2018, at 7:07 AM, Markus Neumann <
> mneumann@meteomatics.com
> >> <ma...@meteomatics.com>> wrote:
> >>>>>
> >>>>> Ok, that's exactly what I did here:
> >>>>> $ java -cp lib/*.jar jena.spatialindexer
> >> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
> >>>>>
> >>>>> Or from outside JENA_HOME:
> >>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
> >> --desc=fuseki-server/run/configuration/mm.ttl
> >>>>> Error: Could not find or load main class
> >> apache-jena-3.8.0.lib.commons-cli-1.4.jar
> >>>>>
> >>>>> Or did I missunderstand something?
> >>>>>
> >>>>>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <
> marco.neumann@gmail.com
> >>> :
> >>>>>>
> >>>>>> don't worry it's a common problem and frequent source of confusion
> >> not only
> >>>>>> with jena but java projects. try to simply inlcude all the jars.
> >>>>>>
> >>>>>> I presume you run this on a linux box with OpenJDK 8. correct?
> >>>>>>
> >>>>>> now once you have set up jena just add the following
> >>>>>> {replace_with_your_path}/apache-jena-3.8.0/lib/*
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <
> >> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
> >> mneumann@meteomatics.com <ma...@meteomatics.com>>>
> >>>>>> wrote:
> >>>>>>
> >>>>>>> This is embarrassing but I don't get it.
> >>>>>>>
> >>>>>>> I've configured $JENA_HOME and adjusted the PATH.
> >>>>>>>
> >>>>>>> Now what classpath should I include when invoking the indexer?
> >>>>>>> What I've tried so far:
> >>>>>>>
> >>>>>>> $ cd $JENA_HOME
> >>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> >>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>>> Error: Could not find or load main class jena.spatialindexer
> >>>>>>> $ java -cp lib/*.jar jena.spatialindexer
> >>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
> >>>>>>>
> >>>>>>> Thanks for your patience
> >>>>>>>
> >>>>>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <
> >> marco.neumann@gmail.com <ma...@gmail.com>>:
> >>>>>>>>
> >>>>>>>> yes correct, this looks good. now include the classpath during
> >> invocation
> >>>>>>>> of the spatialindexer
> >>>>>>>>
> >>>>>>>> in addition it's always a good idea to properly configure jena
> >> along your
> >>>>>>>> java runtime environment settings to avoid jdk / lib conflicts
> >> during
> >>>>>>>> execution.
> >>>>>>>>
> >>>>>>>> https://jena.apache.org/documentation/tools/index.html <
> >> https://jena.apache.org/documentation/tools/index.html> <
> >>>>>>> https://jena.apache.org/documentation/tools/index.html <
> >> https://jena.apache.org/documentation/tools/index.html> <
> >> https://jena.apache.org/documentation/tools/index.html <
> >> https://jena.apache.org/documentation/tools/index.html>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
> >>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com>
> <mailto:
> >> mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:
> >> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
> >> mneumann@meteomatics.com <ma...@meteomatics.com>>>>
> >>>>>>>> wrote:
> >>>>>>>>
> >>>>>>>>> 1.: what do you mean by indexer?
> >>>>>>>>> Probably my biggest problem is, that I have no clue how to find
> >> out,
> >>>>>>> where
> >>>>>>>>> the jena.spatialindexer could be located except for asking here.
> >>>>>>>>>
> >>>>>>>>> Here is the content of the apache jena I downloaded:
> >>>>>>>>> $ ls -lh ../apache-jena-3.8.0/lib
> >>>>>>>>> total 17M
> >>>>>>>>> -rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
> >>>>>>>>> -rw-r--r-- 1 process process  53K Oct 26  2017
> commons-cli-1.4.jar
> >>>>>>>>> -rw-r--r-- 1 process process 328K Mar  5  2018
> >> commons-codec-1.11.jar
> >>>>>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59
> >> commons-compress-1.17.jar
> >>>>>>>>> -rw-r--r-- 1 process process  41K Mar  5  2018
> commons-csv-1.5.jar
> >>>>>>>>> -rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
> >>>>>>>>> -rw-r--r-- 1 process process 425K Oct 26  2017
> >> commons-lang3-3.4.jar
> >>>>>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01
> httpclient-4.5.5.jar
> >>>>>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
> >>>>>>> httpclient-cache-4.5.5.jar
> >>>>>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
> >>>>>>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
> >>>>>>>>> jackson-annotations-2.9.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01
> >> jackson-core-2.9.5.jar
> >>>>>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
> >>>>>>> jackson-databind-2.9.5.jar
> >>>>>>>>> -rw-r--r-- 1 process process  17K Oct 26  2017
> >> jcl-over-slf4j-1.7.25.jar
> >>>>>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01
> jena-base-3.8.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07
> jena-cmds-3.8.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02
> jena-core-3.8.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05
> >> jena-dboe-base-3.8.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05
> >> jena-dboe-index-3.8.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
> >>>>>>>>> jena-dboe-transaction-3.8.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
> >>>>>>>>> jena-dboe-trans-data-3.8.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
> >>>>>>> jena-rdfconnection-3.8.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
> >>>>>>> jena-shaded-guava-3.8.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06
> jena-tdb2-3.8.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01
> >> jsonld-java-0.12.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process 232K Mar  5  2018
> libthrift-0.10.0.jar
> >>>>>>>>> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
> >>>>>>>>> -rw-r--r-- 1 process process  41K Oct 26  2017
> slf4j-api-1.7.25.jar
> >>>>>>>>> -rw-r--r-- 1 process process  12K Oct 26  2017
> >> slf4j-log4j12-1.7.25.jar
> >>>>>>>>>
> >>>>>>>>> 2.: Turns out, I don't need the jts. after commenting out the
> >> affected
> >>>>>>>>> lines, the server still runs fine. (But still without spatial
> >> index)
> >>>>>>>>>
> >>>>>>>>> Best Markus
> >>>>>>>>>
> >>>>>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <
> >> marco.neumann@gmail.com <ma...@gmail.com> <mailto:
> >> marco.neumann@gmail.com <ma...@gmail.com>>
> >>>>>>>> :
> >>>>>>>>>>
> >>>>>>>>>> Ok let's take a look at this.
> >>>>>>>>>>
> >>>>>>>>>> 1. please include in the indexer in the classpath. It's part of
> >> the
> >>>>>>>>> current
> >>>>>>>>>> jena distribution.
> >>>>>>>>>>
> >>>>>>>>>> 2. do you need jts? it's a package that allows you to index
> multi
> >> point
> >>>>>>>>>> geometries. here a sample query would be helpful. If single
> point
> >>>>>>>>>> geometries are indexed and used in conjunction with MBR range
> >> queries.
> >>>>>>>>>> there is no need for jts.
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
> >>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com>
> <mailto:
> >> mneumann@meteomatics.com <ma...@meteomatics.com>>
> >>>>>>>>> <mailto:mneumann@meteomatics.com <mailto:
> mneumann@meteomatics.com>
> >> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>
> >> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>
> >> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>>
> >>>>>>>>>> wrote:
> >>>>>>>>>>
> >>>>>>>>>>> Hi,
> >>>>>>>>>>> (sorry for the long post)
> >>>>>>>>>>>
> >>>>>>>>>>> I've been struggling with the spatial index for a while now.
> >>>>>>>>>>> I've read
> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>>> <
> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>>>> <
> >>>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
> <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>>> <
> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>>>>> and
> >>>>>>>>>>> skipped through about every spatial related thread here on the
> >> list.
> >>>>>>>>>>> I managed to get an in-memory version up and running at some
> >> point
> >>>>>>>>>>> following this
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>> <
> >>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>>>
> >>>>>>>>> <
> >>>>>>>>>
> >>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>> <
> >>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>> <
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>> <
> >>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>>>
> >>>>>>>>> <
> >>>>>>>>>
> >>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>> <
> >>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>> and this
> >>>>>>>>>>>
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>>
> >>>>>>> <
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> >>>>>>>>>
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> >>>>>>>>>>>
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
> >>>>>>>>>>>
> >>>>>>>>>>> But that was on a small dataset that I uploaded via the
> >> web-interface
> >>>>>>> of
> >>>>>>>>>>> Fuseki.
> >>>>>>>>>>>
> >>>>>>>>>>> Now the story is a bit different. I'm building the database
> using
> >>>>>>>>>>> tdbloader2 and would like to create the spatial index upfront.
> >>>>>>>>>>>
> >>>>>>>>>>> java -cp jena-spatial.jar jena.spatialindexer
> >> --desc=assembler_file
> >>>>>>>>>>> I could not figure out, how to get this line to work. I have
> the
> >>>>>>>>> following
> >>>>>>>>>>> possible scenarios:
> >>>>>>>>>>>
> >>>>>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in
> the
> >>>>>>>>> classpath:
> >>>>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> >>>>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>>>>>>> Error: Could not find or load main class jena.spatialindexer
> >>>>>>>>>>>
> >>>>>>>>>>> 2. I use the fuseki-server jar:
> >>>>>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
> >>>>>>>>>>> --desc=./run/configuration/mm.ttl
> >>>>>>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
> >>>>>>>>>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
> >>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not
> >> in a
> >>>>>>>>>>> transaction
> >>>>>>>>>>>
> >>>>>>>>>>> I managed to eliminate the warning about jts by including that
> >> in the
> >>>>>>>>>>> classpath, but the error remains the same (with full trace):
> >>>>>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
> >>>>>>>>>>> --desc=./run/configuration/mm.ttl
> >>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not
> >> in a
> >>>>>>>>>>> transaction
> >>>>>>>>>>>  at
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>>>>>>>>>>  at
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>>>>>>>>>>  at
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>>>>>>>>>>  at
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>>>>>>>>>>  at
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>>>>>>>>>>  at
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>>>>>>>>>>  at
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>>>>>>>>>>  at
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>>>>>>>>>>  at
> >>>>>>>>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>>>>>>>>>>  at
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>>>>>>>>>>  at
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>>>>>>>>>>  at
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>>>>>>>>>>  at
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>>>>>>>>  at
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>>>>>>>>  at jena.spatialindexer.exec(spatialindexer.java:110)
> >>>>>>>>>>>  at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>>>>>>>>>>  at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>>>>>>>>>>  at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>>>>>>>>>>  at jena.spatialindexer.main(spatialindexer.java:53)
> >>>>>>>>>>>
> >>>>>>>>>>> My configuration is the following:
> >>>>>>>>>>> @prefix :      <http://base/#> .
> >>>>>>>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >>>>>>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> >>>>>>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> >>>>>>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> >>>>>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
> >>>>>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
> >>>>>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>>>>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >>>>>>>>>>> # Spatial
> >>>>>>>>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
> >>>>>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> >>>>>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf
> spatial:SpatialIndex .
> >>>>>>>>>>>
> >>>>>>>>>>> :service_tdb_all  a                   fuseki:Service ;
> >>>>>>>>>>>  rdfs:label                    "TDB2 mm" ;
> >>>>>>>>>>>  fuseki:dataset                :spatial_dataset ;
> >>>>>>>>>>>  fuseki:name                   "mm" ;
> >>>>>>>>>>>  fuseki:serviceQuery           "query" , "sparql" ;
> >>>>>>>>>>>  fuseki:serviceReadGraphStore  "get" ;
> >>>>>>>>>>>  fuseki:serviceReadWriteGraphStore
> >>>>>>>>>>>          "data" ;
> >>>>>>>>>>>  fuseki:serviceUpdate          "update" ;
> >>>>>>>>>>>  fuseki:serviceUpload          "upload" .
> >>>>>>>>>>>
> >>>>>>>>>>> :spatial_dataset a spatial:SpatialDataset ;
> >>>>>>>>>>> spatial:dataset   :tdb_dataset_readwrite ;
> >>>>>>>>>>> spatial:index     <#indexLucene> ;
> >>>>>>>>>>> .
> >>>>>>>>>>>
> >>>>>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
> >>>>>>>>>>> spatial:directory <file:Lucene> ;
> >>>>>>>>>>> #spatial:directory "mem" ;
> >>>>>>>>>>> spatial:definition <#definition> ;
> >>>>>>>>>>> .
> >>>>>>>>>>>
> >>>>>>>>>>> <#definition> a spatial:EntityDefinition ;
> >>>>>>>>>>> spatial:entityField      "uri" ;
> >>>>>>>>>>> spatial:geoField     "geo" ;
> >>>>>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format
> >>>>>>>>>>> spatial:hasSpatialPredicatePairs (
> >>>>>>>>>>>   [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
> >>>>>>>>>>>   ) ;
> >>>>>>>>>>> # custom geo predicates for 2) Well Known Text (WKT) Literal
> >>>>>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ;
> >>>>>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT)
> >> Literal
> >>>>>>>>>>> spatial:spatialContextFactory
> >>>>>>>>>>> #
> >> "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
> >>>>>>>>>>>
> >>>>>>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
> >>>>>>>>>>> .
> >>>>>>>>>>>
> >>>>>>>>>>> :tdb_dataset_readwrite
> >>>>>>>>>>>  a              tdb2:DatasetTDB2 ;
> >>>>>>>>>>>  tdb2:location
> >>>>>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
> >>>>>>>>>>>
> >>>>>>>>>>> And I've changed the fuseki script to include the jts jar:
> >>>>>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
> >>>>>>>>>>>
> >>>>>>>>>>> I see no errors or warnings in the server log, when starting
> >> with that
> >>>>>>>>>>> configuration, the Lucene folder is created and populated with
> >>>>>>>>> something:
> >>>>>>>>>>> $ ll run/configuration/Lucene/
> >>>>>>>>>>> total 4
> >>>>>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
> >>>>>>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
> >>>>>>>>>>>
> >>>>>>>>>>> But any spatial query does not return any results.
> >>>>>>>>>>> Any help on how to tackle this would be highly appreciated.
> >>>>>>>>>>>
> >>>>>>>>>>> Best
> >>>>>>>>>>> Markus Neumann
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> --
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> ---
> >>>>>>>>>> Marco Neumann
> >>>>>>>>>> KONA
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>> --
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> ---
> >>>>>>>> Marco Neumann
> >>>>>>>> KONA
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>> --
> >>>>>>
> >>>>>>
> >>>>>> ---
> >>>>>> Marco Neumann
> >>>>>> KONA
> >>>
> >>
> >>
> >>
> >
> > --
> >
> >
> > ---
> > Marco Neumann
> > KONA
>
>
>

-- 


---
Marco Neumann
KONA

Re: Building a spatial index with jena/fuseki

Posted by ajs6f <aj...@apache.org>.
Marco--

I've got a PR at https://github.com/apache/jena/pull/471. Until we hear from Andy, could you perhaps try cloning that PR/branch and trying the new code out? If that is not a reasonable piece of work for you, no problem, but it would help greatly in validating that we've found and fixed the problem.

ajs6f

> On Sep 18, 2018, at 4:51 AM, Marco Neumann <ma...@gmail.com> wrote:
> 
> well spotted Adam, I think that nails it. I guess I was lucky with my setup
> to avoid this glitch so far. Don't want to anticipates Andy's call here but
> what's your plan? wrap the call into a transaction to fix it? If so I'd
> like to see it as an option in the code to work with tdb2 access methods if
> required in addition the current tdb support.
> 
> 
> On Mon, Sep 17, 2018 at 3:26 PM ajs6f <aj...@apache.org> wrote:
> 
>> Okay, I think we've got it. Nice debugging, Markus!
>> 
>> If you look at the line of the spatial indexer code that is throwing an
>> exception:
>> 
>> 
>> https://github.com/apache/jena/blob/master/jena-spatial/src/main/java/jena/spatialindexer.java#L110
>> 
>> indeed, it does not start a transaction against the dataset before
>> starting to read quads to index them. Now, in TDB1 this isn't inherently a
>> problem-- it's possible to work against a dataset without transactions.
>> (Although it's generally not a good idea at all.) But IIRC, TDB2 requires
>> transactions. If that's true (and Andy can verify that for us) then this is
>> a bug and we can fix it in a straightforward way.
>> 
>> Andy, can you confirm that diagnosis? If so, I'll open a ticket and write
>> a PR to use a Txn method to fix this.
>> 
>> ajs6f
>> 
>>> On Sep 17, 2018, at 10:14 AM, Markus Neumann <mn...@meteomatics.com>
>> wrote:
>>> 
>>> It seems I made a mess with absolute and relative paths all together. So
>> I created a minimal setup for testing:
>>> (I include the file-contents at the bottom)
>>> 
>>> $ export JENA_HOME=/srv/linked_data_store/apache-jena-3.8.0
>>> $ export PATH=$PATH:$JENA_HOME/bin
>>> $ tdb2.tdbloader
>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl
>>> 13:50:54 INFO  loader               :: Loader = LoaderPhased
>>> 13:50:54 INFO  loader               :: Data:
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl:
>> 13 mm-loc-mini.ttl 0.06s (Avg: 232)
>>> 13:50:54 INFO  loader               :: Data:
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl: 50
>> mm-rdf.ttl 0.01s (Avg: 6,250)
>>> 13:50:55 INFO  loader               :: Finish - index SPO
>>> 13:50:55 INFO  loader               :: Start replay index SPO
>>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
>> SPO->OSP
>>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
>> SPO->OSP [63 items, 0.0 seconds]
>>> 13:50:55 INFO  loader               :: Finish - index POS
>>> 13:50:55 INFO  loader               :: Finish - index OSP
>>> $ java -cp
>> /srv/linked_data_store/fuseki-server/fuseki-server.jar:/srv/linked_data_store/apache-jena-3.8.0/lib/*
>> jena.spatialindexer
>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>>> SLF4J: Class path contains multiple SLF4J bindings.
>>> SLF4J: Found binding in
>> [jar:file:/srv/linked_data_store/fuseki-server/fuseki-server.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>>> SLF4J: Found binding in
>> [jar:file:/srv/linked_data_store/apache-jena-3.8.0/lib/slf4j-log4j12-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>>> SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
>> explanation.
>>> SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>> transaction
>>>      at
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>      at
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>      at
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>      at
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>      at
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>      at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>      at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>      at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>      at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>      at
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>      at
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>      at
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>      at
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>      at
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>      at jena.spatialindexer.exec(spatialindexer.java:110)
>>>      at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>      at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>      at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>      at jena.spatialindexer.main(spatialindexer.java:53)
>>> 
>>> I can get rid of the SLF4J warnings:
>>> $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar
>> jena.spatialindexer
>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>> transaction
>>>      at
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>      at
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>      at
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>      at
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>      at
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>      at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>      at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>      at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>      at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>      at
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>      at
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>      at
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>      at
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>      at
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>      at jena.spatialindexer.exec(spatialindexer.java:110)
>>>      at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>      at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>      at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>      at jena.spatialindexer.main(spatialindexer.java:53)
>>> 
>>> There is no other java instance running at the time when I run those
>> commands.
>>> All paths are fully qualified and double checked. The destination
>> directory and the Lucene directory were cleared just before.
>>> 
>>> The server does start and serve the data without errors or warnings in
>> the log, but spatial queries do not work.
>>> 
>>> Does anyone see a reason for the TransactionException?
>>> Thanks and best regards
>>> Markus
>>> 
>>> Attachments:
>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
>>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
>>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
>>> @prefix dcterms: <http://purl.org/dc/terms/> .
>>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#>
>>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
>>> 
>>> <http://rdf.meteomatics.com/mm/>
>>>   dcterms:publisher <http://api.meteomatics.com/Imprint.html> ;
>>>   dcterms:title "Meteomatics RDF Vocabulary"@en .
>>> 
>>> mm:location a rdf:Property ;
>>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>   rdfs:label "location" ;
>>>   dcterms:description "Location of a measurement"@en .
>>> 
>>> mm:elevation a rdf:Property ;
>>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>   rdfs:label "elevation" ;
>>>   dcterms:description "Elevation of a location"@en .
>>> 
>>> mm:validdate a rdf:Property ;
>>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>   rdfs:label "validdate" ;
>>>   dcterms:description "Temporal information describing when a
>> Measurement is/was valid"@en .
>>> 
>>> mm:value a rdf:Property ;
>>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>   rdfs:label "value" ;
>>>   dcterms:description "The (observed or predicted) value of a
>> Measurement"@en .
>>> 
>>> mm:parameter a rdf:Property ;
>>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>   rdfs:label "parameter" ;
>>>   dcterms:description "what was measured"@en .
>>> 
>>> mm:station_name a rdf:Property ;
>>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>   rdfs:label "station_name" ;
>>>   dcterms:description "Name of a station"@en .
>>> 
>>> mm:abbreviation a rdf:Property ;
>>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>   rdfs:label "abbreviation" ;
>>>   dcterms:description "Abbreviation of a station name"@en .
>>> 
>>> mm:didok_id a rdf:Property ;
>>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>   rdfs:label "didok_id" ;
>>>   dcterms:description "didok id of a station"@en .
>>> 
>>> mm:unit_symbol a rdf:Property ;
>>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>   rdfs:label "unit symbol" ;
>>>   dcterms:description "unit symbol of a parameter"@en .
>>> 
>>> mm:Measurement a rdf:Class ;
>>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>   rdfs:label "Measurement" ;
>>>   dcterms:description "Measurement of a specific weather parameter at
>> specific location at a specific date (both future or past)" .
>>> 
>>> mm:Location a rdf:Class ;
>>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>   rdfs:label "Location" ;
>>>   dcterms:description "A Point on the globe where we observe
>> weather"@en .
>>> 
>>> mm:Parameter a rdf:Class ;
>>>   rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>   rdfs:label "Parameter" ;
>>>   dcterms:description "A parameter describing an observable aspect of
>> the weather"@en .
>>> 
>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
>>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
>>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
>>> @prefix dcterms: <http://purl.org/dc/terms/> .
>>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
>>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
>>> @prefix mm-measurements: <http://rdf.meteomatics.com/mm/measurements/> .
>>> @prefix mm-locations: <http://rdf.meteomatics.com/mm/locations/> .
>>> 
>>> 
>>> mm-locations:8500015 a mm:Location ;
>>>   a geosparql:Geometry ;
>>>   mm:didok_id 8500015 ;
>>>   geo:lat 47.54259 ;
>>>   geo:long 7.61574 ;
>>>   mm:elevation 273 .
>>> 
>>> 
>>> mm-locations:8504238 a mm:Location ;
>>>   a geosparql:Geometry ;
>>>   geosparql:asWKT "POINT(6.86466645231
>> 47.0840196485)"^^geosparql:wktLiteral ;
>>>   mm:didok_id 8504238 ;
>>>   geo:lat 47.08402 ;
>>>   geo:long 6.86467 ;
>>>   mm:elevation 1086 .
>>> 
>>> /srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>>> @prefix :      <http://base/#> .
>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>> # Spatial
>>> #[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>>> #spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>> #spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>>> 
>>> :service_tdb_all  a                   fuseki:Service ;
>>>       rdfs:label                    "TDB2 mm" ;
>>>       fuseki:dataset                :spatial_dataset ;
>>>       fuseki:name                   "mm" ;
>>>       fuseki:serviceQuery           "query" , "sparql" ;
>>>       fuseki:serviceReadGraphStore  "get" ;
>>>       fuseki:serviceReadWriteGraphStore
>>>               "data" ;
>>>       fuseki:serviceUpdate          "update" ;
>>>       fuseki:serviceUpload          "upload" .
>>> 
>>> :spatial_dataset a spatial:SpatialDataset ;
>>>   spatial:dataset   :tdb_dataset_readwrite ;
>>>   spatial:index     <#indexLucene> ;
>>>   .
>>> 
>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>>   spatial:directory <file:Lucene> ;
>>>   #spatial:directory "mem" ;
>>>   spatial:definition <#definition> ;
>>>   .
>>> 
>>> <#definition> a spatial:EntityDefinition ;
>>>   spatial:entityField      "uri" ;
>>>   spatial:geoField     "geo" ;
>>>   # custom geo predicates for 1) Latitude/Longitude Format
>>>   spatial:hasSpatialPredicatePairs (
>>>        [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>>        ) ;
>>>   # custom geo predicates for 2) Well Known Text (WKT) Literal
>>>   spatial:hasWKTPredicates (geosparql:asWKT) ;
>>>   #spatial:spatialContextFactory
>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>> #     "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>>   .
>>> 
>>> :tdb_dataset_readwrite
>>>       a              tdb2:DatasetTDB2 ;
>>>       tdb2:location
>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>> 
>>> 
>>>> Am 17.09.2018 um 15:15 schrieb ajs6f <aj...@apache.org>:
>>>> 
>>>> I think you might have misunderstood the use of $JENA_HOME, or perhaps
>> the Java classpath. $JENA_HOME, which should generally be an absolute
>> filepath, allows the Jena scripts to find their libraries at runtime.
>> Internally, the scripts use $JENA_HOME to set up the classpaths with which
>> to start running Java code. But in this case, you're not using the scripts.
>> You're calling a Java class directly, which means you have to give it all
>> the libraries directly, using the classpath flag directly. For example,
>> your second attempt:
>>>> 
>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
>> --desc=fuseki-server/run/configuration/mm.ttl
>>>> Error: Could not find or load main class
>> apache-jena-3.8.0.lib.commons-cli-1.4.jar
>>>> 
>>>> may have failed because whatever directory you are in probably doesn't
>> happen to have a Jena distribution in it called "apache-jena-3.8.0".
>> Perhaps try:
>>>> 
>>>> java -cp $JENA_HOME/lib/* jena.spatialindexer
>> --desc=fuseki-server/run/configuration/mm.ttl
>>>> 
>>>> Your first example looks like it might be misusing the -cp flag [1].
>> You probably don't want the *.jar, just *, like
>>>> 
>>>> java -cp lib/* jena.spatialindexer
>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>> 
>>>> especially if you happen to be using Windows. [2] That might not be the
>> entire story, but you can at least try those invocations and see if you get
>> anything different/better.
>>>> 
>>>> ajs6f
>>>> 
>>>> [1]
>> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
>> <
>> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
>>> 
>>>> [2]
>> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
>> <
>> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
>>> 
>>>> 
>>>> 
>>>>> On Sep 17, 2018, at 7:07 AM, Markus Neumann <mneumann@meteomatics.com
>> <ma...@meteomatics.com>> wrote:
>>>>> 
>>>>> Ok, that's exactly what I did here:
>>>>> $ java -cp lib/*.jar jena.spatialindexer
>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>>>>> 
>>>>> Or from outside JENA_HOME:
>>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
>> --desc=fuseki-server/run/configuration/mm.ttl
>>>>> Error: Could not find or load main class
>> apache-jena-3.8.0.lib.commons-cli-1.4.jar
>>>>> 
>>>>> Or did I missunderstand something?
>>>>> 
>>>>>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <marco.neumann@gmail.com
>>> :
>>>>>> 
>>>>>> don't worry it's a common problem and frequent source of confusion
>> not only
>>>>>> with jena but java projects. try to simply inlcude all the jars.
>>>>>> 
>>>>>> I presume you run this on a linux box with OpenJDK 8. correct?
>>>>>> 
>>>>>> now once you have set up jena just add the following
>>>>>> {replace_with_your_path}/apache-jena-3.8.0/lib/*
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <
>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
>> mneumann@meteomatics.com <ma...@meteomatics.com>>>
>>>>>> wrote:
>>>>>> 
>>>>>>> This is embarrassing but I don't get it.
>>>>>>> 
>>>>>>> I've configured $JENA_HOME and adjusted the PATH.
>>>>>>> 
>>>>>>> Now what classpath should I include when invoking the indexer?
>>>>>>> What I've tried so far:
>>>>>>> 
>>>>>>> $ cd $JENA_HOME
>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>>> Error: Could not find or load main class jena.spatialindexer
>>>>>>> $ java -cp lib/*.jar jena.spatialindexer
>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>>>>>>> 
>>>>>>> Thanks for your patience
>>>>>>> 
>>>>>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <
>> marco.neumann@gmail.com <ma...@gmail.com>>:
>>>>>>>> 
>>>>>>>> yes correct, this looks good. now include the classpath during
>> invocation
>>>>>>>> of the spatialindexer
>>>>>>>> 
>>>>>>>> in addition it's always a good idea to properly configure jena
>> along your
>>>>>>>> java runtime environment settings to avoid jdk / lib conflicts
>> during
>>>>>>>> execution.
>>>>>>>> 
>>>>>>>> https://jena.apache.org/documentation/tools/index.html <
>> https://jena.apache.org/documentation/tools/index.html> <
>>>>>>> https://jena.apache.org/documentation/tools/index.html <
>> https://jena.apache.org/documentation/tools/index.html> <
>> https://jena.apache.org/documentation/tools/index.html <
>> https://jena.apache.org/documentation/tools/index.html>>>
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
>>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
>> mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:
>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
>> mneumann@meteomatics.com <ma...@meteomatics.com>>>>
>>>>>>>> wrote:
>>>>>>>> 
>>>>>>>>> 1.: what do you mean by indexer?
>>>>>>>>> Probably my biggest problem is, that I have no clue how to find
>> out,
>>>>>>> where
>>>>>>>>> the jena.spatialindexer could be located except for asking here.
>>>>>>>>> 
>>>>>>>>> Here is the content of the apache jena I downloaded:
>>>>>>>>> $ ls -lh ../apache-jena-3.8.0/lib
>>>>>>>>> total 17M
>>>>>>>>> -rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
>>>>>>>>> -rw-r--r-- 1 process process  53K Oct 26  2017 commons-cli-1.4.jar
>>>>>>>>> -rw-r--r-- 1 process process 328K Mar  5  2018
>> commons-codec-1.11.jar
>>>>>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59
>> commons-compress-1.17.jar
>>>>>>>>> -rw-r--r-- 1 process process  41K Mar  5  2018 commons-csv-1.5.jar
>>>>>>>>> -rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
>>>>>>>>> -rw-r--r-- 1 process process 425K Oct 26  2017
>> commons-lang3-3.4.jar
>>>>>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01 httpclient-4.5.5.jar
>>>>>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
>>>>>>> httpclient-cache-4.5.5.jar
>>>>>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
>>>>>>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
>>>>>>>>> jackson-annotations-2.9.0.jar
>>>>>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01
>> jackson-core-2.9.5.jar
>>>>>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
>>>>>>> jackson-databind-2.9.5.jar
>>>>>>>>> -rw-r--r-- 1 process process  17K Oct 26  2017
>> jcl-over-slf4j-1.7.25.jar
>>>>>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
>>>>>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01 jena-base-3.8.0.jar
>>>>>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07 jena-cmds-3.8.0.jar
>>>>>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02 jena-core-3.8.0.jar
>>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05
>> jena-dboe-base-3.8.0.jar
>>>>>>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05
>> jena-dboe-index-3.8.0.jar
>>>>>>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
>>>>>>>>> jena-dboe-transaction-3.8.0.jar
>>>>>>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
>>>>>>>>> jena-dboe-trans-data-3.8.0.jar
>>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
>>>>>>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
>>>>>>> jena-rdfconnection-3.8.0.jar
>>>>>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
>>>>>>> jena-shaded-guava-3.8.0.jar
>>>>>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06 jena-tdb2-3.8.0.jar
>>>>>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
>>>>>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01
>> jsonld-java-0.12.0.jar
>>>>>>>>> -rw-r--r-- 1 process process 232K Mar  5  2018 libthrift-0.10.0.jar
>>>>>>>>> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
>>>>>>>>> -rw-r--r-- 1 process process  41K Oct 26  2017 slf4j-api-1.7.25.jar
>>>>>>>>> -rw-r--r-- 1 process process  12K Oct 26  2017
>> slf4j-log4j12-1.7.25.jar
>>>>>>>>> 
>>>>>>>>> 2.: Turns out, I don't need the jts. after commenting out the
>> affected
>>>>>>>>> lines, the server still runs fine. (But still without spatial
>> index)
>>>>>>>>> 
>>>>>>>>> Best Markus
>>>>>>>>> 
>>>>>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <
>> marco.neumann@gmail.com <ma...@gmail.com> <mailto:
>> marco.neumann@gmail.com <ma...@gmail.com>>
>>>>>>>> :
>>>>>>>>>> 
>>>>>>>>>> Ok let's take a look at this.
>>>>>>>>>> 
>>>>>>>>>> 1. please include in the indexer in the classpath. It's part of
>> the
>>>>>>>>> current
>>>>>>>>>> jena distribution.
>>>>>>>>>> 
>>>>>>>>>> 2. do you need jts? it's a package that allows you to index multi
>> point
>>>>>>>>>> geometries. here a sample query would be helpful. If single point
>>>>>>>>>> geometries are indexed and used in conjunction with MBR range
>> queries.
>>>>>>>>>> there is no need for jts.
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
>>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
>> mneumann@meteomatics.com <ma...@meteomatics.com>>
>>>>>>>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>
>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>
>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>
>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>>
>>>>>>>>>> wrote:
>>>>>>>>>> 
>>>>>>>>>>> Hi,
>>>>>>>>>>> (sorry for the long post)
>>>>>>>>>>> 
>>>>>>>>>>> I've been struggling with the spatial index for a while now.
>>>>>>>>>>> I've read
>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>>>> <
>>>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>>>>> and
>>>>>>>>>>> skipped through about every spatial related thread here on the
>> list.
>>>>>>>>>>> I managed to get an in-memory version up and running at some
>> point
>>>>>>>>>>> following this
>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> 
>>>>>>> <
>>>>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> 
>>>>>>>> 
>>>>>>>>> <
>>>>>>>>> 
>>>>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> 
>>>>>>> <
>>>>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> 
>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>>> <
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> 
>>>>>>> <
>>>>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> 
>>>>>>>> 
>>>>>>>>> <
>>>>>>>>> 
>>>>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> 
>>>>>>> <
>>>>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> 
>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>>>> 
>>>>>>>>>>> and this
>>>>>>>>>>> 
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>>
>>>>>>> <
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>>>>>> 
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>>>>>>>> 
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>>>>>>>>>>> 
>>>>>>>>>>> But that was on a small dataset that I uploaded via the
>> web-interface
>>>>>>> of
>>>>>>>>>>> Fuseki.
>>>>>>>>>>> 
>>>>>>>>>>> Now the story is a bit different. I'm building the database using
>>>>>>>>>>> tdbloader2 and would like to create the spatial index upfront.
>>>>>>>>>>> 
>>>>>>>>>>> java -cp jena-spatial.jar jena.spatialindexer
>> --desc=assembler_file
>>>>>>>>>>> I could not figure out, how to get this line to work. I have the
>>>>>>>>> following
>>>>>>>>>>> possible scenarios:
>>>>>>>>>>> 
>>>>>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in the
>>>>>>>>> classpath:
>>>>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>>>>>>> Error: Could not find or load main class jena.spatialindexer
>>>>>>>>>>> 
>>>>>>>>>>> 2. I use the fuseki-server jar:
>>>>>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
>>>>>>>>>>> --desc=./run/configuration/mm.ttl
>>>>>>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
>>>>>>>>>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
>>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not
>> in a
>>>>>>>>>>> transaction
>>>>>>>>>>> 
>>>>>>>>>>> I managed to eliminate the warning about jts by including that
>> in the
>>>>>>>>>>> classpath, but the error remains the same (with full trace):
>>>>>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
>>>>>>>>>>> --desc=./run/configuration/mm.ttl
>>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not
>> in a
>>>>>>>>>>> transaction
>>>>>>>>>>>  at
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>>>>>>>>>  at
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>>>>>>>>>  at
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>>>>>>>>>  at
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>>>>>>>>>  at
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>>>>>>>>>  at
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>>>>>>>>>  at
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>>>>>>>>>  at
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>>>>>>>>>  at
>>>>>>>>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>>>>>>>>>  at
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>>>>>>>>>  at
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>>>>>>>>>  at
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>>>>>>>>>  at
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>>>>>>  at
>>>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>>>>>>  at jena.spatialindexer.exec(spatialindexer.java:110)
>>>>>>>>>>>  at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>>>>>>>>>  at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>>>>>>>>>  at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>>>>>>>>>  at jena.spatialindexer.main(spatialindexer.java:53)
>>>>>>>>>>> 
>>>>>>>>>>> My configuration is the following:
>>>>>>>>>>> @prefix :      <http://base/#> .
>>>>>>>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>>>>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>>>>>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>>>>>>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>>>>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>>>>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>>>>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>>>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>>>>>>>>>> # Spatial
>>>>>>>>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>>>>>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>>>>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>>>>>>>>>>> 
>>>>>>>>>>> :service_tdb_all  a                   fuseki:Service ;
>>>>>>>>>>>  rdfs:label                    "TDB2 mm" ;
>>>>>>>>>>>  fuseki:dataset                :spatial_dataset ;
>>>>>>>>>>>  fuseki:name                   "mm" ;
>>>>>>>>>>>  fuseki:serviceQuery           "query" , "sparql" ;
>>>>>>>>>>>  fuseki:serviceReadGraphStore  "get" ;
>>>>>>>>>>>  fuseki:serviceReadWriteGraphStore
>>>>>>>>>>>          "data" ;
>>>>>>>>>>>  fuseki:serviceUpdate          "update" ;
>>>>>>>>>>>  fuseki:serviceUpload          "upload" .
>>>>>>>>>>> 
>>>>>>>>>>> :spatial_dataset a spatial:SpatialDataset ;
>>>>>>>>>>> spatial:dataset   :tdb_dataset_readwrite ;
>>>>>>>>>>> spatial:index     <#indexLucene> ;
>>>>>>>>>>> .
>>>>>>>>>>> 
>>>>>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>>>>>>>>>> spatial:directory <file:Lucene> ;
>>>>>>>>>>> #spatial:directory "mem" ;
>>>>>>>>>>> spatial:definition <#definition> ;
>>>>>>>>>>> .
>>>>>>>>>>> 
>>>>>>>>>>> <#definition> a spatial:EntityDefinition ;
>>>>>>>>>>> spatial:entityField      "uri" ;
>>>>>>>>>>> spatial:geoField     "geo" ;
>>>>>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format
>>>>>>>>>>> spatial:hasSpatialPredicatePairs (
>>>>>>>>>>>   [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>>>>>>>>>>   ) ;
>>>>>>>>>>> # custom geo predicates for 2) Well Known Text (WKT) Literal
>>>>>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ;
>>>>>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT)
>> Literal
>>>>>>>>>>> spatial:spatialContextFactory
>>>>>>>>>>> #
>> "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>>>>>>>>>> 
>>>>>>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>>>>>>>>>> .
>>>>>>>>>>> 
>>>>>>>>>>> :tdb_dataset_readwrite
>>>>>>>>>>>  a              tdb2:DatasetTDB2 ;
>>>>>>>>>>>  tdb2:location
>>>>>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>>>>>>>>>> 
>>>>>>>>>>> And I've changed the fuseki script to include the jts jar:
>>>>>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
>>>>>>>>>>> 
>>>>>>>>>>> I see no errors or warnings in the server log, when starting
>> with that
>>>>>>>>>>> configuration, the Lucene folder is created and populated with
>>>>>>>>> something:
>>>>>>>>>>> $ ll run/configuration/Lucene/
>>>>>>>>>>> total 4
>>>>>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
>>>>>>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
>>>>>>>>>>> 
>>>>>>>>>>> But any spatial query does not return any results.
>>>>>>>>>>> Any help on how to tackle this would be highly appreciated.
>>>>>>>>>>> 
>>>>>>>>>>> Best
>>>>>>>>>>> Markus Neumann
>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> --
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> ---
>>>>>>>>>> Marco Neumann
>>>>>>>>>> KONA
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> 
>>>>>>>> --
>>>>>>>> 
>>>>>>>> 
>>>>>>>> ---
>>>>>>>> Marco Neumann
>>>>>>>> KONA
>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>>> --
>>>>>> 
>>>>>> 
>>>>>> ---
>>>>>> Marco Neumann
>>>>>> KONA
>>> 
>> 
>> 
>> 
> 
> -- 
> 
> 
> ---
> Marco Neumann
> KONA

Re: Building a spatial index with jena/fuseki

Posted by Marco Neumann <ma...@gmail.com>.
well spotted Adam, I think that nails it. I guess I was lucky with my setup
to avoid this glitch so far. Don't want to anticipates Andy's call here but
what's your plan? wrap the call into a transaction to fix it? If so I'd
like to see it as an option in the code to work with tdb2 access methods if
required in addition the current tdb support.


On Mon, Sep 17, 2018 at 3:26 PM ajs6f <aj...@apache.org> wrote:

> Okay, I think we've got it. Nice debugging, Markus!
>
> If you look at the line of the spatial indexer code that is throwing an
> exception:
>
>
> https://github.com/apache/jena/blob/master/jena-spatial/src/main/java/jena/spatialindexer.java#L110
>
> indeed, it does not start a transaction against the dataset before
> starting to read quads to index them. Now, in TDB1 this isn't inherently a
> problem-- it's possible to work against a dataset without transactions.
> (Although it's generally not a good idea at all.) But IIRC, TDB2 requires
> transactions. If that's true (and Andy can verify that for us) then this is
> a bug and we can fix it in a straightforward way.
>
> Andy, can you confirm that diagnosis? If so, I'll open a ticket and write
> a PR to use a Txn method to fix this.
>
> ajs6f
>
> > On Sep 17, 2018, at 10:14 AM, Markus Neumann <mn...@meteomatics.com>
> wrote:
> >
> > It seems I made a mess with absolute and relative paths all together. So
> I created a minimal setup for testing:
> > (I include the file-contents at the bottom)
> >
> > $ export JENA_HOME=/srv/linked_data_store/apache-jena-3.8.0
> > $ export PATH=$PATH:$JENA_HOME/bin
> > $ tdb2.tdbloader
> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl
> > 13:50:54 INFO  loader               :: Loader = LoaderPhased
> > 13:50:54 INFO  loader               :: Data:
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl:
> 13 mm-loc-mini.ttl 0.06s (Avg: 232)
> > 13:50:54 INFO  loader               :: Data:
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl: 50
> mm-rdf.ttl 0.01s (Avg: 6,250)
> > 13:50:55 INFO  loader               :: Finish - index SPO
> > 13:50:55 INFO  loader               :: Start replay index SPO
> > 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
> SPO->OSP
> > 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
> SPO->OSP [63 items, 0.0 seconds]
> > 13:50:55 INFO  loader               :: Finish - index POS
> > 13:50:55 INFO  loader               :: Finish - index OSP
> > $ java -cp
> /srv/linked_data_store/fuseki-server/fuseki-server.jar:/srv/linked_data_store/apache-jena-3.8.0/lib/*
> jena.spatialindexer
> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> > SLF4J: Class path contains multiple SLF4J bindings.
> > SLF4J: Found binding in
> [jar:file:/srv/linked_data_store/fuseki-server/fuseki-server.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> > SLF4J: Found binding in
> [jar:file:/srv/linked_data_store/apache-jena-3.8.0/lib/slf4j-log4j12-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> > SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
> explanation.
> > SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
> > org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> transaction
> >       at
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >       at
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >       at
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >       at
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >       at
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >       at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >       at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >       at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >       at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >       at
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >       at
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >       at
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >       at
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >       at
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >       at jena.spatialindexer.exec(spatialindexer.java:110)
> >       at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >       at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >       at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >       at jena.spatialindexer.main(spatialindexer.java:53)
> >
> > I can get rid of the SLF4J warnings:
> > $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar
> jena.spatialindexer
> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> > org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> transaction
> >       at
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >       at
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >       at
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >       at
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >       at
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >       at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >       at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >       at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >       at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >       at
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >       at
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >       at
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >       at
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >       at
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >       at jena.spatialindexer.exec(spatialindexer.java:110)
> >       at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >       at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >       at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >       at jena.spatialindexer.main(spatialindexer.java:53)
> >
> > There is no other java instance running at the time when I run those
> commands.
> > All paths are fully qualified and double checked. The destination
> directory and the Lucene directory were cleared just before.
> >
> > The server does start and serve the data without errors or warnings in
> the log, but spatial queries do not work.
> >
> > Does anyone see a reason for the TransactionException?
> > Thanks and best regards
> > Markus
> >
> > Attachments:
> > /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
> > @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> > @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> > @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> > @prefix owl: <http://www.w3.org/2002/07/owl#> .
> > @prefix dc: <http://purl.org/dc/elements/1.1/> .
> > @prefix dcterms: <http://purl.org/dc/terms/> .
> > @prefix xsd: <http://www.w3.org/2001/XMLSchema#>
> > @prefix mm: <http://rdf.meteomatics.com/mm/> .
> >
> > <http://rdf.meteomatics.com/mm/>
> >    dcterms:publisher <http://api.meteomatics.com/Imprint.html> ;
> >    dcterms:title "Meteomatics RDF Vocabulary"@en .
> >
> > mm:location a rdf:Property ;
> >    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >    rdfs:label "location" ;
> >    dcterms:description "Location of a measurement"@en .
> >
> > mm:elevation a rdf:Property ;
> >    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >    rdfs:label "elevation" ;
> >    dcterms:description "Elevation of a location"@en .
> >
> > mm:validdate a rdf:Property ;
> >    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >    rdfs:label "validdate" ;
> >    dcterms:description "Temporal information describing when a
> Measurement is/was valid"@en .
> >
> > mm:value a rdf:Property ;
> >    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >    rdfs:label "value" ;
> >    dcterms:description "The (observed or predicted) value of a
> Measurement"@en .
> >
> > mm:parameter a rdf:Property ;
> >    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >    rdfs:label "parameter" ;
> >    dcterms:description "what was measured"@en .
> >
> > mm:station_name a rdf:Property ;
> >    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >    rdfs:label "station_name" ;
> >    dcterms:description "Name of a station"@en .
> >
> > mm:abbreviation a rdf:Property ;
> >    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >    rdfs:label "abbreviation" ;
> >    dcterms:description "Abbreviation of a station name"@en .
> >
> > mm:didok_id a rdf:Property ;
> >    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >    rdfs:label "didok_id" ;
> >    dcterms:description "didok id of a station"@en .
> >
> > mm:unit_symbol a rdf:Property ;
> >    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >    rdfs:label "unit symbol" ;
> >    dcterms:description "unit symbol of a parameter"@en .
> >
> > mm:Measurement a rdf:Class ;
> >    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >    rdfs:label "Measurement" ;
> >    dcterms:description "Measurement of a specific weather parameter at
> specific location at a specific date (both future or past)" .
> >
> > mm:Location a rdf:Class ;
> >    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >    rdfs:label "Location" ;
> >    dcterms:description "A Point on the globe where we observe
> weather"@en .
> >
> > mm:Parameter a rdf:Class ;
> >    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >    rdfs:label "Parameter" ;
> >    dcterms:description "A parameter describing an observable aspect of
> the weather"@en .
> >
> > /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
> > @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> > @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> > @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> > @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> > @prefix owl: <http://www.w3.org/2002/07/owl#> .
> > @prefix dc: <http://purl.org/dc/elements/1.1/> .
> > @prefix dcterms: <http://purl.org/dc/terms/> .
> > @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
> > @prefix mm: <http://rdf.meteomatics.com/mm/> .
> > @prefix mm-measurements: <http://rdf.meteomatics.com/mm/measurements/> .
> > @prefix mm-locations: <http://rdf.meteomatics.com/mm/locations/> .
> >
> >
> > mm-locations:8500015 a mm:Location ;
> >    a geosparql:Geometry ;
> >    mm:didok_id 8500015 ;
> >    geo:lat 47.54259 ;
> >    geo:long 7.61574 ;
> >    mm:elevation 273 .
> >
> >
> > mm-locations:8504238 a mm:Location ;
> >    a geosparql:Geometry ;
> >    geosparql:asWKT "POINT(6.86466645231
> 47.0840196485)"^^geosparql:wktLiteral ;
> >    mm:didok_id 8504238 ;
> >    geo:lat 47.08402 ;
> >    geo:long 6.86467 ;
> >    mm:elevation 1086 .
> >
> > /srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> > @prefix :      <http://base/#> .
> > @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> > @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> > @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> > @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> > @prefix fuseki: <http://jena.apache.org/fuseki#> .
> > @prefix spatial: <http://jena.apache.org/spatial#> .
> > @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> > @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> > # Spatial
> > #[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
> > #spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> > #spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
> >
> > :service_tdb_all  a                   fuseki:Service ;
> >        rdfs:label                    "TDB2 mm" ;
> >        fuseki:dataset                :spatial_dataset ;
> >        fuseki:name                   "mm" ;
> >        fuseki:serviceQuery           "query" , "sparql" ;
> >        fuseki:serviceReadGraphStore  "get" ;
> >        fuseki:serviceReadWriteGraphStore
> >                "data" ;
> >        fuseki:serviceUpdate          "update" ;
> >        fuseki:serviceUpload          "upload" .
> >
> > :spatial_dataset a spatial:SpatialDataset ;
> >    spatial:dataset   :tdb_dataset_readwrite ;
> >    spatial:index     <#indexLucene> ;
> >    .
> >
> > <#indexLucene> a spatial:SpatialIndexLucene ;
> >    spatial:directory <file:Lucene> ;
> >    #spatial:directory "mem" ;
> >    spatial:definition <#definition> ;
> >    .
> >
> > <#definition> a spatial:EntityDefinition ;
> >    spatial:entityField      "uri" ;
> >    spatial:geoField     "geo" ;
> >    # custom geo predicates for 1) Latitude/Longitude Format
> >    spatial:hasSpatialPredicatePairs (
> >         [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
> >         ) ;
> >    # custom geo predicates for 2) Well Known Text (WKT) Literal
> >    spatial:hasWKTPredicates (geosparql:asWKT) ;
> >    #spatial:spatialContextFactory
> > #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
> > #     "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
> >    .
> >
> > :tdb_dataset_readwrite
> >        a              tdb2:DatasetTDB2 ;
> >        tdb2:location
> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
> >
> >
> >> Am 17.09.2018 um 15:15 schrieb ajs6f <aj...@apache.org>:
> >>
> >> I think you might have misunderstood the use of $JENA_HOME, or perhaps
> the Java classpath. $JENA_HOME, which should generally be an absolute
> filepath, allows the Jena scripts to find their libraries at runtime.
> Internally, the scripts use $JENA_HOME to set up the classpaths with which
> to start running Java code. But in this case, you're not using the scripts.
> You're calling a Java class directly, which means you have to give it all
> the libraries directly, using the classpath flag directly. For example,
> your second attempt:
> >>
> >> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
> --desc=fuseki-server/run/configuration/mm.ttl
> >> Error: Could not find or load main class
> apache-jena-3.8.0.lib.commons-cli-1.4.jar
> >>
> >> may have failed because whatever directory you are in probably doesn't
> happen to have a Jena distribution in it called "apache-jena-3.8.0".
> Perhaps try:
> >>
> >> java -cp $JENA_HOME/lib/* jena.spatialindexer
> --desc=fuseki-server/run/configuration/mm.ttl
> >>
> >> Your first example looks like it might be misusing the -cp flag [1].
> You probably don't want the *.jar, just *, like
> >>
> >> java -cp lib/* jena.spatialindexer
> --desc=../fuseki-server/run/configuration/mm.ttl
> >>
> >> especially if you happen to be using Windows. [2] That might not be the
> entire story, but you can at least try those invocations and see if you get
> anything different/better.
> >>
> >> ajs6f
> >>
> >> [1]
> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
> <
> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
> >
> >> [2]
> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
> <
> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
> >
> >>
> >>
> >>> On Sep 17, 2018, at 7:07 AM, Markus Neumann <mneumann@meteomatics.com
> <ma...@meteomatics.com>> wrote:
> >>>
> >>> Ok, that's exactly what I did here:
> >>> $ java -cp lib/*.jar jena.spatialindexer
> --desc=../fuseki-server/run/configuration/mm.ttl
> >>> Error: Could not find or load main class lib.commons-cli-1.4.jar
> >>>
> >>> Or from outside JENA_HOME:
> >>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
> --desc=fuseki-server/run/configuration/mm.ttl
> >>> Error: Could not find or load main class
> apache-jena-3.8.0.lib.commons-cli-1.4.jar
> >>>
> >>> Or did I missunderstand something?
> >>>
> >>>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <marco.neumann@gmail.com
> >:
> >>>>
> >>>> don't worry it's a common problem and frequent source of confusion
> not only
> >>>> with jena but java projects. try to simply inlcude all the jars.
> >>>>
> >>>> I presume you run this on a linux box with OpenJDK 8. correct?
> >>>>
> >>>> now once you have set up jena just add the following
> >>>> {replace_with_your_path}/apache-jena-3.8.0/lib/*
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <
> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
> mneumann@meteomatics.com <ma...@meteomatics.com>>>
> >>>> wrote:
> >>>>
> >>>>> This is embarrassing but I don't get it.
> >>>>>
> >>>>> I've configured $JENA_HOME and adjusted the PATH.
> >>>>>
> >>>>> Now what classpath should I include when invoking the indexer?
> >>>>> What I've tried so far:
> >>>>>
> >>>>> $ cd $JENA_HOME
> >>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> >>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>> Error: Could not find or load main class jena.spatialindexer
> >>>>> $ java -cp lib/*.jar jena.spatialindexer
> >>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
> >>>>>
> >>>>> Thanks for your patience
> >>>>>
> >>>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <
> marco.neumann@gmail.com <ma...@gmail.com>>:
> >>>>>>
> >>>>>> yes correct, this looks good. now include the classpath during
> invocation
> >>>>>> of the spatialindexer
> >>>>>>
> >>>>>> in addition it's always a good idea to properly configure jena
> along your
> >>>>>> java runtime environment settings to avoid jdk / lib conflicts
> during
> >>>>>> execution.
> >>>>>>
> >>>>>> https://jena.apache.org/documentation/tools/index.html <
> https://jena.apache.org/documentation/tools/index.html> <
> >>>>> https://jena.apache.org/documentation/tools/index.html <
> https://jena.apache.org/documentation/tools/index.html> <
> https://jena.apache.org/documentation/tools/index.html <
> https://jena.apache.org/documentation/tools/index.html>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
> >>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
> mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:
> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
> mneumann@meteomatics.com <ma...@meteomatics.com>>>>
> >>>>>> wrote:
> >>>>>>
> >>>>>>> 1.: what do you mean by indexer?
> >>>>>>> Probably my biggest problem is, that I have no clue how to find
> out,
> >>>>> where
> >>>>>>> the jena.spatialindexer could be located except for asking here.
> >>>>>>>
> >>>>>>> Here is the content of the apache jena I downloaded:
> >>>>>>> $ ls -lh ../apache-jena-3.8.0/lib
> >>>>>>> total 17M
> >>>>>>> -rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
> >>>>>>> -rw-r--r-- 1 process process  53K Oct 26  2017 commons-cli-1.4.jar
> >>>>>>> -rw-r--r-- 1 process process 328K Mar  5  2018
> commons-codec-1.11.jar
> >>>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59
> commons-compress-1.17.jar
> >>>>>>> -rw-r--r-- 1 process process  41K Mar  5  2018 commons-csv-1.5.jar
> >>>>>>> -rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
> >>>>>>> -rw-r--r-- 1 process process 425K Oct 26  2017
> commons-lang3-3.4.jar
> >>>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01 httpclient-4.5.5.jar
> >>>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
> >>>>> httpclient-cache-4.5.5.jar
> >>>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
> >>>>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
> >>>>>>> jackson-annotations-2.9.0.jar
> >>>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01
> jackson-core-2.9.5.jar
> >>>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
> >>>>> jackson-databind-2.9.5.jar
> >>>>>>> -rw-r--r-- 1 process process  17K Oct 26  2017
> jcl-over-slf4j-1.7.25.jar
> >>>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
> >>>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01 jena-base-3.8.0.jar
> >>>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07 jena-cmds-3.8.0.jar
> >>>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02 jena-core-3.8.0.jar
> >>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05
> jena-dboe-base-3.8.0.jar
> >>>>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05
> jena-dboe-index-3.8.0.jar
> >>>>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
> >>>>>>> jena-dboe-transaction-3.8.0.jar
> >>>>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
> >>>>>>> jena-dboe-trans-data-3.8.0.jar
> >>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
> >>>>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
> >>>>> jena-rdfconnection-3.8.0.jar
> >>>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
> >>>>> jena-shaded-guava-3.8.0.jar
> >>>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06 jena-tdb2-3.8.0.jar
> >>>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
> >>>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01
> jsonld-java-0.12.0.jar
> >>>>>>> -rw-r--r-- 1 process process 232K Mar  5  2018 libthrift-0.10.0.jar
> >>>>>>> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
> >>>>>>> -rw-r--r-- 1 process process  41K Oct 26  2017 slf4j-api-1.7.25.jar
> >>>>>>> -rw-r--r-- 1 process process  12K Oct 26  2017
> slf4j-log4j12-1.7.25.jar
> >>>>>>>
> >>>>>>> 2.: Turns out, I don't need the jts. after commenting out the
> affected
> >>>>>>> lines, the server still runs fine. (But still without spatial
> index)
> >>>>>>>
> >>>>>>> Best Markus
> >>>>>>>
> >>>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <
> marco.neumann@gmail.com <ma...@gmail.com> <mailto:
> marco.neumann@gmail.com <ma...@gmail.com>>
> >>>>>> :
> >>>>>>>>
> >>>>>>>> Ok let's take a look at this.
> >>>>>>>>
> >>>>>>>> 1. please include in the indexer in the classpath. It's part of
> the
> >>>>>>> current
> >>>>>>>> jena distribution.
> >>>>>>>>
> >>>>>>>> 2. do you need jts? it's a package that allows you to index multi
> point
> >>>>>>>> geometries. here a sample query would be helpful. If single point
> >>>>>>>> geometries are indexed and used in conjunction with MBR range
> queries.
> >>>>>>>> there is no need for jts.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
> >>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
> mneumann@meteomatics.com <ma...@meteomatics.com>>
> >>>>>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>
> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>
> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>
> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>>
> >>>>>>>> wrote:
> >>>>>>>>
> >>>>>>>>> Hi,
> >>>>>>>>> (sorry for the long post)
> >>>>>>>>>
> >>>>>>>>> I've been struggling with the spatial index for a while now.
> >>>>>>>>> I've read
> >>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>>> <
> >>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>>>> <
> >>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>>> <
> >>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>>>>> and
> >>>>>>>>> skipped through about every spatial related thread here on the
> list.
> >>>>>>>>> I managed to get an in-memory version up and running at some
> point
> >>>>>>>>> following this
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>> <
> >>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>>>
> >>>>>>> <
> >>>>>>>
> >>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>> <
> >>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>>>
> >>>>>>>>
> >>>>>>>>> <
> >>>>>>>>>
> >>>>>>>
> >>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>> <
> >>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>>>
> >>>>>>> <
> >>>>>>>
> >>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>> <
> >>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>>>
> >>>>>>>>
> >>>>>>>>>>
> >>>>>>>>> and this
> >>>>>>>>>
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>>
> >>>>> <
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> >>>>>>>
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> >>>>>>>>>
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
> >>>>>>>>>
> >>>>>>>>> But that was on a small dataset that I uploaded via the
> web-interface
> >>>>> of
> >>>>>>>>> Fuseki.
> >>>>>>>>>
> >>>>>>>>> Now the story is a bit different. I'm building the database using
> >>>>>>>>> tdbloader2 and would like to create the spatial index upfront.
> >>>>>>>>>
> >>>>>>>>> java -cp jena-spatial.jar jena.spatialindexer
> --desc=assembler_file
> >>>>>>>>> I could not figure out, how to get this line to work. I have the
> >>>>>>> following
> >>>>>>>>> possible scenarios:
> >>>>>>>>>
> >>>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in the
> >>>>>>> classpath:
> >>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> >>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>>>>> Error: Could not find or load main class jena.spatialindexer
> >>>>>>>>>
> >>>>>>>>> 2. I use the fuseki-server jar:
> >>>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
> >>>>>>>>> --desc=./run/configuration/mm.ttl
> >>>>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
> >>>>>>>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
> >>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not
> in a
> >>>>>>>>> transaction
> >>>>>>>>>
> >>>>>>>>> I managed to eliminate the warning about jts by including that
> in the
> >>>>>>>>> classpath, but the error remains the same (with full trace):
> >>>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
> >>>>>>>>> --desc=./run/configuration/mm.ttl
> >>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not
> in a
> >>>>>>>>> transaction
> >>>>>>>>>   at
> >>>>>>>>>
> >>>>>>>
> >>>>>
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>>>>>>>>   at
> >>>>>>>>>
> >>>>>>>
> >>>>>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>>>>>>>>   at
> >>>>>>>>>
> >>>>>>>
> >>>>>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>>>>>>>>   at
> >>>>>>>>>
> >>>>>>>
> >>>>>
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>>>>>>>>   at
> >>>>>>>>>
> >>>>>>>
> >>>>>
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>>>>>>>>   at
> >>>>>>>>>
> >>>>>>>
> >>>>>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>>>>>>>>   at
> >>>>>>>>>
> >>>>>>>
> >>>>>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>>>>>>>>   at
> >>>>>>>>>
> >>>>>>>
> >>>>>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>>>>>>>>   at
> >>>>>>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>>>>>>>>   at
> >>>>>>>>>
> >>>>>>>
> >>>>>
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>>>>>>>>   at
> >>>>>>>>>
> >>>>>>>
> >>>>>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>>>>>>>>   at
> >>>>>>>>>
> >>>>>>>
> >>>>>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>>>>>>>>   at
> >>>>>>>>>
> >>>>>>>
> >>>>>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>>>>>>   at
> >>>>>>>>>
> >>>>>>>
> >>>>>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>>>>>>   at jena.spatialindexer.exec(spatialindexer.java:110)
> >>>>>>>>>   at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>>>>>>>>   at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>>>>>>>>   at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>>>>>>>>   at jena.spatialindexer.main(spatialindexer.java:53)
> >>>>>>>>>
> >>>>>>>>> My configuration is the following:
> >>>>>>>>> @prefix :      <http://base/#> .
> >>>>>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >>>>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> >>>>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> >>>>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> >>>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
> >>>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
> >>>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >>>>>>>>> # Spatial
> >>>>>>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
> >>>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> >>>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
> >>>>>>>>>
> >>>>>>>>> :service_tdb_all  a                   fuseki:Service ;
> >>>>>>>>>   rdfs:label                    "TDB2 mm" ;
> >>>>>>>>>   fuseki:dataset                :spatial_dataset ;
> >>>>>>>>>   fuseki:name                   "mm" ;
> >>>>>>>>>   fuseki:serviceQuery           "query" , "sparql" ;
> >>>>>>>>>   fuseki:serviceReadGraphStore  "get" ;
> >>>>>>>>>   fuseki:serviceReadWriteGraphStore
> >>>>>>>>>           "data" ;
> >>>>>>>>>   fuseki:serviceUpdate          "update" ;
> >>>>>>>>>   fuseki:serviceUpload          "upload" .
> >>>>>>>>>
> >>>>>>>>> :spatial_dataset a spatial:SpatialDataset ;
> >>>>>>>>> spatial:dataset   :tdb_dataset_readwrite ;
> >>>>>>>>> spatial:index     <#indexLucene> ;
> >>>>>>>>> .
> >>>>>>>>>
> >>>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
> >>>>>>>>> spatial:directory <file:Lucene> ;
> >>>>>>>>> #spatial:directory "mem" ;
> >>>>>>>>> spatial:definition <#definition> ;
> >>>>>>>>> .
> >>>>>>>>>
> >>>>>>>>> <#definition> a spatial:EntityDefinition ;
> >>>>>>>>> spatial:entityField      "uri" ;
> >>>>>>>>> spatial:geoField     "geo" ;
> >>>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format
> >>>>>>>>> spatial:hasSpatialPredicatePairs (
> >>>>>>>>>    [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
> >>>>>>>>>    ) ;
> >>>>>>>>> # custom geo predicates for 2) Well Known Text (WKT) Literal
> >>>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ;
> >>>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT)
> Literal
> >>>>>>>>> spatial:spatialContextFactory
> >>>>>>>>> #
>  "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
> >>>>>>>>>
> >>>>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
> >>>>>>>>> .
> >>>>>>>>>
> >>>>>>>>> :tdb_dataset_readwrite
> >>>>>>>>>   a              tdb2:DatasetTDB2 ;
> >>>>>>>>>   tdb2:location
> >>>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
> >>>>>>>>>
> >>>>>>>>> And I've changed the fuseki script to include the jts jar:
> >>>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
> >>>>>>>>>
> >>>>>>>>> I see no errors or warnings in the server log, when starting
> with that
> >>>>>>>>> configuration, the Lucene folder is created and populated with
> >>>>>>> something:
> >>>>>>>>> $ ll run/configuration/Lucene/
> >>>>>>>>> total 4
> >>>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
> >>>>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
> >>>>>>>>>
> >>>>>>>>> But any spatial query does not return any results.
> >>>>>>>>> Any help on how to tackle this would be highly appreciated.
> >>>>>>>>>
> >>>>>>>>> Best
> >>>>>>>>> Markus Neumann
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>> --
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> ---
> >>>>>>>> Marco Neumann
> >>>>>>>> KONA
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>> --
> >>>>>>
> >>>>>>
> >>>>>> ---
> >>>>>> Marco Neumann
> >>>>>> KONA
> >>>>>
> >>>>>
> >>>>
> >>>> --
> >>>>
> >>>>
> >>>> ---
> >>>> Marco Neumann
> >>>> KONA
> >
>
>
>

-- 


---
Marco Neumann
KONA

Re: Building a spatial index with jena/fuseki

Posted by Marco Neumann <ma...@gmail.com>.
indeed Andy, I got confused with the naming here. same in the code
actually. it might be a good idea to come up with a new name for TDB2 to
reduce scope for confusion.


On Wed, Sep 19, 2018 at 1:47 PM Andy Seaborne <an...@apache.org> wrote:

>
>
> On 19/09/18 11:24, Marco Neumann wrote:
> > On Wed, Sep 19, 2018 at 11:04 AM Andy Seaborne <an...@apache.org> wrote:
> >
> >>
> >>
> >> On 17/09/18 15:26, ajs6f wrote:
> >>> Okay, I think we've got it. Nice debugging, Markus!
> >>>
> >>> If you look at the line of the spatial indexer code that is throwing an
> >> exception:
> >>>
> >>>
> >>
> https://github.com/apache/jena/blob/master/jena-spatial/src/main/java/jena/spatialindexer.java#L110
> >>>
> >>> indeed, it does not start a transaction against the dataset before
> >> starting to read quads to index them. Now, in TDB1 this isn't
> inherently a
> >> problem-- it's possible to work against a dataset without transactions.
> >> (Although it's generally not a good idea at all.) But IIRC, TDB2
> requires
> >> transactions. If that's true (and Andy can verify that for us) then
> this is
> >> a bug and we can fix it in a straightforward way.
> >>>
> >>> Andy, can you confirm that diagnosis?
> >>
> >> Yes - TDB2 only works transactionally.
> >>
> >>
> > Andy--
> >
> > I am just looking at the file system, I noticed that there is no binary
> > difference between tdb and tdb2 indexes. would it be fair to describe
> tdb2
> > as a tdb+txn with different access methods?
>
> Are you looking at tdblaod vs tdbloader2 (unfortunately named
>
> The TBD2 loader is tdb2.tdbloader.
>
> The disk format for TDB2 is different - it is pushed down one level plus
> the node table and the indexes are different byte structures.  The
> indexes are nearly the same but not quite (there is no link field in the
> leaf blocks; tere is an extra control file ".bpt" per index).
>
> The journal in TDB1 can grow big, the journal in TDB2 is small - a few
> hundrad bytes maximum.
>
> And (by accident!) you can have both in the same directory.  This is not
> a good idea.
>
>      Andy
>
>
> TDB2:
> DB2:
> Data-0001/  tdb.lock
>
> DB2/Data-0001:
> GOSP.bpt  GSPO.bpt        OSP.bpt   POSG.dat           SPO.dat
> GOSP.dat  GSPO.dat        OSP.dat   POSG.idn           SPOG.bpt
> GOSP.idn  GSPO.idn        OSPG.bpt  POS.idn            SPOG.dat
> GPOS.bpt  journal.jrnl    OSPG.dat  prefixes.bpt       SPOG.idn
> GPOS.dat  nodes.bpt       OSPG.idn  prefixes.dat       SPO.idn
> GPOS.idn  nodes.dat       OSP.idn   prefixes-data.bdf  tdb.lock
> GPU.bpt   nodes-data.bdf  POS.bpt   prefixes-data.obj
> GPU.dat   nodes-data.obj  POS.dat   prefixes.idn
> GPU.idn   nodes.idn       POSG.bpt  SPO.bpt
>
> TDB1:
> DB1:
> GOSP.dat  journal.jrnl  OSPG.idn  prefix2id.dat  SPOG.dat
> GOSP.idn  node2id.dat   OSP.idn   prefix2id.idn  SPOG.idn
> GPOS.dat  node2id.idn   POS.dat   prefixes.dat   SPO.idn
> GPOS.idn  nodes.dat     POSG.dat  prefixIdx.dat  stats.opt
> GSPO.dat  OSP.dat       POSG.idn  prefixIdx.idn
> GSPO.idn  OSPG.dat      POS.idn   SPO.dat
>
>
> >
> >
> >>
> >>> If so, I'll open a ticket and write a PR to use a Txn method to fix
> this.
> >>
> >> which ajs6f has merged into the development system.
> >>
> >>>
> >>> ajs6f
> >>>
> >>>> On Sep 17, 2018, at 10:14 AM, Markus Neumann <
> mneumann@meteomatics.com>
> >> wrote:
> >>>>
> >>>> It seems I made a mess with absolute and relative paths all together.
> >> So I created a minimal setup for testing:
> >>>> (I include the file-contents at the bottom)
> >>>>
> >>>> $ export JENA_HOME=/srv/linked_data_store/apache-jena-3.8.0
> >>>> $ export PATH=$PATH:$JENA_HOME/bin
> >>>> $ tdb2.tdbloader
> >> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
> >> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl
> >>>> 13:50:54 INFO  loader               :: Loader = LoaderPhased
> >>>> 13:50:54 INFO  loader               :: Data:
> >>
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl:
> >> 13 mm-loc-mini.ttl 0.06s (Avg: 232)
> >>>> 13:50:54 INFO  loader               :: Data:
> >> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl: 50
> >> mm-rdf.ttl 0.01s (Avg: 6,250)
> >>>> 13:50:55 INFO  loader               :: Finish - index SPO
> >>>> 13:50:55 INFO  loader               :: Start replay index SPO
> >>>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
> >> SPO->OSP
> >>>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
> >> SPO->OSP [63 items, 0.0 seconds]
> >>>> 13:50:55 INFO  loader               :: Finish - index POS
> >>>> 13:50:55 INFO  loader               :: Finish - index OSP
> >>>> $ java -cp
> >>
> /srv/linked_data_store/fuseki-server/fuseki-server.jar:/srv/linked_data_store/apache-jena-3.8.0/lib/*
> >> jena.spatialindexer
> >> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >>>> SLF4J: Class path contains multiple SLF4J bindings.
> >>>> SLF4J: Found binding in
> >>
> [jar:file:/srv/linked_data_store/fuseki-server/fuseki-server.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> >>>> SLF4J: Found binding in
> >>
> [jar:file:/srv/linked_data_store/apache-jena-3.8.0/lib/slf4j-log4j12-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> >>>> SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
> >> explanation.
> >>>> SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
> >>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> >> transaction
> >>>>       at
> >>
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>>>       at
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>>>       at
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>>>       at
> >>
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>>>       at
> >>
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>>>       at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>>>       at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>>>       at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>>>       at
> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>>>       at
> >>
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>>>       at
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>>>       at
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>>>       at
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>       at
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>       at jena.spatialindexer.exec(spatialindexer.java:110)
> >>>>       at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>>>       at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>>>       at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>>>       at jena.spatialindexer.main(spatialindexer.java:53)
> >>>>
> >>>> I can get rid of the SLF4J warnings:
> >>>> $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar
> >> jena.spatialindexer
> >> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> >> transaction
> >>>>       at
> >>
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>>>       at
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>>>       at
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>>>       at
> >>
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>>>       at
> >>
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>>>       at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>>>       at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>>>       at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>>>       at
> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>>>       at
> >>
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>>>       at
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>>>       at
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>>>       at
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>       at
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>       at jena.spatialindexer.exec(spatialindexer.java:110)
> >>>>       at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>>>       at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>>>       at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>>>       at jena.spatialindexer.main(spatialindexer.java:53)
> >>>>
> >>>> There is no other java instance running at the time when I run those
> >> commands.
> >>>> All paths are fully qualified and double checked. The destination
> >> directory and the Lucene directory were cleared just before.
> >>>>
> >>>> The server does start and serve the data without errors or warnings in
> >> the log, but spatial queries do not work.
> >>>>
> >>>> Does anyone see a reason for the TransactionException?
> >>>> Thanks and best regards
> >>>> Markus
> >>>>
> >>>> Attachments:
> >>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
> >>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> >>>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
> >>>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
> >>>> @prefix dcterms: <http://purl.org/dc/terms/> .
> >>>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#>
> >>>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
> >>>>
> >>>> <http://rdf.meteomatics.com/mm/>
> >>>>      dcterms:publisher <http://api.meteomatics.com/Imprint.html> ;
> >>>>      dcterms:title "Meteomatics RDF Vocabulary"@en .
> >>>>
> >>>> mm:location a rdf:Property ;
> >>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>      rdfs:label "location" ;
> >>>>      dcterms:description "Location of a measurement"@en .
> >>>>
> >>>> mm:elevation a rdf:Property ;
> >>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>      rdfs:label "elevation" ;
> >>>>      dcterms:description "Elevation of a location"@en .
> >>>>
> >>>> mm:validdate a rdf:Property ;
> >>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>      rdfs:label "validdate" ;
> >>>>      dcterms:description "Temporal information describing when a
> >> Measurement is/was valid"@en .
> >>>>
> >>>> mm:value a rdf:Property ;
> >>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>      rdfs:label "value" ;
> >>>>      dcterms:description "The (observed or predicted) value of a
> >> Measurement"@en .
> >>>>
> >>>> mm:parameter a rdf:Property ;
> >>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>      rdfs:label "parameter" ;
> >>>>      dcterms:description "what was measured"@en .
> >>>>
> >>>> mm:station_name a rdf:Property ;
> >>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>      rdfs:label "station_name" ;
> >>>>      dcterms:description "Name of a station"@en .
> >>>>
> >>>> mm:abbreviation a rdf:Property ;
> >>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>      rdfs:label "abbreviation" ;
> >>>>      dcterms:description "Abbreviation of a station name"@en .
> >>>>
> >>>> mm:didok_id a rdf:Property ;
> >>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>      rdfs:label "didok_id" ;
> >>>>      dcterms:description "didok id of a station"@en .
> >>>>
> >>>> mm:unit_symbol a rdf:Property ;
> >>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>      rdfs:label "unit symbol" ;
> >>>>      dcterms:description "unit symbol of a parameter"@en .
> >>>>
> >>>> mm:Measurement a rdf:Class ;
> >>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>      rdfs:label "Measurement" ;
> >>>>      dcterms:description "Measurement of a specific weather parameter
> at
> >> specific location at a specific date (both future or past)" .
> >>>>
> >>>> mm:Location a rdf:Class ;
> >>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>      rdfs:label "Location" ;
> >>>>      dcterms:description "A Point on the globe where we observe
> >> weather"@en .
> >>>>
> >>>> mm:Parameter a rdf:Class ;
> >>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>>>      rdfs:label "Parameter" ;
> >>>>      dcterms:description "A parameter describing an observable aspect
> of
> >> the weather"@en .
> >>>>
> >>>>
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
> >>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> >>>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
> >>>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
> >>>> @prefix dcterms: <http://purl.org/dc/terms/> .
> >>>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
> >>>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
> >>>> @prefix mm-measurements: <http://rdf.meteomatics.com/mm/measurements/
> >
> >> .
> >>>> @prefix mm-locations: <http://rdf.meteomatics.com/mm/locations/> .
> >>>>
> >>>>
> >>>> mm-locations:8500015 a mm:Location ;
> >>>>      a geosparql:Geometry ;
> >>>>      mm:didok_id 8500015 ;
> >>>>      geo:lat 47.54259 ;
> >>>>      geo:long 7.61574 ;
> >>>>      mm:elevation 273 .
> >>>>
> >>>>
> >>>> mm-locations:8504238 a mm:Location ;
> >>>>      a geosparql:Geometry ;
> >>>>      geosparql:asWKT "POINT(6.86466645231
> >> 47.0840196485)"^^geosparql:wktLiteral ;
> >>>>      mm:didok_id 8504238 ;
> >>>>      geo:lat 47.08402 ;
> >>>>      geo:long 6.86467 ;
> >>>>      mm:elevation 1086 .
> >>>>
> >>>> /srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >>>> @prefix :      <http://base/#> .
> >>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> >>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> >>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> >>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
> >>>> @prefix spatial: <http://jena.apache.org/spatial#> .
> >>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >>>> # Spatial
> >>>> #[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
> >>>> #spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> >>>> #spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
> >>>>
> >>>> :service_tdb_all  a                   fuseki:Service ;
> >>>>          rdfs:label                    "TDB2 mm" ;
> >>>>          fuseki:dataset                :spatial_dataset ;
> >>>>          fuseki:name                   "mm" ;
> >>>>          fuseki:serviceQuery           "query" , "sparql" ;
> >>>>          fuseki:serviceReadGraphStore  "get" ;
> >>>>          fuseki:serviceReadWriteGraphStore
> >>>>                  "data" ;
> >>>>          fuseki:serviceUpdate          "update" ;
> >>>>          fuseki:serviceUpload          "upload" .
> >>>>
> >>>> :spatial_dataset a spatial:SpatialDataset ;
> >>>>      spatial:dataset   :tdb_dataset_readwrite ;
> >>>>      spatial:index     <#indexLucene> ;
> >>>>      .
> >>>>
> >>>> <#indexLucene> a spatial:SpatialIndexLucene ;
> >>>>      spatial:directory <file:Lucene> ;
> >>>>      #spatial:directory "mem" ;
> >>>>      spatial:definition <#definition> ;
> >>>>      .
> >>>>
> >>>> <#definition> a spatial:EntityDefinition ;
> >>>>      spatial:entityField      "uri" ;
> >>>>      spatial:geoField     "geo" ;
> >>>>      # custom geo predicates for 1) Latitude/Longitude Format
> >>>>      spatial:hasSpatialPredicatePairs (
> >>>>           [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
> >>>>           ) ;
> >>>>      # custom geo predicates for 2) Well Known Text (WKT) Literal
> >>>>      spatial:hasWKTPredicates (geosparql:asWKT) ;
> >>>>      #spatial:spatialContextFactory
> >>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
> >>>> #    "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
> >>>>      .
> >>>>
> >>>> :tdb_dataset_readwrite
> >>>>          a              tdb2:DatasetTDB2 ;
> >>>>          tdb2:location
> >> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
> >>>>
> >>>>
> >>>>> Am 17.09.2018 um 15:15 schrieb ajs6f <aj...@apache.org>:
> >>>>>
> >>>>> I think you might have misunderstood the use of $JENA_HOME, or
> perhaps
> >> the Java classpath. $JENA_HOME, which should generally be an absolute
> >> filepath, allows the Jena scripts to find their libraries at runtime.
> >> Internally, the scripts use $JENA_HOME to set up the classpaths with
> which
> >> to start running Java code. But in this case, you're not using the
> scripts.
> >> You're calling a Java class directly, which means you have to give it
> all
> >> the libraries directly, using the classpath flag directly. For example,
> >> your second attempt:
> >>>>>
> >>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
> >> --desc=fuseki-server/run/configuration/mm.ttl
> >>>>> Error: Could not find or load main class
> >> apache-jena-3.8.0.lib.commons-cli-1.4.jar
> >>>>>
> >>>>> may have failed because whatever directory you are in probably
> doesn't
> >> happen to have a Jena distribution in it called "apache-jena-3.8.0".
> >> Perhaps try:
> >>>>>
> >>>>> java -cp $JENA_HOME/lib/* jena.spatialindexer
> >> --desc=fuseki-server/run/configuration/mm.ttl
> >>>>>
> >>>>> Your first example looks like it might be misusing the -cp flag [1].
> >> You probably don't want the *.jar, just *, like
> >>>>>
> >>>>> java -cp lib/* jena.spatialindexer
> >> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>
> >>>>> especially if you happen to be using Windows. [2] That might not be
> >> the entire story, but you can at least try those invocations and see if
> you
> >> get anything different/better.
> >>>>>
> >>>>> ajs6f
> >>>>>
> >>>>> [1]
> >>
> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
> >> <
> >>
> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
> >>>
> >>>>> [2]
> >>
> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
> >> <
> >>
> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
> >>>
> >>>>>
> >>>>>
> >>>>>> On Sep 17, 2018, at 7:07 AM, Markus Neumann <
> mneumann@meteomatics.com
> >> <ma...@meteomatics.com>> wrote:
> >>>>>>
> >>>>>> Ok, that's exactly what I did here:
> >>>>>> $ java -cp lib/*.jar jena.spatialindexer
> >> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
> >>>>>>
> >>>>>> Or from outside JENA_HOME:
> >>>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
> >> --desc=fuseki-server/run/configuration/mm.ttl
> >>>>>> Error: Could not find or load main class
> >> apache-jena-3.8.0.lib.commons-cli-1.4.jar
> >>>>>>
> >>>>>> Or did I missunderstand something?
> >>>>>>
> >>>>>>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <
> >> marco.neumann@gmail.com>:
> >>>>>>>
> >>>>>>> don't worry it's a common problem and frequent source of confusion
> >> not only
> >>>>>>> with jena but java projects. try to simply inlcude all the jars.
> >>>>>>>
> >>>>>>> I presume you run this on a linux box with OpenJDK 8. correct?
> >>>>>>>
> >>>>>>> now once you have set up jena just add the following
> >>>>>>> {replace_with_your_path}/apache-jena-3.8.0/lib/*
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <
> >> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
> >> mneumann@meteomatics.com <ma...@meteomatics.com>>>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>>> This is embarrassing but I don't get it.
> >>>>>>>>
> >>>>>>>> I've configured $JENA_HOME and adjusted the PATH.
> >>>>>>>>
> >>>>>>>> Now what classpath should I include when invoking the indexer?
> >>>>>>>> What I've tried so far:
> >>>>>>>>
> >>>>>>>> $ cd $JENA_HOME
> >>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> >>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>>>> Error: Could not find or load main class jena.spatialindexer
> >>>>>>>> $ java -cp lib/*.jar jena.spatialindexer
> >>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
> >>>>>>>>
> >>>>>>>> Thanks for your patience
> >>>>>>>>
> >>>>>>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <
> >> marco.neumann@gmail.com <ma...@gmail.com>>:
> >>>>>>>>>
> >>>>>>>>> yes correct, this looks good. now include the classpath during
> >> invocation
> >>>>>>>>> of the spatialindexer
> >>>>>>>>>
> >>>>>>>>> in addition it's always a good idea to properly configure jena
> >> along your
> >>>>>>>>> java runtime environment settings to avoid jdk / lib conflicts
> >> during
> >>>>>>>>> execution.
> >>>>>>>>>
> >>>>>>>>> https://jena.apache.org/documentation/tools/index.html <
> >> https://jena.apache.org/documentation/tools/index.html> <
> >>>>>>>> https://jena.apache.org/documentation/tools/index.html <
> >> https://jena.apache.org/documentation/tools/index.html> <
> >> https://jena.apache.org/documentation/tools/index.html <
> >> https://jena.apache.org/documentation/tools/index.html>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
> >>>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com>
> <mailto:
> >> mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:
> >> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
> >> mneumann@meteomatics.com <ma...@meteomatics.com>>>>
> >>>>>>>>> wrote:
> >>>>>>>>>
> >>>>>>>>>> 1.: what do you mean by indexer?
> >>>>>>>>>> Probably my biggest problem is, that I have no clue how to find
> >> out,
> >>>>>>>> where
> >>>>>>>>>> the jena.spatialindexer could be located except for asking here.
> >>>>>>>>>>
> >>>>>>>>>> Here is the content of the apache jena I downloaded:
> >>>>>>>>>> $ ls -lh ../apache-jena-3.8.0/lib
> >>>>>>>>>> total 17M
> >>>>>>>>>> -rw-r--r-- 1 process process 162K Oct 26  2017
> collection-0.7.jar
> >>>>>>>>>> -rw-r--r-- 1 process process  53K Oct 26  2017
> commons-cli-1.4.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 328K Mar  5  2018
> >> commons-codec-1.11.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59
> >> commons-compress-1.17.jar
> >>>>>>>>>> -rw-r--r-- 1 process process  41K Mar  5  2018
> commons-csv-1.5.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 210K Mar  5  2018
> commons-io-2.6.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 425K Oct 26  2017
> >> commons-lang3-3.4.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01
> >> httpclient-4.5.5.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
> >>>>>>>> httpclient-cache-4.5.5.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01
> httpcore-4.4.9.jar
> >>>>>>>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
> >>>>>>>>>> jackson-annotations-2.9.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01
> >> jackson-core-2.9.5.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
> >>>>>>>> jackson-databind-2.9.5.jar
> >>>>>>>>>> -rw-r--r-- 1 process process  17K Oct 26  2017
> >> jcl-over-slf4j-1.7.25.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03
> jena-arq-3.8.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01
> jena-base-3.8.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07
> jena-cmds-3.8.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02
> jena-core-3.8.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05
> >> jena-dboe-base-3.8.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05
> >> jena-dboe-index-3.8.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
> >>>>>>>>>> jena-dboe-transaction-3.8.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
> >>>>>>>>>> jena-dboe-trans-data-3.8.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01
> jena-iri-3.8.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
> >>>>>>>> jena-rdfconnection-3.8.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
> >>>>>>>> jena-shaded-guava-3.8.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06
> jena-tdb2-3.8.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04
> jena-tdb-3.8.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01
> >> jsonld-java-0.12.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 232K Mar  5  2018
> >> libthrift-0.10.0.jar
> >>>>>>>>>> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
> >>>>>>>>>> -rw-r--r-- 1 process process  41K Oct 26  2017
> >> slf4j-api-1.7.25.jar
> >>>>>>>>>> -rw-r--r-- 1 process process  12K Oct 26  2017
> >> slf4j-log4j12-1.7.25.jar
> >>>>>>>>>>
> >>>>>>>>>> 2.: Turns out, I don't need the jts. after commenting out the
> >> affected
> >>>>>>>>>> lines, the server still runs fine. (But still without spatial
> >> index)
> >>>>>>>>>>
> >>>>>>>>>> Best Markus
> >>>>>>>>>>
> >>>>>>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <
> >> marco.neumann@gmail.com <ma...@gmail.com> <mailto:
> >> marco.neumann@gmail.com <ma...@gmail.com>>
> >>>>>>>>> :
> >>>>>>>>>>>
> >>>>>>>>>>> Ok let's take a look at this.
> >>>>>>>>>>>
> >>>>>>>>>>> 1. please include in the indexer in the classpath. It's part of
> >> the
> >>>>>>>>>> current
> >>>>>>>>>>> jena distribution.
> >>>>>>>>>>>
> >>>>>>>>>>> 2. do you need jts? it's a package that allows you to index
> >> multi point
> >>>>>>>>>>> geometries. here a sample query would be helpful. If single
> point
> >>>>>>>>>>> geometries are indexed and used in conjunction with MBR range
> >> queries.
> >>>>>>>>>>> there is no need for jts.
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
> >>>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com>
> <mailto:
> >> mneumann@meteomatics.com <ma...@meteomatics.com>>
> >>>>>>>>>> <mailto:mneumann@meteomatics.com <mailto:
> mneumann@meteomatics.com>
> >> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>
> >> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>
> >> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>>
> >>>>>>>>>>> wrote:
> >>>>>>>>>>>
> >>>>>>>>>>>> Hi,
> >>>>>>>>>>>> (sorry for the long post)
> >>>>>>>>>>>>
> >>>>>>>>>>>> I've been struggling with the spatial index for a while now.
> >>>>>>>>>>>> I've read
> >>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
> <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>>> <
> >>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
> <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>>>> <
> >>>>>>>>>>>>
> https://jena.apache.org/documentation/query/spatial-query.html
> >> <https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>>> <
> >>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
> <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> >> https://jena.apache.org/documentation/query/spatial-query.html>>>>> and
> >>>>>>>>>>>> skipped through about every spatial related thread here on the
> >> list.
> >>>>>>>>>>>> I managed to get an in-memory version up and running at some
> >> point
> >>>>>>>>>>>> following this
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>>> <
> >>>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>>>>
> >>>>>>>>>> <
> >>>>>>>>>>
> >>>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>>> <
> >>>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>> <
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>>> <
> >>>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>>>>
> >>>>>>>>>> <
> >>>>>>>>>>
> >>>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>>> <
> >>>>>>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>>>
> >>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>> and this
> >>>>>>>>>>>>
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>>
> >>>>>>>> <
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> >>>>>>>>>>
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> >>>>>>>>>>>>
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
> >>>>>>>>>>>>
> >>>>>>>>>>>> But that was on a small dataset that I uploaded via the
> >> web-interface
> >>>>>>>> of
> >>>>>>>>>>>> Fuseki.
> >>>>>>>>>>>>
> >>>>>>>>>>>> Now the story is a bit different. I'm building the database
> >> using
> >>>>>>>>>>>> tdbloader2 and would like to create the spatial index upfront.
> >>>>>>>>>>>>
> >>>>>>>>>>>> java -cp jena-spatial.jar jena.spatialindexer
> >> --desc=assembler_file
> >>>>>>>>>>>> I could not figure out, how to get this line to work. I have
> the
> >>>>>>>>>> following
> >>>>>>>>>>>> possible scenarios:
> >>>>>>>>>>>>
> >>>>>>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in
> the
> >>>>>>>>>> classpath:
> >>>>>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> >>>>>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>>>>>>>> Error: Could not find or load main class jena.spatialindexer
> >>>>>>>>>>>>
> >>>>>>>>>>>> 2. I use the fuseki-server jar:
> >>>>>>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
> >>>>>>>>>>>> --desc=./run/configuration/mm.ttl
> >>>>>>>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
> >>>>>>>>>>>>
> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
> >>>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not
> >> in a
> >>>>>>>>>>>> transaction
> >>>>>>>>>>>>
> >>>>>>>>>>>> I managed to eliminate the warning about jts by including that
> >> in the
> >>>>>>>>>>>> classpath, but the error remains the same (with full trace):
> >>>>>>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
> >>>>>>>>>>>> --desc=./run/configuration/mm.ttl
> >>>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not
> >> in a
> >>>>>>>>>>>> transaction
> >>>>>>>>>>>>     at
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>>>>>>>>>>>     at
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>>>>>>>>>>>     at
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>>>>>>>>>>>     at
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>>>>>>>>>>>     at
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>>>>>>>>>>>     at
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>>>>>>>>>>>     at
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>>>>>>>>>>>     at
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>>>>>>>>>>>     at
> >>>>>>>>>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>>>>>>>>>>>     at
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>>>>>>>>>>>     at
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>>>>>>>>>>>     at
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>>>>>>>>>>>     at
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>>>>>>>>>     at
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>>>>>>>>>     at jena.spatialindexer.exec(spatialindexer.java:110)
> >>>>>>>>>>>>     at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>>>>>>>>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>>>>>>>>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>>>>>>>>>>>     at jena.spatialindexer.main(spatialindexer.java:53)
> >>>>>>>>>>>>
> >>>>>>>>>>>> My configuration is the following:
> >>>>>>>>>>>> @prefix :      <http://base/#> .
> >>>>>>>>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
> .
> >>>>>>>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> >>>>>>>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> >>>>>>>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> >>>>>>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
> >>>>>>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
> >>>>>>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>>>>>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >>>>>>>>>>>> # Spatial
> >>>>>>>>>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
> >>>>>>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> >>>>>>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf
> spatial:SpatialIndex
> >> .
> >>>>>>>>>>>>
> >>>>>>>>>>>> :service_tdb_all  a                   fuseki:Service ;
> >>>>>>>>>>>>     rdfs:label                    "TDB2 mm" ;
> >>>>>>>>>>>>     fuseki:dataset                :spatial_dataset ;
> >>>>>>>>>>>>     fuseki:name                   "mm" ;
> >>>>>>>>>>>>     fuseki:serviceQuery           "query" , "sparql" ;
> >>>>>>>>>>>>     fuseki:serviceReadGraphStore  "get" ;
> >>>>>>>>>>>>     fuseki:serviceReadWriteGraphStore
> >>>>>>>>>>>>             "data" ;
> >>>>>>>>>>>>     fuseki:serviceUpdate          "update" ;
> >>>>>>>>>>>>     fuseki:serviceUpload          "upload" .
> >>>>>>>>>>>>
> >>>>>>>>>>>> :spatial_dataset a spatial:SpatialDataset ;
> >>>>>>>>>>>> spatial:dataset   :tdb_dataset_readwrite ;
> >>>>>>>>>>>> spatial:index     <#indexLucene> ;
> >>>>>>>>>>>> .
> >>>>>>>>>>>>
> >>>>>>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
> >>>>>>>>>>>> spatial:directory <file:Lucene> ;
> >>>>>>>>>>>> #spatial:directory "mem" ;
> >>>>>>>>>>>> spatial:definition <#definition> ;
> >>>>>>>>>>>> .
> >>>>>>>>>>>>
> >>>>>>>>>>>> <#definition> a spatial:EntityDefinition ;
> >>>>>>>>>>>> spatial:entityField      "uri" ;
> >>>>>>>>>>>> spatial:geoField     "geo" ;
> >>>>>>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format
> >>>>>>>>>>>> spatial:hasSpatialPredicatePairs (
> >>>>>>>>>>>>      [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
> >>>>>>>>>>>>      ) ;
> >>>>>>>>>>>> # custom geo predicates for 2) Well Known Text (WKT) Literal
> >>>>>>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ;
> >>>>>>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT)
> >> Literal
> >>>>>>>>>>>> spatial:spatialContextFactory
> >>>>>>>>>>>> #
> >>   "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
> >>>>>>>>>>>>
> >>>>>>>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
> >>>>>>>>>>>> .
> >>>>>>>>>>>>
> >>>>>>>>>>>> :tdb_dataset_readwrite
> >>>>>>>>>>>>     a              tdb2:DatasetTDB2 ;
> >>>>>>>>>>>>     tdb2:location
> >>>>>>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
> >>>>>>>>>>>>
> >>>>>>>>>>>> And I've changed the fuseki script to include the jts jar:
> >>>>>>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
> >>>>>>>>>>>>
> >>>>>>>>>>>> I see no errors or warnings in the server log, when starting
> >> with that
> >>>>>>>>>>>> configuration, the Lucene folder is created and populated with
> >>>>>>>>>> something:
> >>>>>>>>>>>> $ ll run/configuration/Lucene/
> >>>>>>>>>>>> total 4
> >>>>>>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
> >>>>>>>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
> >>>>>>>>>>>>
> >>>>>>>>>>>> But any spatial query does not return any results.
> >>>>>>>>>>>> Any help on how to tackle this would be highly appreciated.
> >>>>>>>>>>>>
> >>>>>>>>>>>> Best
> >>>>>>>>>>>> Markus Neumann
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> --
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> ---
> >>>>>>>>>>> Marco Neumann
> >>>>>>>>>>> KONA
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> ---
> >>>>>>>>> Marco Neumann
> >>>>>>>>> KONA
> >>>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>> --
> >>>>>>>
> >>>>>>>
> >>>>>>> ---
> >>>>>>> Marco Neumann
> >>>>>>> KONA
> >>>>
> >>>
> >>>
> >>
> >>
> >
>
>

-- 


---
Marco Neumann
KONA

Re: Building a spatial index with jena/fuseki

Posted by Andy Seaborne <an...@apache.org>.

On 19/09/18 11:24, Marco Neumann wrote:
> On Wed, Sep 19, 2018 at 11:04 AM Andy Seaborne <an...@apache.org> wrote:
> 
>>
>>
>> On 17/09/18 15:26, ajs6f wrote:
>>> Okay, I think we've got it. Nice debugging, Markus!
>>>
>>> If you look at the line of the spatial indexer code that is throwing an
>> exception:
>>>
>>>
>> https://github.com/apache/jena/blob/master/jena-spatial/src/main/java/jena/spatialindexer.java#L110
>>>
>>> indeed, it does not start a transaction against the dataset before
>> starting to read quads to index them. Now, in TDB1 this isn't inherently a
>> problem-- it's possible to work against a dataset without transactions.
>> (Although it's generally not a good idea at all.) But IIRC, TDB2 requires
>> transactions. If that's true (and Andy can verify that for us) then this is
>> a bug and we can fix it in a straightforward way.
>>>
>>> Andy, can you confirm that diagnosis?
>>
>> Yes - TDB2 only works transactionally.
>>
>>
> Andy--
> 
> I am just looking at the file system, I noticed that there is no binary
> difference between tdb and tdb2 indexes. would it be fair to describe tdb2
> as a tdb+txn with different access methods?

Are you looking at tdblaod vs tdbloader2 (unfortunately named

The TBD2 loader is tdb2.tdbloader.

The disk format for TDB2 is different - it is pushed down one level plus 
the node table and the indexes are different byte structures.  The 
indexes are nearly the same but not quite (there is no link field in the 
leaf blocks; tere is an extra control file ".bpt" per index).

The journal in TDB1 can grow big, the journal in TDB2 is small - a few 
hundrad bytes maximum.

And (by accident!) you can have both in the same directory.  This is not 
a good idea.

     Andy


TDB2:
DB2:
Data-0001/  tdb.lock

DB2/Data-0001:
GOSP.bpt  GSPO.bpt	  OSP.bpt   POSG.dat	       SPO.dat
GOSP.dat  GSPO.dat	  OSP.dat   POSG.idn	       SPOG.bpt
GOSP.idn  GSPO.idn	  OSPG.bpt  POS.idn	       SPOG.dat
GPOS.bpt  journal.jrnl	  OSPG.dat  prefixes.bpt       SPOG.idn
GPOS.dat  nodes.bpt	  OSPG.idn  prefixes.dat       SPO.idn
GPOS.idn  nodes.dat	  OSP.idn   prefixes-data.bdf  tdb.lock
GPU.bpt   nodes-data.bdf  POS.bpt   prefixes-data.obj
GPU.dat   nodes-data.obj  POS.dat   prefixes.idn
GPU.idn   nodes.idn	  POSG.bpt  SPO.bpt

TDB1:
DB1:
GOSP.dat  journal.jrnl	OSPG.idn  prefix2id.dat  SPOG.dat
GOSP.idn  node2id.dat	OSP.idn   prefix2id.idn  SPOG.idn
GPOS.dat  node2id.idn	POS.dat   prefixes.dat	 SPO.idn
GPOS.idn  nodes.dat	POSG.dat  prefixIdx.dat  stats.opt
GSPO.dat  OSP.dat	POSG.idn  prefixIdx.idn
GSPO.idn  OSPG.dat	POS.idn   SPO.dat


> 
> 
>>
>>> If so, I'll open a ticket and write a PR to use a Txn method to fix this.
>>
>> which ajs6f has merged into the development system.
>>
>>>
>>> ajs6f
>>>
>>>> On Sep 17, 2018, at 10:14 AM, Markus Neumann <mn...@meteomatics.com>
>> wrote:
>>>>
>>>> It seems I made a mess with absolute and relative paths all together.
>> So I created a minimal setup for testing:
>>>> (I include the file-contents at the bottom)
>>>>
>>>> $ export JENA_HOME=/srv/linked_data_store/apache-jena-3.8.0
>>>> $ export PATH=$PATH:$JENA_HOME/bin
>>>> $ tdb2.tdbloader
>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl
>>>> 13:50:54 INFO  loader               :: Loader = LoaderPhased
>>>> 13:50:54 INFO  loader               :: Data:
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl:
>> 13 mm-loc-mini.ttl 0.06s (Avg: 232)
>>>> 13:50:54 INFO  loader               :: Data:
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl: 50
>> mm-rdf.ttl 0.01s (Avg: 6,250)
>>>> 13:50:55 INFO  loader               :: Finish - index SPO
>>>> 13:50:55 INFO  loader               :: Start replay index SPO
>>>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
>> SPO->OSP
>>>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
>> SPO->OSP [63 items, 0.0 seconds]
>>>> 13:50:55 INFO  loader               :: Finish - index POS
>>>> 13:50:55 INFO  loader               :: Finish - index OSP
>>>> $ java -cp
>> /srv/linked_data_store/fuseki-server/fuseki-server.jar:/srv/linked_data_store/apache-jena-3.8.0/lib/*
>> jena.spatialindexer
>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>>>> SLF4J: Class path contains multiple SLF4J bindings.
>>>> SLF4J: Found binding in
>> [jar:file:/srv/linked_data_store/fuseki-server/fuseki-server.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>>>> SLF4J: Found binding in
>> [jar:file:/srv/linked_data_store/apache-jena-3.8.0/lib/slf4j-log4j12-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>>>> SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
>> explanation.
>>>> SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>> transaction
>>>>       at
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>>       at
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>>       at
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>>       at
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>>       at
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>>       at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>>       at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>>       at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>>       at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>>       at
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>>       at
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>>       at
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>>       at
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>       at
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>       at jena.spatialindexer.exec(spatialindexer.java:110)
>>>>       at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>>       at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>>       at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>>       at jena.spatialindexer.main(spatialindexer.java:53)
>>>>
>>>> I can get rid of the SLF4J warnings:
>>>> $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar
>> jena.spatialindexer
>> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>> transaction
>>>>       at
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>>       at
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>>       at
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>>       at
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>>       at
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>>       at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>>       at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>>       at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>>       at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>>       at
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>>       at
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>>       at
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>>       at
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>       at
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>       at jena.spatialindexer.exec(spatialindexer.java:110)
>>>>       at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>>       at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>>       at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>>       at jena.spatialindexer.main(spatialindexer.java:53)
>>>>
>>>> There is no other java instance running at the time when I run those
>> commands.
>>>> All paths are fully qualified and double checked. The destination
>> directory and the Lucene directory were cleared just before.
>>>>
>>>> The server does start and serve the data without errors or warnings in
>> the log, but spatial queries do not work.
>>>>
>>>> Does anyone see a reason for the TransactionException?
>>>> Thanks and best regards
>>>> Markus
>>>>
>>>> Attachments:
>>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
>>>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
>>>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
>>>> @prefix dcterms: <http://purl.org/dc/terms/> .
>>>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#>
>>>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
>>>>
>>>> <http://rdf.meteomatics.com/mm/>
>>>>      dcterms:publisher <http://api.meteomatics.com/Imprint.html> ;
>>>>      dcterms:title "Meteomatics RDF Vocabulary"@en .
>>>>
>>>> mm:location a rdf:Property ;
>>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>      rdfs:label "location" ;
>>>>      dcterms:description "Location of a measurement"@en .
>>>>
>>>> mm:elevation a rdf:Property ;
>>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>      rdfs:label "elevation" ;
>>>>      dcterms:description "Elevation of a location"@en .
>>>>
>>>> mm:validdate a rdf:Property ;
>>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>      rdfs:label "validdate" ;
>>>>      dcterms:description "Temporal information describing when a
>> Measurement is/was valid"@en .
>>>>
>>>> mm:value a rdf:Property ;
>>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>      rdfs:label "value" ;
>>>>      dcterms:description "The (observed or predicted) value of a
>> Measurement"@en .
>>>>
>>>> mm:parameter a rdf:Property ;
>>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>      rdfs:label "parameter" ;
>>>>      dcterms:description "what was measured"@en .
>>>>
>>>> mm:station_name a rdf:Property ;
>>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>      rdfs:label "station_name" ;
>>>>      dcterms:description "Name of a station"@en .
>>>>
>>>> mm:abbreviation a rdf:Property ;
>>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>      rdfs:label "abbreviation" ;
>>>>      dcterms:description "Abbreviation of a station name"@en .
>>>>
>>>> mm:didok_id a rdf:Property ;
>>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>      rdfs:label "didok_id" ;
>>>>      dcterms:description "didok id of a station"@en .
>>>>
>>>> mm:unit_symbol a rdf:Property ;
>>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>      rdfs:label "unit symbol" ;
>>>>      dcterms:description "unit symbol of a parameter"@en .
>>>>
>>>> mm:Measurement a rdf:Class ;
>>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>      rdfs:label "Measurement" ;
>>>>      dcterms:description "Measurement of a specific weather parameter at
>> specific location at a specific date (both future or past)" .
>>>>
>>>> mm:Location a rdf:Class ;
>>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>      rdfs:label "Location" ;
>>>>      dcterms:description "A Point on the globe where we observe
>> weather"@en .
>>>>
>>>> mm:Parameter a rdf:Class ;
>>>>      rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>>>      rdfs:label "Parameter" ;
>>>>      dcterms:description "A parameter describing an observable aspect of
>> the weather"@en .
>>>>
>>>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
>>>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
>>>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
>>>> @prefix dcterms: <http://purl.org/dc/terms/> .
>>>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
>>>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
>>>> @prefix mm-measurements: <http://rdf.meteomatics.com/mm/measurements/>
>> .
>>>> @prefix mm-locations: <http://rdf.meteomatics.com/mm/locations/> .
>>>>
>>>>
>>>> mm-locations:8500015 a mm:Location ;
>>>>      a geosparql:Geometry ;
>>>>      mm:didok_id 8500015 ;
>>>>      geo:lat 47.54259 ;
>>>>      geo:long 7.61574 ;
>>>>      mm:elevation 273 .
>>>>
>>>>
>>>> mm-locations:8504238 a mm:Location ;
>>>>      a geosparql:Geometry ;
>>>>      geosparql:asWKT "POINT(6.86466645231
>> 47.0840196485)"^^geosparql:wktLiteral ;
>>>>      mm:didok_id 8504238 ;
>>>>      geo:lat 47.08402 ;
>>>>      geo:long 6.86467 ;
>>>>      mm:elevation 1086 .
>>>>
>>>> /srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>>>> @prefix :      <http://base/#> .
>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>>> # Spatial
>>>> #[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>>>> #spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>>> #spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>>>>
>>>> :service_tdb_all  a                   fuseki:Service ;
>>>>          rdfs:label                    "TDB2 mm" ;
>>>>          fuseki:dataset                :spatial_dataset ;
>>>>          fuseki:name                   "mm" ;
>>>>          fuseki:serviceQuery           "query" , "sparql" ;
>>>>          fuseki:serviceReadGraphStore  "get" ;
>>>>          fuseki:serviceReadWriteGraphStore
>>>>                  "data" ;
>>>>          fuseki:serviceUpdate          "update" ;
>>>>          fuseki:serviceUpload          "upload" .
>>>>
>>>> :spatial_dataset a spatial:SpatialDataset ;
>>>>      spatial:dataset   :tdb_dataset_readwrite ;
>>>>      spatial:index     <#indexLucene> ;
>>>>      .
>>>>
>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>>>      spatial:directory <file:Lucene> ;
>>>>      #spatial:directory "mem" ;
>>>>      spatial:definition <#definition> ;
>>>>      .
>>>>
>>>> <#definition> a spatial:EntityDefinition ;
>>>>      spatial:entityField      "uri" ;
>>>>      spatial:geoField     "geo" ;
>>>>      # custom geo predicates for 1) Latitude/Longitude Format
>>>>      spatial:hasSpatialPredicatePairs (
>>>>           [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>>>           ) ;
>>>>      # custom geo predicates for 2) Well Known Text (WKT) Literal
>>>>      spatial:hasWKTPredicates (geosparql:asWKT) ;
>>>>      #spatial:spatialContextFactory
>>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>>> #    "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>>>      .
>>>>
>>>> :tdb_dataset_readwrite
>>>>          a              tdb2:DatasetTDB2 ;
>>>>          tdb2:location
>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>>>
>>>>
>>>>> Am 17.09.2018 um 15:15 schrieb ajs6f <aj...@apache.org>:
>>>>>
>>>>> I think you might have misunderstood the use of $JENA_HOME, or perhaps
>> the Java classpath. $JENA_HOME, which should generally be an absolute
>> filepath, allows the Jena scripts to find their libraries at runtime.
>> Internally, the scripts use $JENA_HOME to set up the classpaths with which
>> to start running Java code. But in this case, you're not using the scripts.
>> You're calling a Java class directly, which means you have to give it all
>> the libraries directly, using the classpath flag directly. For example,
>> your second attempt:
>>>>>
>>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
>> --desc=fuseki-server/run/configuration/mm.ttl
>>>>> Error: Could not find or load main class
>> apache-jena-3.8.0.lib.commons-cli-1.4.jar
>>>>>
>>>>> may have failed because whatever directory you are in probably doesn't
>> happen to have a Jena distribution in it called "apache-jena-3.8.0".
>> Perhaps try:
>>>>>
>>>>> java -cp $JENA_HOME/lib/* jena.spatialindexer
>> --desc=fuseki-server/run/configuration/mm.ttl
>>>>>
>>>>> Your first example looks like it might be misusing the -cp flag [1].
>> You probably don't want the *.jar, just *, like
>>>>>
>>>>> java -cp lib/* jena.spatialindexer
>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>
>>>>> especially if you happen to be using Windows. [2] That might not be
>> the entire story, but you can at least try those invocations and see if you
>> get anything different/better.
>>>>>
>>>>> ajs6f
>>>>>
>>>>> [1]
>> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
>> <
>> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
>>>
>>>>> [2]
>> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
>> <
>> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
>>>
>>>>>
>>>>>
>>>>>> On Sep 17, 2018, at 7:07 AM, Markus Neumann <mneumann@meteomatics.com
>> <ma...@meteomatics.com>> wrote:
>>>>>>
>>>>>> Ok, that's exactly what I did here:
>>>>>> $ java -cp lib/*.jar jena.spatialindexer
>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>>>>>>
>>>>>> Or from outside JENA_HOME:
>>>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
>> --desc=fuseki-server/run/configuration/mm.ttl
>>>>>> Error: Could not find or load main class
>> apache-jena-3.8.0.lib.commons-cli-1.4.jar
>>>>>>
>>>>>> Or did I missunderstand something?
>>>>>>
>>>>>>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <
>> marco.neumann@gmail.com>:
>>>>>>>
>>>>>>> don't worry it's a common problem and frequent source of confusion
>> not only
>>>>>>> with jena but java projects. try to simply inlcude all the jars.
>>>>>>>
>>>>>>> I presume you run this on a linux box with OpenJDK 8. correct?
>>>>>>>
>>>>>>> now once you have set up jena just add the following
>>>>>>> {replace_with_your_path}/apache-jena-3.8.0/lib/*
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <
>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
>> mneumann@meteomatics.com <ma...@meteomatics.com>>>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> This is embarrassing but I don't get it.
>>>>>>>>
>>>>>>>> I've configured $JENA_HOME and adjusted the PATH.
>>>>>>>>
>>>>>>>> Now what classpath should I include when invoking the indexer?
>>>>>>>> What I've tried so far:
>>>>>>>>
>>>>>>>> $ cd $JENA_HOME
>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>>>> Error: Could not find or load main class jena.spatialindexer
>>>>>>>> $ java -cp lib/*.jar jena.spatialindexer
>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>>>>>>>>
>>>>>>>> Thanks for your patience
>>>>>>>>
>>>>>>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <
>> marco.neumann@gmail.com <ma...@gmail.com>>:
>>>>>>>>>
>>>>>>>>> yes correct, this looks good. now include the classpath during
>> invocation
>>>>>>>>> of the spatialindexer
>>>>>>>>>
>>>>>>>>> in addition it's always a good idea to properly configure jena
>> along your
>>>>>>>>> java runtime environment settings to avoid jdk / lib conflicts
>> during
>>>>>>>>> execution.
>>>>>>>>>
>>>>>>>>> https://jena.apache.org/documentation/tools/index.html <
>> https://jena.apache.org/documentation/tools/index.html> <
>>>>>>>> https://jena.apache.org/documentation/tools/index.html <
>> https://jena.apache.org/documentation/tools/index.html> <
>> https://jena.apache.org/documentation/tools/index.html <
>> https://jena.apache.org/documentation/tools/index.html>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
>>>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
>> mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:
>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
>> mneumann@meteomatics.com <ma...@meteomatics.com>>>>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> 1.: what do you mean by indexer?
>>>>>>>>>> Probably my biggest problem is, that I have no clue how to find
>> out,
>>>>>>>> where
>>>>>>>>>> the jena.spatialindexer could be located except for asking here.
>>>>>>>>>>
>>>>>>>>>> Here is the content of the apache jena I downloaded:
>>>>>>>>>> $ ls -lh ../apache-jena-3.8.0/lib
>>>>>>>>>> total 17M
>>>>>>>>>> -rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
>>>>>>>>>> -rw-r--r-- 1 process process  53K Oct 26  2017 commons-cli-1.4.jar
>>>>>>>>>> -rw-r--r-- 1 process process 328K Mar  5  2018
>> commons-codec-1.11.jar
>>>>>>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59
>> commons-compress-1.17.jar
>>>>>>>>>> -rw-r--r-- 1 process process  41K Mar  5  2018 commons-csv-1.5.jar
>>>>>>>>>> -rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
>>>>>>>>>> -rw-r--r-- 1 process process 425K Oct 26  2017
>> commons-lang3-3.4.jar
>>>>>>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01
>> httpclient-4.5.5.jar
>>>>>>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
>>>>>>>> httpclient-cache-4.5.5.jar
>>>>>>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
>>>>>>>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
>>>>>>>>>> jackson-annotations-2.9.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01
>> jackson-core-2.9.5.jar
>>>>>>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
>>>>>>>> jackson-databind-2.9.5.jar
>>>>>>>>>> -rw-r--r-- 1 process process  17K Oct 26  2017
>> jcl-over-slf4j-1.7.25.jar
>>>>>>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01 jena-base-3.8.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07 jena-cmds-3.8.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02 jena-core-3.8.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05
>> jena-dboe-base-3.8.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05
>> jena-dboe-index-3.8.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
>>>>>>>>>> jena-dboe-transaction-3.8.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
>>>>>>>>>> jena-dboe-trans-data-3.8.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
>>>>>>>> jena-rdfconnection-3.8.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
>>>>>>>> jena-shaded-guava-3.8.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06 jena-tdb2-3.8.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01
>> jsonld-java-0.12.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process 232K Mar  5  2018
>> libthrift-0.10.0.jar
>>>>>>>>>> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
>>>>>>>>>> -rw-r--r-- 1 process process  41K Oct 26  2017
>> slf4j-api-1.7.25.jar
>>>>>>>>>> -rw-r--r-- 1 process process  12K Oct 26  2017
>> slf4j-log4j12-1.7.25.jar
>>>>>>>>>>
>>>>>>>>>> 2.: Turns out, I don't need the jts. after commenting out the
>> affected
>>>>>>>>>> lines, the server still runs fine. (But still without spatial
>> index)
>>>>>>>>>>
>>>>>>>>>> Best Markus
>>>>>>>>>>
>>>>>>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <
>> marco.neumann@gmail.com <ma...@gmail.com> <mailto:
>> marco.neumann@gmail.com <ma...@gmail.com>>
>>>>>>>>> :
>>>>>>>>>>>
>>>>>>>>>>> Ok let's take a look at this.
>>>>>>>>>>>
>>>>>>>>>>> 1. please include in the indexer in the classpath. It's part of
>> the
>>>>>>>>>> current
>>>>>>>>>>> jena distribution.
>>>>>>>>>>>
>>>>>>>>>>> 2. do you need jts? it's a package that allows you to index
>> multi point
>>>>>>>>>>> geometries. here a sample query would be helpful. If single point
>>>>>>>>>>> geometries are indexed and used in conjunction with MBR range
>> queries.
>>>>>>>>>>> there is no need for jts.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
>>>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
>> mneumann@meteomatics.com <ma...@meteomatics.com>>
>>>>>>>>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>
>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>
>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>
>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi,
>>>>>>>>>>>> (sorry for the long post)
>>>>>>>>>>>>
>>>>>>>>>>>> I've been struggling with the spatial index for a while now.
>>>>>>>>>>>> I've read
>>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>>>> <
>>>>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
>> <https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <
>> https://jena.apache.org/documentation/query/spatial-query.html>>>>> and
>>>>>>>>>>>> skipped through about every spatial related thread here on the
>> list.
>>>>>>>>>>>> I managed to get an in-memory version up and running at some
>> point
>>>>>>>>>>>> following this
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>
>>>>>>>> <
>>>>>>>>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>
>>>>>>>>>
>>>>>>>>>> <
>>>>>>>>>>
>>>>>>>>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>
>>>>>>>> <
>>>>>>>>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>
>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> <
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>
>>>>>>>> <
>>>>>>>>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>
>>>>>>>>>
>>>>>>>>>> <
>>>>>>>>>>
>>>>>>>>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>
>>>>>>>> <
>>>>>>>>
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>>
>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>> and this
>>>>>>>>>>>>
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>>
>>>>>>>> <
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>>>>>>>
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>>>>>>>>>
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>>>>>>>>>>>>
>>>>>>>>>>>> But that was on a small dataset that I uploaded via the
>> web-interface
>>>>>>>> of
>>>>>>>>>>>> Fuseki.
>>>>>>>>>>>>
>>>>>>>>>>>> Now the story is a bit different. I'm building the database
>> using
>>>>>>>>>>>> tdbloader2 and would like to create the spatial index upfront.
>>>>>>>>>>>>
>>>>>>>>>>>> java -cp jena-spatial.jar jena.spatialindexer
>> --desc=assembler_file
>>>>>>>>>>>> I could not figure out, how to get this line to work. I have the
>>>>>>>>>> following
>>>>>>>>>>>> possible scenarios:
>>>>>>>>>>>>
>>>>>>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in the
>>>>>>>>>> classpath:
>>>>>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>>>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>>>>>>>> Error: Could not find or load main class jena.spatialindexer
>>>>>>>>>>>>
>>>>>>>>>>>> 2. I use the fuseki-server jar:
>>>>>>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
>>>>>>>>>>>> --desc=./run/configuration/mm.ttl
>>>>>>>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
>>>>>>>>>>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
>>>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not
>> in a
>>>>>>>>>>>> transaction
>>>>>>>>>>>>
>>>>>>>>>>>> I managed to eliminate the warning about jts by including that
>> in the
>>>>>>>>>>>> classpath, but the error remains the same (with full trace):
>>>>>>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
>>>>>>>>>>>> --desc=./run/configuration/mm.ttl
>>>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not
>> in a
>>>>>>>>>>>> transaction
>>>>>>>>>>>>     at
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>>>>>>>>>>     at
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>>>>>>>>>>     at
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>>>>>>>>>>     at
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>>>>>>>>>>     at
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>>>>>>>>>>     at
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>>>>>>>>>>     at
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>>>>>>>>>>     at
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>>>>>>>>>>     at
>>>>>>>>>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>>>>>>>>>>     at
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>>>>>>>>>>     at
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>>>>>>>>>>     at
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>>>>>>>>>>     at
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>>>>>>>     at
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>>>>>>>     at jena.spatialindexer.exec(spatialindexer.java:110)
>>>>>>>>>>>>     at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>>>>>>>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>>>>>>>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>>>>>>>>>>     at jena.spatialindexer.main(spatialindexer.java:53)
>>>>>>>>>>>>
>>>>>>>>>>>> My configuration is the following:
>>>>>>>>>>>> @prefix :      <http://base/#> .
>>>>>>>>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>>>>>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>>>>>>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>>>>>>>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>>>>>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>>>>>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>>>>>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>>>>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>>>>>>>>>>> # Spatial
>>>>>>>>>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>>>>>>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>>>>>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex
>> .
>>>>>>>>>>>>
>>>>>>>>>>>> :service_tdb_all  a                   fuseki:Service ;
>>>>>>>>>>>>     rdfs:label                    "TDB2 mm" ;
>>>>>>>>>>>>     fuseki:dataset                :spatial_dataset ;
>>>>>>>>>>>>     fuseki:name                   "mm" ;
>>>>>>>>>>>>     fuseki:serviceQuery           "query" , "sparql" ;
>>>>>>>>>>>>     fuseki:serviceReadGraphStore  "get" ;
>>>>>>>>>>>>     fuseki:serviceReadWriteGraphStore
>>>>>>>>>>>>             "data" ;
>>>>>>>>>>>>     fuseki:serviceUpdate          "update" ;
>>>>>>>>>>>>     fuseki:serviceUpload          "upload" .
>>>>>>>>>>>>
>>>>>>>>>>>> :spatial_dataset a spatial:SpatialDataset ;
>>>>>>>>>>>> spatial:dataset   :tdb_dataset_readwrite ;
>>>>>>>>>>>> spatial:index     <#indexLucene> ;
>>>>>>>>>>>> .
>>>>>>>>>>>>
>>>>>>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>>>>>>>>>>> spatial:directory <file:Lucene> ;
>>>>>>>>>>>> #spatial:directory "mem" ;
>>>>>>>>>>>> spatial:definition <#definition> ;
>>>>>>>>>>>> .
>>>>>>>>>>>>
>>>>>>>>>>>> <#definition> a spatial:EntityDefinition ;
>>>>>>>>>>>> spatial:entityField      "uri" ;
>>>>>>>>>>>> spatial:geoField     "geo" ;
>>>>>>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format
>>>>>>>>>>>> spatial:hasSpatialPredicatePairs (
>>>>>>>>>>>>      [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>>>>>>>>>>>      ) ;
>>>>>>>>>>>> # custom geo predicates for 2) Well Known Text (WKT) Literal
>>>>>>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ;
>>>>>>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT)
>> Literal
>>>>>>>>>>>> spatial:spatialContextFactory
>>>>>>>>>>>> #
>>   "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>>>>>>>>>>>
>>>>>>>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>>>>>>>>>>> .
>>>>>>>>>>>>
>>>>>>>>>>>> :tdb_dataset_readwrite
>>>>>>>>>>>>     a              tdb2:DatasetTDB2 ;
>>>>>>>>>>>>     tdb2:location
>>>>>>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>>>>>>>>>>>
>>>>>>>>>>>> And I've changed the fuseki script to include the jts jar:
>>>>>>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
>>>>>>>>>>>>
>>>>>>>>>>>> I see no errors or warnings in the server log, when starting
>> with that
>>>>>>>>>>>> configuration, the Lucene folder is created and populated with
>>>>>>>>>> something:
>>>>>>>>>>>> $ ll run/configuration/Lucene/
>>>>>>>>>>>> total 4
>>>>>>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
>>>>>>>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
>>>>>>>>>>>>
>>>>>>>>>>>> But any spatial query does not return any results.
>>>>>>>>>>>> Any help on how to tackle this would be highly appreciated.
>>>>>>>>>>>>
>>>>>>>>>>>> Best
>>>>>>>>>>>> Markus Neumann
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ---
>>>>>>>>>>> Marco Neumann
>>>>>>>>>>> KONA
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ---
>>>>>>>>> Marco Neumann
>>>>>>>>> KONA
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>>
>>>>>>> ---
>>>>>>> Marco Neumann
>>>>>>> KONA
>>>>
>>>
>>>
>>
>>
>

Re: Building a spatial index with jena/fuseki

Posted by Marco Neumann <ma...@gmail.com>.
On Wed, Sep 19, 2018 at 11:04 AM Andy Seaborne <an...@apache.org> wrote:

>
>
> On 17/09/18 15:26, ajs6f wrote:
> > Okay, I think we've got it. Nice debugging, Markus!
> >
> > If you look at the line of the spatial indexer code that is throwing an
> exception:
> >
> >
> https://github.com/apache/jena/blob/master/jena-spatial/src/main/java/jena/spatialindexer.java#L110
> >
> > indeed, it does not start a transaction against the dataset before
> starting to read quads to index them. Now, in TDB1 this isn't inherently a
> problem-- it's possible to work against a dataset without transactions.
> (Although it's generally not a good idea at all.) But IIRC, TDB2 requires
> transactions. If that's true (and Andy can verify that for us) then this is
> a bug and we can fix it in a straightforward way.
> >
> > Andy, can you confirm that diagnosis?
>
> Yes - TDB2 only works transactionally.
>
>
Andy--

I am just looking at the file system, I noticed that there is no binary
difference between tdb and tdb2 indexes. would it be fair to describe tdb2
as a tdb+txn with different access methods?


>
> > If so, I'll open a ticket and write a PR to use a Txn method to fix this.
>
> which ajs6f has merged into the development system.
>
> >
> > ajs6f
> >
> >> On Sep 17, 2018, at 10:14 AM, Markus Neumann <mn...@meteomatics.com>
> wrote:
> >>
> >> It seems I made a mess with absolute and relative paths all together.
> So I created a minimal setup for testing:
> >> (I include the file-contents at the bottom)
> >>
> >> $ export JENA_HOME=/srv/linked_data_store/apache-jena-3.8.0
> >> $ export PATH=$PATH:$JENA_HOME/bin
> >> $ tdb2.tdbloader
> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl
> >> 13:50:54 INFO  loader               :: Loader = LoaderPhased
> >> 13:50:54 INFO  loader               :: Data:
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl:
> 13 mm-loc-mini.ttl 0.06s (Avg: 232)
> >> 13:50:54 INFO  loader               :: Data:
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl: 50
> mm-rdf.ttl 0.01s (Avg: 6,250)
> >> 13:50:55 INFO  loader               :: Finish - index SPO
> >> 13:50:55 INFO  loader               :: Start replay index SPO
> >> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
> SPO->OSP
> >> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS,
> SPO->OSP [63 items, 0.0 seconds]
> >> 13:50:55 INFO  loader               :: Finish - index POS
> >> 13:50:55 INFO  loader               :: Finish - index OSP
> >> $ java -cp
> /srv/linked_data_store/fuseki-server/fuseki-server.jar:/srv/linked_data_store/apache-jena-3.8.0/lib/*
> jena.spatialindexer
> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >> SLF4J: Class path contains multiple SLF4J bindings.
> >> SLF4J: Found binding in
> [jar:file:/srv/linked_data_store/fuseki-server/fuseki-server.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> >> SLF4J: Found binding in
> [jar:file:/srv/linked_data_store/apache-jena-3.8.0/lib/slf4j-log4j12-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> >> SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
> explanation.
> >> SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
> >> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> transaction
> >>      at
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>      at
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>      at
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>      at
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>      at
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>      at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>      at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>      at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>      at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>      at
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>      at
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>      at
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>      at
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>      at
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>      at jena.spatialindexer.exec(spatialindexer.java:110)
> >>      at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>      at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>      at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>      at jena.spatialindexer.main(spatialindexer.java:53)
> >>
> >> I can get rid of the SLF4J warnings:
> >> $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar
> jena.spatialindexer
> --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> transaction
> >>      at
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>      at
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>      at
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>      at
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>      at
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>      at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>      at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>      at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>      at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>      at
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>      at
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>      at
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>      at
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>      at
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>      at jena.spatialindexer.exec(spatialindexer.java:110)
> >>      at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>      at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>      at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>      at jena.spatialindexer.main(spatialindexer.java:53)
> >>
> >> There is no other java instance running at the time when I run those
> commands.
> >> All paths are fully qualified and double checked. The destination
> directory and the Lucene directory were cleared just before.
> >>
> >> The server does start and serve the data without errors or warnings in
> the log, but spatial queries do not work.
> >>
> >> Does anyone see a reason for the TransactionException?
> >> Thanks and best regards
> >> Markus
> >>
> >> Attachments:
> >> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
> >> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> >> @prefix owl: <http://www.w3.org/2002/07/owl#> .
> >> @prefix dc: <http://purl.org/dc/elements/1.1/> .
> >> @prefix dcterms: <http://purl.org/dc/terms/> .
> >> @prefix xsd: <http://www.w3.org/2001/XMLSchema#>
> >> @prefix mm: <http://rdf.meteomatics.com/mm/> .
> >>
> >> <http://rdf.meteomatics.com/mm/>
> >>     dcterms:publisher <http://api.meteomatics.com/Imprint.html> ;
> >>     dcterms:title "Meteomatics RDF Vocabulary"@en .
> >>
> >> mm:location a rdf:Property ;
> >>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>     rdfs:label "location" ;
> >>     dcterms:description "Location of a measurement"@en .
> >>
> >> mm:elevation a rdf:Property ;
> >>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>     rdfs:label "elevation" ;
> >>     dcterms:description "Elevation of a location"@en .
> >>
> >> mm:validdate a rdf:Property ;
> >>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>     rdfs:label "validdate" ;
> >>     dcterms:description "Temporal information describing when a
> Measurement is/was valid"@en .
> >>
> >> mm:value a rdf:Property ;
> >>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>     rdfs:label "value" ;
> >>     dcterms:description "The (observed or predicted) value of a
> Measurement"@en .
> >>
> >> mm:parameter a rdf:Property ;
> >>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>     rdfs:label "parameter" ;
> >>     dcterms:description "what was measured"@en .
> >>
> >> mm:station_name a rdf:Property ;
> >>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>     rdfs:label "station_name" ;
> >>     dcterms:description "Name of a station"@en .
> >>
> >> mm:abbreviation a rdf:Property ;
> >>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>     rdfs:label "abbreviation" ;
> >>     dcterms:description "Abbreviation of a station name"@en .
> >>
> >> mm:didok_id a rdf:Property ;
> >>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>     rdfs:label "didok_id" ;
> >>     dcterms:description "didok id of a station"@en .
> >>
> >> mm:unit_symbol a rdf:Property ;
> >>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>     rdfs:label "unit symbol" ;
> >>     dcterms:description "unit symbol of a parameter"@en .
> >>
> >> mm:Measurement a rdf:Class ;
> >>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>     rdfs:label "Measurement" ;
> >>     dcterms:description "Measurement of a specific weather parameter at
> specific location at a specific date (both future or past)" .
> >>
> >> mm:Location a rdf:Class ;
> >>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>     rdfs:label "Location" ;
> >>     dcterms:description "A Point on the globe where we observe
> weather"@en .
> >>
> >> mm:Parameter a rdf:Class ;
> >>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
> >>     rdfs:label "Parameter" ;
> >>     dcterms:description "A parameter describing an observable aspect of
> the weather"@en .
> >>
> >> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
> >> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> >> @prefix owl: <http://www.w3.org/2002/07/owl#> .
> >> @prefix dc: <http://purl.org/dc/elements/1.1/> .
> >> @prefix dcterms: <http://purl.org/dc/terms/> .
> >> @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
> >> @prefix mm: <http://rdf.meteomatics.com/mm/> .
> >> @prefix mm-measurements: <http://rdf.meteomatics.com/mm/measurements/>
> .
> >> @prefix mm-locations: <http://rdf.meteomatics.com/mm/locations/> .
> >>
> >>
> >> mm-locations:8500015 a mm:Location ;
> >>     a geosparql:Geometry ;
> >>     mm:didok_id 8500015 ;
> >>     geo:lat 47.54259 ;
> >>     geo:long 7.61574 ;
> >>     mm:elevation 273 .
> >>
> >>
> >> mm-locations:8504238 a mm:Location ;
> >>     a geosparql:Geometry ;
> >>     geosparql:asWKT "POINT(6.86466645231
> 47.0840196485)"^^geosparql:wktLiteral ;
> >>     mm:didok_id 8504238 ;
> >>     geo:lat 47.08402 ;
> >>     geo:long 6.86467 ;
> >>     mm:elevation 1086 .
> >>
> >> /srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> >> @prefix :      <http://base/#> .
> >> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> >> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> >> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> >> @prefix fuseki: <http://jena.apache.org/fuseki#> .
> >> @prefix spatial: <http://jena.apache.org/spatial#> .
> >> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >> # Spatial
> >> #[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
> >> #spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> >> #spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
> >>
> >> :service_tdb_all  a                   fuseki:Service ;
> >>         rdfs:label                    "TDB2 mm" ;
> >>         fuseki:dataset                :spatial_dataset ;
> >>         fuseki:name                   "mm" ;
> >>         fuseki:serviceQuery           "query" , "sparql" ;
> >>         fuseki:serviceReadGraphStore  "get" ;
> >>         fuseki:serviceReadWriteGraphStore
> >>                 "data" ;
> >>         fuseki:serviceUpdate          "update" ;
> >>         fuseki:serviceUpload          "upload" .
> >>
> >> :spatial_dataset a spatial:SpatialDataset ;
> >>     spatial:dataset   :tdb_dataset_readwrite ;
> >>     spatial:index     <#indexLucene> ;
> >>     .
> >>
> >> <#indexLucene> a spatial:SpatialIndexLucene ;
> >>     spatial:directory <file:Lucene> ;
> >>     #spatial:directory "mem" ;
> >>     spatial:definition <#definition> ;
> >>     .
> >>
> >> <#definition> a spatial:EntityDefinition ;
> >>     spatial:entityField      "uri" ;
> >>     spatial:geoField     "geo" ;
> >>     # custom geo predicates for 1) Latitude/Longitude Format
> >>     spatial:hasSpatialPredicatePairs (
> >>          [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
> >>          ) ;
> >>     # custom geo predicates for 2) Well Known Text (WKT) Literal
> >>     spatial:hasWKTPredicates (geosparql:asWKT) ;
> >>     #spatial:spatialContextFactory
> >> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
> >> #    "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
> >>     .
> >>
> >> :tdb_dataset_readwrite
> >>         a              tdb2:DatasetTDB2 ;
> >>         tdb2:location
> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
> >>
> >>
> >>> Am 17.09.2018 um 15:15 schrieb ajs6f <aj...@apache.org>:
> >>>
> >>> I think you might have misunderstood the use of $JENA_HOME, or perhaps
> the Java classpath. $JENA_HOME, which should generally be an absolute
> filepath, allows the Jena scripts to find their libraries at runtime.
> Internally, the scripts use $JENA_HOME to set up the classpaths with which
> to start running Java code. But in this case, you're not using the scripts.
> You're calling a Java class directly, which means you have to give it all
> the libraries directly, using the classpath flag directly. For example,
> your second attempt:
> >>>
> >>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
> --desc=fuseki-server/run/configuration/mm.ttl
> >>> Error: Could not find or load main class
> apache-jena-3.8.0.lib.commons-cli-1.4.jar
> >>>
> >>> may have failed because whatever directory you are in probably doesn't
> happen to have a Jena distribution in it called "apache-jena-3.8.0".
> Perhaps try:
> >>>
> >>> java -cp $JENA_HOME/lib/* jena.spatialindexer
> --desc=fuseki-server/run/configuration/mm.ttl
> >>>
> >>> Your first example looks like it might be misusing the -cp flag [1].
> You probably don't want the *.jar, just *, like
> >>>
> >>> java -cp lib/* jena.spatialindexer
> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>
> >>> especially if you happen to be using Windows. [2] That might not be
> the entire story, but you can at least try those invocations and see if you
> get anything different/better.
> >>>
> >>> ajs6f
> >>>
> >>> [1]
> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
> <
> https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
> >
> >>> [2]
> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
> <
> https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath
> >
> >>>
> >>>
> >>>> On Sep 17, 2018, at 7:07 AM, Markus Neumann <mneumann@meteomatics.com
> <ma...@meteomatics.com>> wrote:
> >>>>
> >>>> Ok, that's exactly what I did here:
> >>>> $ java -cp lib/*.jar jena.spatialindexer
> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
> >>>>
> >>>> Or from outside JENA_HOME:
> >>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer
> --desc=fuseki-server/run/configuration/mm.ttl
> >>>> Error: Could not find or load main class
> apache-jena-3.8.0.lib.commons-cli-1.4.jar
> >>>>
> >>>> Or did I missunderstand something?
> >>>>
> >>>>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <
> marco.neumann@gmail.com>:
> >>>>>
> >>>>> don't worry it's a common problem and frequent source of confusion
> not only
> >>>>> with jena but java projects. try to simply inlcude all the jars.
> >>>>>
> >>>>> I presume you run this on a linux box with OpenJDK 8. correct?
> >>>>>
> >>>>> now once you have set up jena just add the following
> >>>>> {replace_with_your_path}/apache-jena-3.8.0/lib/*
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <
> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
> mneumann@meteomatics.com <ma...@meteomatics.com>>>
> >>>>> wrote:
> >>>>>
> >>>>>> This is embarrassing but I don't get it.
> >>>>>>
> >>>>>> I've configured $JENA_HOME and adjusted the PATH.
> >>>>>>
> >>>>>> Now what classpath should I include when invoking the indexer?
> >>>>>> What I've tried so far:
> >>>>>>
> >>>>>> $ cd $JENA_HOME
> >>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> >>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>> Error: Could not find or load main class jena.spatialindexer
> >>>>>> $ java -cp lib/*.jar jena.spatialindexer
> >>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
> >>>>>>
> >>>>>> Thanks for your patience
> >>>>>>
> >>>>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <
> marco.neumann@gmail.com <ma...@gmail.com>>:
> >>>>>>>
> >>>>>>> yes correct, this looks good. now include the classpath during
> invocation
> >>>>>>> of the spatialindexer
> >>>>>>>
> >>>>>>> in addition it's always a good idea to properly configure jena
> along your
> >>>>>>> java runtime environment settings to avoid jdk / lib conflicts
> during
> >>>>>>> execution.
> >>>>>>>
> >>>>>>> https://jena.apache.org/documentation/tools/index.html <
> https://jena.apache.org/documentation/tools/index.html> <
> >>>>>> https://jena.apache.org/documentation/tools/index.html <
> https://jena.apache.org/documentation/tools/index.html> <
> https://jena.apache.org/documentation/tools/index.html <
> https://jena.apache.org/documentation/tools/index.html>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
> >>>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
> mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:
> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
> mneumann@meteomatics.com <ma...@meteomatics.com>>>>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>>> 1.: what do you mean by indexer?
> >>>>>>>> Probably my biggest problem is, that I have no clue how to find
> out,
> >>>>>> where
> >>>>>>>> the jena.spatialindexer could be located except for asking here.
> >>>>>>>>
> >>>>>>>> Here is the content of the apache jena I downloaded:
> >>>>>>>> $ ls -lh ../apache-jena-3.8.0/lib
> >>>>>>>> total 17M
> >>>>>>>> -rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
> >>>>>>>> -rw-r--r-- 1 process process  53K Oct 26  2017 commons-cli-1.4.jar
> >>>>>>>> -rw-r--r-- 1 process process 328K Mar  5  2018
> commons-codec-1.11.jar
> >>>>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59
> commons-compress-1.17.jar
> >>>>>>>> -rw-r--r-- 1 process process  41K Mar  5  2018 commons-csv-1.5.jar
> >>>>>>>> -rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
> >>>>>>>> -rw-r--r-- 1 process process 425K Oct 26  2017
> commons-lang3-3.4.jar
> >>>>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01
> httpclient-4.5.5.jar
> >>>>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
> >>>>>> httpclient-cache-4.5.5.jar
> >>>>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
> >>>>>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
> >>>>>>>> jackson-annotations-2.9.0.jar
> >>>>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01
> jackson-core-2.9.5.jar
> >>>>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
> >>>>>> jackson-databind-2.9.5.jar
> >>>>>>>> -rw-r--r-- 1 process process  17K Oct 26  2017
> jcl-over-slf4j-1.7.25.jar
> >>>>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
> >>>>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01 jena-base-3.8.0.jar
> >>>>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07 jena-cmds-3.8.0.jar
> >>>>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02 jena-core-3.8.0.jar
> >>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05
> jena-dboe-base-3.8.0.jar
> >>>>>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05
> jena-dboe-index-3.8.0.jar
> >>>>>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
> >>>>>>>> jena-dboe-transaction-3.8.0.jar
> >>>>>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
> >>>>>>>> jena-dboe-trans-data-3.8.0.jar
> >>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
> >>>>>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
> >>>>>> jena-rdfconnection-3.8.0.jar
> >>>>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
> >>>>>> jena-shaded-guava-3.8.0.jar
> >>>>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06 jena-tdb2-3.8.0.jar
> >>>>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
> >>>>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01
> jsonld-java-0.12.0.jar
> >>>>>>>> -rw-r--r-- 1 process process 232K Mar  5  2018
> libthrift-0.10.0.jar
> >>>>>>>> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
> >>>>>>>> -rw-r--r-- 1 process process  41K Oct 26  2017
> slf4j-api-1.7.25.jar
> >>>>>>>> -rw-r--r-- 1 process process  12K Oct 26  2017
> slf4j-log4j12-1.7.25.jar
> >>>>>>>>
> >>>>>>>> 2.: Turns out, I don't need the jts. after commenting out the
> affected
> >>>>>>>> lines, the server still runs fine. (But still without spatial
> index)
> >>>>>>>>
> >>>>>>>> Best Markus
> >>>>>>>>
> >>>>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <
> marco.neumann@gmail.com <ma...@gmail.com> <mailto:
> marco.neumann@gmail.com <ma...@gmail.com>>
> >>>>>>> :
> >>>>>>>>>
> >>>>>>>>> Ok let's take a look at this.
> >>>>>>>>>
> >>>>>>>>> 1. please include in the indexer in the classpath. It's part of
> the
> >>>>>>>> current
> >>>>>>>>> jena distribution.
> >>>>>>>>>
> >>>>>>>>> 2. do you need jts? it's a package that allows you to index
> multi point
> >>>>>>>>> geometries. here a sample query would be helpful. If single point
> >>>>>>>>> geometries are indexed and used in conjunction with MBR range
> queries.
> >>>>>>>>> there is no need for jts.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
> >>>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:
> mneumann@meteomatics.com <ma...@meteomatics.com>>
> >>>>>>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>
> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>
> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>
> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>>
> >>>>>>>>> wrote:
> >>>>>>>>>
> >>>>>>>>>> Hi,
> >>>>>>>>>> (sorry for the long post)
> >>>>>>>>>>
> >>>>>>>>>> I've been struggling with the spatial index for a while now.
> >>>>>>>>>> I've read
> >>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>>> <
> >>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>>>> <
> >>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html
> <https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>>> <
> >>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>>>>> and
> >>>>>>>>>> skipped through about every spatial related thread here on the
> list.
> >>>>>>>>>> I managed to get an in-memory version up and running at some
> point
> >>>>>>>>>> following this
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>>> <
> >>>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>>>>
> >>>>>>>> <
> >>>>>>>>
> >>>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>>> <
> >>>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>>>> <
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>>> <
> >>>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>>>>
> >>>>>>>> <
> >>>>>>>>
> >>>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>>> <
> >>>>>>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> ><
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>> and this
> >>>>>>>>>>
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>>
> >>>>>> <
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> >>>>>>>>
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> >>>>>>>>>>
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
> >>>>>>>>>>
> >>>>>>>>>> But that was on a small dataset that I uploaded via the
> web-interface
> >>>>>> of
> >>>>>>>>>> Fuseki.
> >>>>>>>>>>
> >>>>>>>>>> Now the story is a bit different. I'm building the database
> using
> >>>>>>>>>> tdbloader2 and would like to create the spatial index upfront.
> >>>>>>>>>>
> >>>>>>>>>> java -cp jena-spatial.jar jena.spatialindexer
> --desc=assembler_file
> >>>>>>>>>> I could not figure out, how to get this line to work. I have the
> >>>>>>>> following
> >>>>>>>>>> possible scenarios:
> >>>>>>>>>>
> >>>>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in the
> >>>>>>>> classpath:
> >>>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> >>>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>>>>>>>> Error: Could not find or load main class jena.spatialindexer
> >>>>>>>>>>
> >>>>>>>>>> 2. I use the fuseki-server jar:
> >>>>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
> >>>>>>>>>> --desc=./run/configuration/mm.ttl
> >>>>>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
> >>>>>>>>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
> >>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not
> in a
> >>>>>>>>>> transaction
> >>>>>>>>>>
> >>>>>>>>>> I managed to eliminate the warning about jts by including that
> in the
> >>>>>>>>>> classpath, but the error remains the same (with full trace):
> >>>>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
> >>>>>>>>>> --desc=./run/configuration/mm.ttl
> >>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not
> in a
> >>>>>>>>>> transaction
> >>>>>>>>>>    at
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>>>>>>>>>    at
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>>>>>>>>>    at
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>>>>>>>>>    at
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>>>>>>>>>    at
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>>>>>>>>>    at
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>>>>>>>>>    at
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>>>>>>>>>    at
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>>>>>>>>>    at
> >>>>>>>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>>>>>>>>>    at
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>>>>>>>>>    at
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>>>>>>>>>    at
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>>>>>>>>>    at
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>>>>>>>    at
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>>>>>>>    at jena.spatialindexer.exec(spatialindexer.java:110)
> >>>>>>>>>>    at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>>>>>>>>>    at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>>>>>>>>>    at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>>>>>>>>>    at jena.spatialindexer.main(spatialindexer.java:53)
> >>>>>>>>>>
> >>>>>>>>>> My configuration is the following:
> >>>>>>>>>> @prefix :      <http://base/#> .
> >>>>>>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >>>>>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> >>>>>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> >>>>>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> >>>>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
> >>>>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
> >>>>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>>>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >>>>>>>>>> # Spatial
> >>>>>>>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
> >>>>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> >>>>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex
> .
> >>>>>>>>>>
> >>>>>>>>>> :service_tdb_all  a                   fuseki:Service ;
> >>>>>>>>>>    rdfs:label                    "TDB2 mm" ;
> >>>>>>>>>>    fuseki:dataset                :spatial_dataset ;
> >>>>>>>>>>    fuseki:name                   "mm" ;
> >>>>>>>>>>    fuseki:serviceQuery           "query" , "sparql" ;
> >>>>>>>>>>    fuseki:serviceReadGraphStore  "get" ;
> >>>>>>>>>>    fuseki:serviceReadWriteGraphStore
> >>>>>>>>>>            "data" ;
> >>>>>>>>>>    fuseki:serviceUpdate          "update" ;
> >>>>>>>>>>    fuseki:serviceUpload          "upload" .
> >>>>>>>>>>
> >>>>>>>>>> :spatial_dataset a spatial:SpatialDataset ;
> >>>>>>>>>> spatial:dataset   :tdb_dataset_readwrite ;
> >>>>>>>>>> spatial:index     <#indexLucene> ;
> >>>>>>>>>> .
> >>>>>>>>>>
> >>>>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
> >>>>>>>>>> spatial:directory <file:Lucene> ;
> >>>>>>>>>> #spatial:directory "mem" ;
> >>>>>>>>>> spatial:definition <#definition> ;
> >>>>>>>>>> .
> >>>>>>>>>>
> >>>>>>>>>> <#definition> a spatial:EntityDefinition ;
> >>>>>>>>>> spatial:entityField      "uri" ;
> >>>>>>>>>> spatial:geoField     "geo" ;
> >>>>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format
> >>>>>>>>>> spatial:hasSpatialPredicatePairs (
> >>>>>>>>>>     [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
> >>>>>>>>>>     ) ;
> >>>>>>>>>> # custom geo predicates for 2) Well Known Text (WKT) Literal
> >>>>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ;
> >>>>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT)
> Literal
> >>>>>>>>>> spatial:spatialContextFactory
> >>>>>>>>>> #
>  "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
> >>>>>>>>>>
> >>>>>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
> >>>>>>>>>> .
> >>>>>>>>>>
> >>>>>>>>>> :tdb_dataset_readwrite
> >>>>>>>>>>    a              tdb2:DatasetTDB2 ;
> >>>>>>>>>>    tdb2:location
> >>>>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
> >>>>>>>>>>
> >>>>>>>>>> And I've changed the fuseki script to include the jts jar:
> >>>>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
> >>>>>>>>>>
> >>>>>>>>>> I see no errors or warnings in the server log, when starting
> with that
> >>>>>>>>>> configuration, the Lucene folder is created and populated with
> >>>>>>>> something:
> >>>>>>>>>> $ ll run/configuration/Lucene/
> >>>>>>>>>> total 4
> >>>>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
> >>>>>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
> >>>>>>>>>>
> >>>>>>>>>> But any spatial query does not return any results.
> >>>>>>>>>> Any help on how to tackle this would be highly appreciated.
> >>>>>>>>>>
> >>>>>>>>>> Best
> >>>>>>>>>> Markus Neumann
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> ---
> >>>>>>>>> Marco Neumann
> >>>>>>>>> KONA
> >>>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>> --
> >>>>>>>
> >>>>>>>
> >>>>>>> ---
> >>>>>>> Marco Neumann
> >>>>>>> KONA
> >>>>>>
> >>>>>>
> >>>>>
> >>>>> --
> >>>>>
> >>>>>
> >>>>> ---
> >>>>> Marco Neumann
> >>>>> KONA
> >>
> >
> >
>
>

-- 


---
Marco Neumann
KONA

Re: Building a spatial index with jena/fuseki

Posted by Andy Seaborne <an...@apache.org>.

On 17/09/18 15:26, ajs6f wrote:
> Okay, I think we've got it. Nice debugging, Markus!
> 
> If you look at the line of the spatial indexer code that is throwing an exception:
> 
> https://github.com/apache/jena/blob/master/jena-spatial/src/main/java/jena/spatialindexer.java#L110
> 
> indeed, it does not start a transaction against the dataset before starting to read quads to index them. Now, in TDB1 this isn't inherently a problem-- it's possible to work against a dataset without transactions. (Although it's generally not a good idea at all.) But IIRC, TDB2 requires transactions. If that's true (and Andy can verify that for us) then this is a bug and we can fix it in a straightforward way.
> 
> Andy, can you confirm that diagnosis?

Yes - TDB2 only works transactionally.


> If so, I'll open a ticket and write a PR to use a Txn method to fix this.

which ajs6f has merged into the development system.

> 
> ajs6f
> 
>> On Sep 17, 2018, at 10:14 AM, Markus Neumann <mn...@meteomatics.com> wrote:
>>
>> It seems I made a mess with absolute and relative paths all together. So I created a minimal setup for testing:
>> (I include the file-contents at the bottom)
>>
>> $ export JENA_HOME=/srv/linked_data_store/apache-jena-3.8.0
>> $ export PATH=$PATH:$JENA_HOME/bin
>> $ tdb2.tdbloader --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl
>> 13:50:54 INFO  loader               :: Loader = LoaderPhased
>> 13:50:54 INFO  loader               :: Data: /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl: 13 mm-loc-mini.ttl 0.06s (Avg: 232)
>> 13:50:54 INFO  loader               :: Data: /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl: 50 mm-rdf.ttl 0.01s (Avg: 6,250)
>> 13:50:55 INFO  loader               :: Finish - index SPO
>> 13:50:55 INFO  loader               :: Start replay index SPO
>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS, SPO->OSP
>> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS, SPO->OSP [63 items, 0.0 seconds]
>> 13:50:55 INFO  loader               :: Finish - index POS
>> 13:50:55 INFO  loader               :: Finish - index OSP
>> $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar:/srv/linked_data_store/apache-jena-3.8.0/lib/* jena.spatialindexer --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>> SLF4J: Class path contains multiple SLF4J bindings.
>> SLF4J: Found binding in [jar:file:/srv/linked_data_store/fuseki-server/fuseki-server.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>> SLF4J: Found binding in [jar:file:/srv/linked_data_store/apache-jena-3.8.0/lib/slf4j-log4j12-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>> SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
>> SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a transaction
>> 	at org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>> 	at org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>> 	at org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>> 	at org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>> 	at org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>> 	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>> 	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>> 	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>> 	at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>> 	at org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>> 	at org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>> 	at org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>> 	at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>> 	at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>> 	at jena.spatialindexer.exec(spatialindexer.java:110)
>> 	at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>> 	at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>> 	at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>> 	at jena.spatialindexer.main(spatialindexer.java:53)
>>
>> I can get rid of the SLF4J warnings:
>> $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar jena.spatialindexer --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a transaction
>> 	at org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>> 	at org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>> 	at org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>> 	at org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>> 	at org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>> 	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>> 	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>> 	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>> 	at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>> 	at org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>> 	at org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>> 	at org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>> 	at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>> 	at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>> 	at jena.spatialindexer.exec(spatialindexer.java:110)
>> 	at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>> 	at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>> 	at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>> 	at jena.spatialindexer.main(spatialindexer.java:53)
>>
>> There is no other java instance running at the time when I run those commands.
>> All paths are fully qualified and double checked. The destination directory and the Lucene directory were cleared just before.
>>
>> The server does start and serve the data without errors or warnings in the log, but spatial queries do not work.
>>
>> Does anyone see a reason for the TransactionException?
>> Thanks and best regards
>> Markus
>>
>> Attachments:
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
>> @prefix dcterms: <http://purl.org/dc/terms/> .
>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#>
>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
>>
>> <http://rdf.meteomatics.com/mm/>
>>     dcterms:publisher <http://api.meteomatics.com/Imprint.html> ;
>>     dcterms:title "Meteomatics RDF Vocabulary"@en .
>>
>> mm:location a rdf:Property ;
>>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>     rdfs:label "location" ;
>>     dcterms:description "Location of a measurement"@en .
>>
>> mm:elevation a rdf:Property ;
>>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>     rdfs:label "elevation" ;
>>     dcterms:description "Elevation of a location"@en .
>>
>> mm:validdate a rdf:Property ;
>>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>     rdfs:label "validdate" ;
>>     dcterms:description "Temporal information describing when a Measurement is/was valid"@en .
>>
>> mm:value a rdf:Property ;
>>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>     rdfs:label "value" ;
>>     dcterms:description "The (observed or predicted) value of a Measurement"@en .
>>
>> mm:parameter a rdf:Property ;
>>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>     rdfs:label "parameter" ;
>>     dcterms:description "what was measured"@en .
>>
>> mm:station_name a rdf:Property ;
>>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>     rdfs:label "station_name" ;
>>     dcterms:description "Name of a station"@en .
>>
>> mm:abbreviation a rdf:Property ;
>>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>     rdfs:label "abbreviation" ;
>>     dcterms:description "Abbreviation of a station name"@en .
>>
>> mm:didok_id a rdf:Property ;
>>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>     rdfs:label "didok_id" ;
>>     dcterms:description "didok id of a station"@en .
>>
>> mm:unit_symbol a rdf:Property ;
>>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>     rdfs:label "unit symbol" ;
>>     dcterms:description "unit symbol of a parameter"@en .
>>
>> mm:Measurement a rdf:Class ;
>>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>     rdfs:label "Measurement" ;
>>     dcterms:description "Measurement of a specific weather parameter at specific location at a specific date (both future or past)" .
>>
>> mm:Location a rdf:Class ;
>>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>     rdfs:label "Location" ;
>>     dcterms:description "A Point on the globe where we observe weather"@en .
>>
>> mm:Parameter a rdf:Class ;
>>     rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>>     rdfs:label "Parameter" ;
>>     dcterms:description "A parameter describing an observable aspect of the weather"@en .
>>
>> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
>> @prefix owl: <http://www.w3.org/2002/07/owl#> .
>> @prefix dc: <http://purl.org/dc/elements/1.1/> .
>> @prefix dcterms: <http://purl.org/dc/terms/> .
>> @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
>> @prefix mm: <http://rdf.meteomatics.com/mm/> .
>> @prefix mm-measurements: <http://rdf.meteomatics.com/mm/measurements/> .
>> @prefix mm-locations: <http://rdf.meteomatics.com/mm/locations/> .
>>
>>
>> mm-locations:8500015 a mm:Location ;
>>     a geosparql:Geometry ;
>>     mm:didok_id 8500015 ;
>>     geo:lat 47.54259 ;
>>     geo:long 7.61574 ;
>>     mm:elevation 273 .
>>
>>
>> mm-locations:8504238 a mm:Location ;
>>     a geosparql:Geometry ;
>>     geosparql:asWKT "POINT(6.86466645231 47.0840196485)"^^geosparql:wktLiteral ;
>>     mm:didok_id 8504238 ;
>>     geo:lat 47.08402 ;
>>     geo:long 6.86467 ;
>>     mm:elevation 1086 .
>>
>> /srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
>> @prefix :      <http://base/#> .
>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>> @prefix spatial: <http://jena.apache.org/spatial#> .
>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>> # Spatial
>> #[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>> #spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>> #spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>>
>> :service_tdb_all  a                   fuseki:Service ;
>>         rdfs:label                    "TDB2 mm" ;
>>         fuseki:dataset                :spatial_dataset ;
>>         fuseki:name                   "mm" ;
>>         fuseki:serviceQuery           "query" , "sparql" ;
>>         fuseki:serviceReadGraphStore  "get" ;
>>         fuseki:serviceReadWriteGraphStore
>>                 "data" ;
>>         fuseki:serviceUpdate          "update" ;
>>         fuseki:serviceUpload          "upload" .
>>
>> :spatial_dataset a spatial:SpatialDataset ;
>>     spatial:dataset   :tdb_dataset_readwrite ;
>>     spatial:index     <#indexLucene> ;
>>     .
>>
>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>     spatial:directory <file:Lucene> ;
>>     #spatial:directory "mem" ;
>>     spatial:definition <#definition> ;
>>     .
>>
>> <#definition> a spatial:EntityDefinition ;
>>     spatial:entityField      "uri" ;
>>     spatial:geoField     "geo" ;
>>     # custom geo predicates for 1) Latitude/Longitude Format
>>     spatial:hasSpatialPredicatePairs (
>>          [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>          ) ;
>>     # custom geo predicates for 2) Well Known Text (WKT) Literal
>>     spatial:hasWKTPredicates (geosparql:asWKT) ;
>>     #spatial:spatialContextFactory
>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>> #	"org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>     .
>>
>> :tdb_dataset_readwrite
>>         a              tdb2:DatasetTDB2 ;
>>         tdb2:location  "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>
>>
>>> Am 17.09.2018 um 15:15 schrieb ajs6f <aj...@apache.org>:
>>>
>>> I think you might have misunderstood the use of $JENA_HOME, or perhaps the Java classpath. $JENA_HOME, which should generally be an absolute filepath, allows the Jena scripts to find their libraries at runtime. Internally, the scripts use $JENA_HOME to set up the classpaths with which to start running Java code. But in this case, you're not using the scripts. You're calling a Java class directly, which means you have to give it all the libraries directly, using the classpath flag directly. For example, your second attempt:
>>>
>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer --desc=fuseki-server/run/configuration/mm.ttl
>>> Error: Could not find or load main class apache-jena-3.8.0.lib.commons-cli-1.4.jar
>>>
>>> may have failed because whatever directory you are in probably doesn't happen to have a Jena distribution in it called "apache-jena-3.8.0". Perhaps try:
>>>
>>> java -cp $JENA_HOME/lib/* jena.spatialindexer --desc=fuseki-server/run/configuration/mm.ttl
>>>
>>> Your first example looks like it might be misusing the -cp flag [1]. You probably don't want the *.jar, just *, like
>>>
>>> java -cp lib/* jena.spatialindexer --desc=../fuseki-server/run/configuration/mm.ttl
>>>
>>> especially if you happen to be using Windows. [2] That might not be the entire story, but you can at least try those invocations and see if you get anything different/better.
>>>
>>> ajs6f
>>>
>>> [1] https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762 <https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762>
>>> [2] https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath <https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath>
>>>
>>>
>>>> On Sep 17, 2018, at 7:07 AM, Markus Neumann <mneumann@meteomatics.com <ma...@meteomatics.com>> wrote:
>>>>
>>>> Ok, that's exactly what I did here:
>>>> $ java -cp lib/*.jar jena.spatialindexer --desc=../fuseki-server/run/configuration/mm.ttl
>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>>>>
>>>> Or from outside JENA_HOME:
>>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer --desc=fuseki-server/run/configuration/mm.ttl
>>>> Error: Could not find or load main class apache-jena-3.8.0.lib.commons-cli-1.4.jar
>>>>
>>>> Or did I missunderstand something?
>>>>
>>>>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <ma...@gmail.com>:
>>>>>
>>>>> don't worry it's a common problem and frequent source of confusion not only
>>>>> with jena but java projects. try to simply inlcude all the jars.
>>>>>
>>>>> I presume you run this on a linux box with OpenJDK 8. correct?
>>>>>
>>>>> now once you have set up jena just add the following
>>>>> {replace_with_your_path}/apache-jena-3.8.0/lib/*
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>
>>>>> wrote:
>>>>>
>>>>>> This is embarrassing but I don't get it.
>>>>>>
>>>>>> I've configured $JENA_HOME and adjusted the PATH.
>>>>>>
>>>>>> Now what classpath should I include when invoking the indexer?
>>>>>> What I've tried so far:
>>>>>>
>>>>>> $ cd $JENA_HOME
>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>> Error: Could not find or load main class jena.spatialindexer
>>>>>> $ java -cp lib/*.jar jena.spatialindexer
>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>>>>>>
>>>>>> Thanks for your patience
>>>>>>
>>>>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <marco.neumann@gmail.com <ma...@gmail.com>>:
>>>>>>>
>>>>>>> yes correct, this looks good. now include the classpath during invocation
>>>>>>> of the spatialindexer
>>>>>>>
>>>>>>> in addition it's always a good idea to properly configure jena along your
>>>>>>> java runtime environment settings to avoid jdk / lib conflicts during
>>>>>>> execution.
>>>>>>>
>>>>>>> https://jena.apache.org/documentation/tools/index.html <https://jena.apache.org/documentation/tools/index.html> <
>>>>>> https://jena.apache.org/documentation/tools/index.html <https://jena.apache.org/documentation/tools/index.html> <https://jena.apache.org/documentation/tools/index.html <https://jena.apache.org/documentation/tools/index.html>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> 1.: what do you mean by indexer?
>>>>>>>> Probably my biggest problem is, that I have no clue how to find out,
>>>>>> where
>>>>>>>> the jena.spatialindexer could be located except for asking here.
>>>>>>>>
>>>>>>>> Here is the content of the apache jena I downloaded:
>>>>>>>> $ ls -lh ../apache-jena-3.8.0/lib
>>>>>>>> total 17M
>>>>>>>> -rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
>>>>>>>> -rw-r--r-- 1 process process  53K Oct 26  2017 commons-cli-1.4.jar
>>>>>>>> -rw-r--r-- 1 process process 328K Mar  5  2018 commons-codec-1.11.jar
>>>>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59 commons-compress-1.17.jar
>>>>>>>> -rw-r--r-- 1 process process  41K Mar  5  2018 commons-csv-1.5.jar
>>>>>>>> -rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
>>>>>>>> -rw-r--r-- 1 process process 425K Oct 26  2017 commons-lang3-3.4.jar
>>>>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01 httpclient-4.5.5.jar
>>>>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
>>>>>> httpclient-cache-4.5.5.jar
>>>>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
>>>>>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
>>>>>>>> jackson-annotations-2.9.0.jar
>>>>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01 jackson-core-2.9.5.jar
>>>>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
>>>>>> jackson-databind-2.9.5.jar
>>>>>>>> -rw-r--r-- 1 process process  17K Oct 26  2017 jcl-over-slf4j-1.7.25.jar
>>>>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
>>>>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01 jena-base-3.8.0.jar
>>>>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07 jena-cmds-3.8.0.jar
>>>>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02 jena-core-3.8.0.jar
>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05 jena-dboe-base-3.8.0.jar
>>>>>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05 jena-dboe-index-3.8.0.jar
>>>>>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
>>>>>>>> jena-dboe-transaction-3.8.0.jar
>>>>>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
>>>>>>>> jena-dboe-trans-data-3.8.0.jar
>>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
>>>>>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
>>>>>> jena-rdfconnection-3.8.0.jar
>>>>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
>>>>>> jena-shaded-guava-3.8.0.jar
>>>>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06 jena-tdb2-3.8.0.jar
>>>>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
>>>>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01 jsonld-java-0.12.0.jar
>>>>>>>> -rw-r--r-- 1 process process 232K Mar  5  2018 libthrift-0.10.0.jar
>>>>>>>> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
>>>>>>>> -rw-r--r-- 1 process process  41K Oct 26  2017 slf4j-api-1.7.25.jar
>>>>>>>> -rw-r--r-- 1 process process  12K Oct 26  2017 slf4j-log4j12-1.7.25.jar
>>>>>>>>
>>>>>>>> 2.: Turns out, I don't need the jts. after commenting out the affected
>>>>>>>> lines, the server still runs fine. (But still without spatial index)
>>>>>>>>
>>>>>>>> Best Markus
>>>>>>>>
>>>>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <marco.neumann@gmail.com <ma...@gmail.com> <mailto:marco.neumann@gmail.com <ma...@gmail.com>>
>>>>>>> :
>>>>>>>>>
>>>>>>>>> Ok let's take a look at this.
>>>>>>>>>
>>>>>>>>> 1. please include in the indexer in the classpath. It's part of the
>>>>>>>> current
>>>>>>>>> jena distribution.
>>>>>>>>>
>>>>>>>>> 2. do you need jts? it's a package that allows you to index multi point
>>>>>>>>> geometries. here a sample query would be helpful. If single point
>>>>>>>>> geometries are indexed and used in conjunction with MBR range queries.
>>>>>>>>> there is no need for jts.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
>>>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>
>>>>>>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>> (sorry for the long post)
>>>>>>>>>>
>>>>>>>>>> I've been struggling with the spatial index for a while now.
>>>>>>>>>> I've read
>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>>> <
>>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>>>> and
>>>>>>>>>> skipped through about every spatial related thread here on the list.
>>>>>>>>>> I managed to get an in-memory version up and running at some point
>>>>>>>>>> following this
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>>> <
>>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>>>>
>>>>>>>> <
>>>>>>>>
>>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>>> <
>>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>>>>
>>>>>>>>>
>>>>>>>>>> <
>>>>>>>>>>
>>>>>>>>
>>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>>> <
>>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>>>>
>>>>>>>> <
>>>>>>>>
>>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>>> <
>>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>>>>
>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>> and this
>>>>>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>>
>>>>>> <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>>>>>>>>>>
>>>>>>>>>> But that was on a small dataset that I uploaded via the web-interface
>>>>>> of
>>>>>>>>>> Fuseki.
>>>>>>>>>>
>>>>>>>>>> Now the story is a bit different. I'm building the database using
>>>>>>>>>> tdbloader2 and would like to create the spatial index upfront.
>>>>>>>>>>
>>>>>>>>>> java -cp jena-spatial.jar jena.spatialindexer --desc=assembler_file
>>>>>>>>>> I could not figure out, how to get this line to work. I have the
>>>>>>>> following
>>>>>>>>>> possible scenarios:
>>>>>>>>>>
>>>>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in the
>>>>>>>> classpath:
>>>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>>>>>> Error: Could not find or load main class jena.spatialindexer
>>>>>>>>>>
>>>>>>>>>> 2. I use the fuseki-server jar:
>>>>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
>>>>>>>>>> --desc=./run/configuration/mm.ttl
>>>>>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
>>>>>>>>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>>>>>>>>> transaction
>>>>>>>>>>
>>>>>>>>>> I managed to eliminate the warning about jts by including that in the
>>>>>>>>>> classpath, but the error remains the same (with full trace):
>>>>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
>>>>>>>>>> --desc=./run/configuration/mm.ttl
>>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>>>>>>>>> transaction
>>>>>>>>>>    at
>>>>>>>>>>
>>>>>>>>
>>>>>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>>>>>>>>    at
>>>>>>>>>>
>>>>>>>>
>>>>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>>>>>>>>    at
>>>>>>>>>>
>>>>>>>>
>>>>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>>>>>>>>    at
>>>>>>>>>>
>>>>>>>>
>>>>>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>>>>>>>>    at
>>>>>>>>>>
>>>>>>>>
>>>>>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>>>>>>>>    at
>>>>>>>>>>
>>>>>>>>
>>>>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>>>>>>>>    at
>>>>>>>>>>
>>>>>>>>
>>>>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>>>>>>>>    at
>>>>>>>>>>
>>>>>>>>
>>>>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>>>>>>>>    at
>>>>>>>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>>>>>>>>    at
>>>>>>>>>>
>>>>>>>>
>>>>>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>>>>>>>>    at
>>>>>>>>>>
>>>>>>>>
>>>>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>>>>>>>>    at
>>>>>>>>>>
>>>>>>>>
>>>>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>>>>>>>>    at
>>>>>>>>>>
>>>>>>>>
>>>>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>>>>>    at
>>>>>>>>>>
>>>>>>>>
>>>>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>>>>>    at jena.spatialindexer.exec(spatialindexer.java:110)
>>>>>>>>>>    at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>>>>>>>>    at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>>>>>>>>    at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>>>>>>>>    at jena.spatialindexer.main(spatialindexer.java:53)
>>>>>>>>>>
>>>>>>>>>> My configuration is the following:
>>>>>>>>>> @prefix :      <http://base/#> .
>>>>>>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>>>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>>>>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>>>>>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>>>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>>>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>>>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>>>>>>>>> # Spatial
>>>>>>>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>>>>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>>>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>>>>>>>>>>
>>>>>>>>>> :service_tdb_all  a                   fuseki:Service ;
>>>>>>>>>>    rdfs:label                    "TDB2 mm" ;
>>>>>>>>>>    fuseki:dataset                :spatial_dataset ;
>>>>>>>>>>    fuseki:name                   "mm" ;
>>>>>>>>>>    fuseki:serviceQuery           "query" , "sparql" ;
>>>>>>>>>>    fuseki:serviceReadGraphStore  "get" ;
>>>>>>>>>>    fuseki:serviceReadWriteGraphStore
>>>>>>>>>>            "data" ;
>>>>>>>>>>    fuseki:serviceUpdate          "update" ;
>>>>>>>>>>    fuseki:serviceUpload          "upload" .
>>>>>>>>>>
>>>>>>>>>> :spatial_dataset a spatial:SpatialDataset ;
>>>>>>>>>> spatial:dataset   :tdb_dataset_readwrite ;
>>>>>>>>>> spatial:index     <#indexLucene> ;
>>>>>>>>>> .
>>>>>>>>>>
>>>>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>>>>>>>>> spatial:directory <file:Lucene> ;
>>>>>>>>>> #spatial:directory "mem" ;
>>>>>>>>>> spatial:definition <#definition> ;
>>>>>>>>>> .
>>>>>>>>>>
>>>>>>>>>> <#definition> a spatial:EntityDefinition ;
>>>>>>>>>> spatial:entityField      "uri" ;
>>>>>>>>>> spatial:geoField     "geo" ;
>>>>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format
>>>>>>>>>> spatial:hasSpatialPredicatePairs (
>>>>>>>>>>     [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>>>>>>>>>     ) ;
>>>>>>>>>> # custom geo predicates for 2) Well Known Text (WKT) Literal
>>>>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ;
>>>>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT) Literal
>>>>>>>>>> spatial:spatialContextFactory
>>>>>>>>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>>>>>>>>>
>>>>>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>>>>>>>>> .
>>>>>>>>>>
>>>>>>>>>> :tdb_dataset_readwrite
>>>>>>>>>>    a              tdb2:DatasetTDB2 ;
>>>>>>>>>>    tdb2:location
>>>>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>>>>>>>>>
>>>>>>>>>> And I've changed the fuseki script to include the jts jar:
>>>>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
>>>>>>>>>>
>>>>>>>>>> I see no errors or warnings in the server log, when starting with that
>>>>>>>>>> configuration, the Lucene folder is created and populated with
>>>>>>>> something:
>>>>>>>>>> $ ll run/configuration/Lucene/
>>>>>>>>>> total 4
>>>>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
>>>>>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
>>>>>>>>>>
>>>>>>>>>> But any spatial query does not return any results.
>>>>>>>>>> Any help on how to tackle this would be highly appreciated.
>>>>>>>>>>
>>>>>>>>>> Best
>>>>>>>>>> Markus Neumann
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ---
>>>>>>>>> Marco Neumann
>>>>>>>>> KONA
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>>
>>>>>>> ---
>>>>>>> Marco Neumann
>>>>>>> KONA
>>>>>>
>>>>>>
>>>>>
>>>>> -- 
>>>>>
>>>>>
>>>>> ---
>>>>> Marco Neumann
>>>>> KONA
>>
> 
>

Re: Building a spatial index with jena/fuseki

Posted by ajs6f <aj...@apache.org>.
Okay, I think we've got it. Nice debugging, Markus!

If you look at the line of the spatial indexer code that is throwing an exception:

https://github.com/apache/jena/blob/master/jena-spatial/src/main/java/jena/spatialindexer.java#L110

indeed, it does not start a transaction against the dataset before starting to read quads to index them. Now, in TDB1 this isn't inherently a problem-- it's possible to work against a dataset without transactions. (Although it's generally not a good idea at all.) But IIRC, TDB2 requires transactions. If that's true (and Andy can verify that for us) then this is a bug and we can fix it in a straightforward way.

Andy, can you confirm that diagnosis? If so, I'll open a ticket and write a PR to use a Txn method to fix this.

ajs6f

> On Sep 17, 2018, at 10:14 AM, Markus Neumann <mn...@meteomatics.com> wrote:
> 
> It seems I made a mess with absolute and relative paths all together. So I created a minimal setup for testing:
> (I include the file-contents at the bottom)
> 
> $ export JENA_HOME=/srv/linked_data_store/apache-jena-3.8.0
> $ export PATH=$PATH:$JENA_HOME/bin
> $ tdb2.tdbloader --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl 
> 13:50:54 INFO  loader               :: Loader = LoaderPhased
> 13:50:54 INFO  loader               :: Data: /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl: 13 mm-loc-mini.ttl 0.06s (Avg: 232)
> 13:50:54 INFO  loader               :: Data: /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl: 50 mm-rdf.ttl 0.01s (Avg: 6,250)
> 13:50:55 INFO  loader               :: Finish - index SPO
> 13:50:55 INFO  loader               :: Start replay index SPO
> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS, SPO->OSP
> 13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS, SPO->OSP [63 items, 0.0 seconds]
> 13:50:55 INFO  loader               :: Finish - index POS
> 13:50:55 INFO  loader               :: Finish - index OSP
> $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar:/srv/linked_data_store/apache-jena-3.8.0/lib/* jena.spatialindexer --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> SLF4J: Class path contains multiple SLF4J bindings.
> SLF4J: Found binding in [jar:file:/srv/linked_data_store/fuseki-server/fuseki-server.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> SLF4J: Found binding in [jar:file:/srv/linked_data_store/apache-jena-3.8.0/lib/slf4j-log4j12-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
> SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a transaction
> 	at org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> 	at org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> 	at org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> 	at org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> 	at org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> 	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> 	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> 	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> 	at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> 	at org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> 	at org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> 	at org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> 	at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> 	at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> 	at jena.spatialindexer.exec(spatialindexer.java:110)
> 	at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> 	at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> 	at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> 	at jena.spatialindexer.main(spatialindexer.java:53)
> 
> I can get rid of the SLF4J warnings:
> $ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar jena.spatialindexer --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a transaction
> 	at org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> 	at org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> 	at org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> 	at org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> 	at org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> 	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> 	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> 	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> 	at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> 	at org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> 	at org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> 	at org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> 	at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> 	at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> 	at jena.spatialindexer.exec(spatialindexer.java:110)
> 	at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> 	at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> 	at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> 	at jena.spatialindexer.main(spatialindexer.java:53)
> 
> There is no other java instance running at the time when I run those commands.
> All paths are fully qualified and double checked. The destination directory and the Lucene directory were cleared just before.
> 
> The server does start and serve the data without errors or warnings in the log, but spatial queries do not work.
> 
> Does anyone see a reason for the TransactionException?
> Thanks and best regards
> Markus
> 
> Attachments:
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . 
> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> @prefix owl: <http://www.w3.org/2002/07/owl#> .
> @prefix dc: <http://purl.org/dc/elements/1.1/> .
> @prefix dcterms: <http://purl.org/dc/terms/> .
> @prefix xsd: <http://www.w3.org/2001/XMLSchema#>
> @prefix mm: <http://rdf.meteomatics.com/mm/> .
> 
> <http://rdf.meteomatics.com/mm/>
>    dcterms:publisher <http://api.meteomatics.com/Imprint.html> ;
>    dcterms:title "Meteomatics RDF Vocabulary"@en .
> 
> mm:location a rdf:Property ;
>    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>    rdfs:label "location" ;
>    dcterms:description "Location of a measurement"@en .
> 
> mm:elevation a rdf:Property ;
>    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>    rdfs:label "elevation" ;
>    dcterms:description "Elevation of a location"@en .
> 
> mm:validdate a rdf:Property ;
>    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>    rdfs:label "validdate" ;
>    dcterms:description "Temporal information describing when a Measurement is/was valid"@en .
> 
> mm:value a rdf:Property ;
>    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>    rdfs:label "value" ;
>    dcterms:description "The (observed or predicted) value of a Measurement"@en .
> 
> mm:parameter a rdf:Property ;
>    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>    rdfs:label "parameter" ;
>    dcterms:description "what was measured"@en .
> 
> mm:station_name a rdf:Property ;
>    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>    rdfs:label "station_name" ;
>    dcterms:description "Name of a station"@en .
> 
> mm:abbreviation a rdf:Property ;
>    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>    rdfs:label "abbreviation" ;
>    dcterms:description "Abbreviation of a station name"@en .
> 
> mm:didok_id a rdf:Property ;
>    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>    rdfs:label "didok_id" ;
>    dcterms:description "didok id of a station"@en .
> 
> mm:unit_symbol a rdf:Property ;
>    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>    rdfs:label "unit symbol" ;
>    dcterms:description "unit symbol of a parameter"@en .
> 
> mm:Measurement a rdf:Class ;
>    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>    rdfs:label "Measurement" ;
>    dcterms:description "Measurement of a specific weather parameter at specific location at a specific date (both future or past)" .
> 
> mm:Location a rdf:Class ;
>    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>    rdfs:label "Location" ;
>    dcterms:description "A Point on the globe where we observe weather"@en .
> 
> mm:Parameter a rdf:Class ;
>    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
>    rdfs:label "Parameter" ;
>    dcterms:description "A parameter describing an observable aspect of the weather"@en .
> 
> /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> @prefix owl: <http://www.w3.org/2002/07/owl#> .
> @prefix dc: <http://purl.org/dc/elements/1.1/> .
> @prefix dcterms: <http://purl.org/dc/terms/> .
> @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
> @prefix mm: <http://rdf.meteomatics.com/mm/> .
> @prefix mm-measurements: <http://rdf.meteomatics.com/mm/measurements/> .
> @prefix mm-locations: <http://rdf.meteomatics.com/mm/locations/> .
> 
> 
> mm-locations:8500015 a mm:Location ;
>    a geosparql:Geometry ;
>    mm:didok_id 8500015 ;
>    geo:lat 47.54259 ;
>    geo:long 7.61574 ;
>    mm:elevation 273 .
> 
> 
> mm-locations:8504238 a mm:Location ;
>    a geosparql:Geometry ;
>    geosparql:asWKT "POINT(6.86466645231 47.0840196485)"^^geosparql:wktLiteral ;
>    mm:didok_id 8504238 ;
>    geo:lat 47.08402 ;
>    geo:long 6.86467 ;
>    mm:elevation 1086 .
> 
> /srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
> @prefix :      <http://base/#> .
> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> @prefix fuseki: <http://jena.apache.org/fuseki#> .
> @prefix spatial: <http://jena.apache.org/spatial#> .
> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> # Spatial
> #[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
> #spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> #spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
> 
> :service_tdb_all  a                   fuseki:Service ;
>        rdfs:label                    "TDB2 mm" ;
>        fuseki:dataset                :spatial_dataset ;
>        fuseki:name                   "mm" ;
>        fuseki:serviceQuery           "query" , "sparql" ;
>        fuseki:serviceReadGraphStore  "get" ;
>        fuseki:serviceReadWriteGraphStore
>                "data" ;
>        fuseki:serviceUpdate          "update" ;
>        fuseki:serviceUpload          "upload" .
> 
> :spatial_dataset a spatial:SpatialDataset ;
>    spatial:dataset   :tdb_dataset_readwrite ;
>    spatial:index     <#indexLucene> ;
>    .
> 
> <#indexLucene> a spatial:SpatialIndexLucene ;
>    spatial:directory <file:Lucene> ;
>    #spatial:directory "mem" ;
>    spatial:definition <#definition> ;
>    .
> 
> <#definition> a spatial:EntityDefinition ;
>    spatial:entityField      "uri" ;
>    spatial:geoField     "geo" ;
>    # custom geo predicates for 1) Latitude/Longitude Format
>    spatial:hasSpatialPredicatePairs (
>         [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>         ) ;
>    # custom geo predicates for 2) Well Known Text (WKT) Literal
>    spatial:hasWKTPredicates (geosparql:asWKT) ;
>    #spatial:spatialContextFactory
> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
> #	"org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>    .
> 
> :tdb_dataset_readwrite
>        a              tdb2:DatasetTDB2 ;
>        tdb2:location  "/srv/linked_data_store/fuseki-server/run/databases/mm" .
> 
> 
>> Am 17.09.2018 um 15:15 schrieb ajs6f <aj...@apache.org>:
>> 
>> I think you might have misunderstood the use of $JENA_HOME, or perhaps the Java classpath. $JENA_HOME, which should generally be an absolute filepath, allows the Jena scripts to find their libraries at runtime. Internally, the scripts use $JENA_HOME to set up the classpaths with which to start running Java code. But in this case, you're not using the scripts. You're calling a Java class directly, which means you have to give it all the libraries directly, using the classpath flag directly. For example, your second attempt:
>> 
>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer --desc=fuseki-server/run/configuration/mm.ttl
>> Error: Could not find or load main class apache-jena-3.8.0.lib.commons-cli-1.4.jar
>> 
>> may have failed because whatever directory you are in probably doesn't happen to have a Jena distribution in it called "apache-jena-3.8.0". Perhaps try:
>> 
>> java -cp $JENA_HOME/lib/* jena.spatialindexer --desc=fuseki-server/run/configuration/mm.ttl
>> 
>> Your first example looks like it might be misusing the -cp flag [1]. You probably don't want the *.jar, just *, like
>> 
>> java -cp lib/* jena.spatialindexer --desc=../fuseki-server/run/configuration/mm.ttl
>> 
>> especially if you happen to be using Windows. [2] That might not be the entire story, but you can at least try those invocations and see if you get anything different/better.
>> 
>> ajs6f
>> 
>> [1] https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762 <https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762>
>> [2] https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath <https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath>
>> 
>> 
>>> On Sep 17, 2018, at 7:07 AM, Markus Neumann <mneumann@meteomatics.com <ma...@meteomatics.com>> wrote:
>>> 
>>> Ok, that's exactly what I did here:
>>> $ java -cp lib/*.jar jena.spatialindexer --desc=../fuseki-server/run/configuration/mm.ttl
>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>>> 
>>> Or from outside JENA_HOME:
>>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer --desc=fuseki-server/run/configuration/mm.ttl
>>> Error: Could not find or load main class apache-jena-3.8.0.lib.commons-cli-1.4.jar
>>> 
>>> Or did I missunderstand something?
>>> 
>>>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <ma...@gmail.com>:
>>>> 
>>>> don't worry it's a common problem and frequent source of confusion not only
>>>> with jena but java projects. try to simply inlcude all the jars.
>>>> 
>>>> I presume you run this on a linux box with OpenJDK 8. correct?
>>>> 
>>>> now once you have set up jena just add the following
>>>> {replace_with_your_path}/apache-jena-3.8.0/lib/*
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>
>>>> wrote:
>>>> 
>>>>> This is embarrassing but I don't get it.
>>>>> 
>>>>> I've configured $JENA_HOME and adjusted the PATH.
>>>>> 
>>>>> Now what classpath should I include when invoking the indexer?
>>>>> What I've tried so far:
>>>>> 
>>>>> $ cd $JENA_HOME
>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>> Error: Could not find or load main class jena.spatialindexer
>>>>> $ java -cp lib/*.jar jena.spatialindexer
>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>>>>> 
>>>>> Thanks for your patience
>>>>> 
>>>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <marco.neumann@gmail.com <ma...@gmail.com>>:
>>>>>> 
>>>>>> yes correct, this looks good. now include the classpath during invocation
>>>>>> of the spatialindexer
>>>>>> 
>>>>>> in addition it's always a good idea to properly configure jena along your
>>>>>> java runtime environment settings to avoid jdk / lib conflicts during
>>>>>> execution.
>>>>>> 
>>>>>> https://jena.apache.org/documentation/tools/index.html <https://jena.apache.org/documentation/tools/index.html> <
>>>>> https://jena.apache.org/documentation/tools/index.html <https://jena.apache.org/documentation/tools/index.html> <https://jena.apache.org/documentation/tools/index.html <https://jena.apache.org/documentation/tools/index.html>>>
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
>>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>
>>>>>> wrote:
>>>>>> 
>>>>>>> 1.: what do you mean by indexer?
>>>>>>> Probably my biggest problem is, that I have no clue how to find out,
>>>>> where
>>>>>>> the jena.spatialindexer could be located except for asking here.
>>>>>>> 
>>>>>>> Here is the content of the apache jena I downloaded:
>>>>>>> $ ls -lh ../apache-jena-3.8.0/lib
>>>>>>> total 17M
>>>>>>> -rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
>>>>>>> -rw-r--r-- 1 process process  53K Oct 26  2017 commons-cli-1.4.jar
>>>>>>> -rw-r--r-- 1 process process 328K Mar  5  2018 commons-codec-1.11.jar
>>>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59 commons-compress-1.17.jar
>>>>>>> -rw-r--r-- 1 process process  41K Mar  5  2018 commons-csv-1.5.jar
>>>>>>> -rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
>>>>>>> -rw-r--r-- 1 process process 425K Oct 26  2017 commons-lang3-3.4.jar
>>>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01 httpclient-4.5.5.jar
>>>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
>>>>> httpclient-cache-4.5.5.jar
>>>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
>>>>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
>>>>>>> jackson-annotations-2.9.0.jar
>>>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01 jackson-core-2.9.5.jar
>>>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
>>>>> jackson-databind-2.9.5.jar
>>>>>>> -rw-r--r-- 1 process process  17K Oct 26  2017 jcl-over-slf4j-1.7.25.jar
>>>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
>>>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01 jena-base-3.8.0.jar
>>>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07 jena-cmds-3.8.0.jar
>>>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02 jena-core-3.8.0.jar
>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05 jena-dboe-base-3.8.0.jar
>>>>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05 jena-dboe-index-3.8.0.jar
>>>>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
>>>>>>> jena-dboe-transaction-3.8.0.jar
>>>>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
>>>>>>> jena-dboe-trans-data-3.8.0.jar
>>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
>>>>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
>>>>> jena-rdfconnection-3.8.0.jar
>>>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
>>>>> jena-shaded-guava-3.8.0.jar
>>>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06 jena-tdb2-3.8.0.jar
>>>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
>>>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01 jsonld-java-0.12.0.jar
>>>>>>> -rw-r--r-- 1 process process 232K Mar  5  2018 libthrift-0.10.0.jar
>>>>>>> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
>>>>>>> -rw-r--r-- 1 process process  41K Oct 26  2017 slf4j-api-1.7.25.jar
>>>>>>> -rw-r--r-- 1 process process  12K Oct 26  2017 slf4j-log4j12-1.7.25.jar
>>>>>>> 
>>>>>>> 2.: Turns out, I don't need the jts. after commenting out the affected
>>>>>>> lines, the server still runs fine. (But still without spatial index)
>>>>>>> 
>>>>>>> Best Markus
>>>>>>> 
>>>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <marco.neumann@gmail.com <ma...@gmail.com> <mailto:marco.neumann@gmail.com <ma...@gmail.com>>
>>>>>> :
>>>>>>>> 
>>>>>>>> Ok let's take a look at this.
>>>>>>>> 
>>>>>>>> 1. please include in the indexer in the classpath. It's part of the
>>>>>>> current
>>>>>>>> jena distribution.
>>>>>>>> 
>>>>>>>> 2. do you need jts? it's a package that allows you to index multi point
>>>>>>>> geometries. here a sample query would be helpful. If single point
>>>>>>>> geometries are indexed and used in conjunction with MBR range queries.
>>>>>>>> there is no need for jts.
>>>>>>>> 
>>>>>>>> 
>>>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
>>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>
>>>>>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>>
>>>>>>>> wrote:
>>>>>>>> 
>>>>>>>>> Hi,
>>>>>>>>> (sorry for the long post)
>>>>>>>>> 
>>>>>>>>> I've been struggling with the spatial index for a while now.
>>>>>>>>> I've read
>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>>> <
>>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>>>> and
>>>>>>>>> skipped through about every spatial related thread here on the list.
>>>>>>>>> I managed to get an in-memory version up and running at some point
>>>>>>>>> following this
>>>>>>>>> 
>>>>>>>>> 
>>>>>>> 
>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>> <
>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>>> 
>>>>>>> <
>>>>>>> 
>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>> <
>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>>> 
>>>>>>>> 
>>>>>>>>> <
>>>>>>>>> 
>>>>>>> 
>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>> <
>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>>> 
>>>>>>> <
>>>>>>> 
>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>> <
>>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>>> 
>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>> and this
>>>>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>>
>>>>> <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>>>>>>>>> 
>>>>>>>>> But that was on a small dataset that I uploaded via the web-interface
>>>>> of
>>>>>>>>> Fuseki.
>>>>>>>>> 
>>>>>>>>> Now the story is a bit different. I'm building the database using
>>>>>>>>> tdbloader2 and would like to create the spatial index upfront.
>>>>>>>>> 
>>>>>>>>> java -cp jena-spatial.jar jena.spatialindexer --desc=assembler_file
>>>>>>>>> I could not figure out, how to get this line to work. I have the
>>>>>>> following
>>>>>>>>> possible scenarios:
>>>>>>>>> 
>>>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in the
>>>>>>> classpath:
>>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>>>>> Error: Could not find or load main class jena.spatialindexer
>>>>>>>>> 
>>>>>>>>> 2. I use the fuseki-server jar:
>>>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
>>>>>>>>> --desc=./run/configuration/mm.ttl
>>>>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
>>>>>>>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>>>>>>>> transaction
>>>>>>>>> 
>>>>>>>>> I managed to eliminate the warning about jts by including that in the
>>>>>>>>> classpath, but the error remains the same (with full trace):
>>>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
>>>>>>>>> --desc=./run/configuration/mm.ttl
>>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>>>>>>>> transaction
>>>>>>>>>   at
>>>>>>>>> 
>>>>>>> 
>>>>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>>>>>>>   at
>>>>>>>>> 
>>>>>>> 
>>>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>>>>>>>   at
>>>>>>>>> 
>>>>>>> 
>>>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>>>>>>>   at
>>>>>>>>> 
>>>>>>> 
>>>>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>>>>>>>   at
>>>>>>>>> 
>>>>>>> 
>>>>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>>>>>>>   at
>>>>>>>>> 
>>>>>>> 
>>>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>>>>>>>   at
>>>>>>>>> 
>>>>>>> 
>>>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>>>>>>>   at
>>>>>>>>> 
>>>>>>> 
>>>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>>>>>>>   at
>>>>>>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>>>>>>>   at
>>>>>>>>> 
>>>>>>> 
>>>>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>>>>>>>   at
>>>>>>>>> 
>>>>>>> 
>>>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>>>>>>>   at
>>>>>>>>> 
>>>>>>> 
>>>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>>>>>>>   at
>>>>>>>>> 
>>>>>>> 
>>>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>>>>   at
>>>>>>>>> 
>>>>>>> 
>>>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>>>>   at jena.spatialindexer.exec(spatialindexer.java:110)
>>>>>>>>>   at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>>>>>>>   at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>>>>>>>   at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>>>>>>>   at jena.spatialindexer.main(spatialindexer.java:53)
>>>>>>>>> 
>>>>>>>>> My configuration is the following:
>>>>>>>>> @prefix :      <http://base/#> .
>>>>>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>>>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>>>>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>>>>>>>> # Spatial
>>>>>>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>>>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>>>>>>>>> 
>>>>>>>>> :service_tdb_all  a                   fuseki:Service ;
>>>>>>>>>   rdfs:label                    "TDB2 mm" ;
>>>>>>>>>   fuseki:dataset                :spatial_dataset ;
>>>>>>>>>   fuseki:name                   "mm" ;
>>>>>>>>>   fuseki:serviceQuery           "query" , "sparql" ;
>>>>>>>>>   fuseki:serviceReadGraphStore  "get" ;
>>>>>>>>>   fuseki:serviceReadWriteGraphStore
>>>>>>>>>           "data" ;
>>>>>>>>>   fuseki:serviceUpdate          "update" ;
>>>>>>>>>   fuseki:serviceUpload          "upload" .
>>>>>>>>> 
>>>>>>>>> :spatial_dataset a spatial:SpatialDataset ;
>>>>>>>>> spatial:dataset   :tdb_dataset_readwrite ;
>>>>>>>>> spatial:index     <#indexLucene> ;
>>>>>>>>> .
>>>>>>>>> 
>>>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>>>>>>>> spatial:directory <file:Lucene> ;
>>>>>>>>> #spatial:directory "mem" ;
>>>>>>>>> spatial:definition <#definition> ;
>>>>>>>>> .
>>>>>>>>> 
>>>>>>>>> <#definition> a spatial:EntityDefinition ;
>>>>>>>>> spatial:entityField      "uri" ;
>>>>>>>>> spatial:geoField     "geo" ;
>>>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format
>>>>>>>>> spatial:hasSpatialPredicatePairs (
>>>>>>>>>    [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>>>>>>>>    ) ;
>>>>>>>>> # custom geo predicates for 2) Well Known Text (WKT) Literal
>>>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ;
>>>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT) Literal
>>>>>>>>> spatial:spatialContextFactory
>>>>>>>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>>>>>>>> 
>>>>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>>>>>>>> .
>>>>>>>>> 
>>>>>>>>> :tdb_dataset_readwrite
>>>>>>>>>   a              tdb2:DatasetTDB2 ;
>>>>>>>>>   tdb2:location
>>>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>>>>>>>> 
>>>>>>>>> And I've changed the fuseki script to include the jts jar:
>>>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
>>>>>>>>> 
>>>>>>>>> I see no errors or warnings in the server log, when starting with that
>>>>>>>>> configuration, the Lucene folder is created and populated with
>>>>>>> something:
>>>>>>>>> $ ll run/configuration/Lucene/
>>>>>>>>> total 4
>>>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
>>>>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
>>>>>>>>> 
>>>>>>>>> But any spatial query does not return any results.
>>>>>>>>> Any help on how to tackle this would be highly appreciated.
>>>>>>>>> 
>>>>>>>>> Best
>>>>>>>>> Markus Neumann
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> 
>>>>>>>> --
>>>>>>>> 
>>>>>>>> 
>>>>>>>> ---
>>>>>>>> Marco Neumann
>>>>>>>> KONA
>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>>> --
>>>>>> 
>>>>>> 
>>>>>> ---
>>>>>> Marco Neumann
>>>>>> KONA
>>>>> 
>>>>> 
>>>> 
>>>> -- 
>>>> 
>>>> 
>>>> ---
>>>> Marco Neumann
>>>> KONA
>

Re: Building a spatial index with jena/fuseki

Posted by Markus Neumann <mn...@meteomatics.com>.
It seems I made a mess with absolute and relative paths all together. So I created a minimal setup for testing:
(I include the file-contents at the bottom)

$ export JENA_HOME=/srv/linked_data_store/apache-jena-3.8.0
$ export PATH=$PATH:$JENA_HOME/bin
$ tdb2.tdbloader --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl 
13:50:54 INFO  loader               :: Loader = LoaderPhased
13:50:54 INFO  loader               :: Data: /srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl: 13 mm-loc-mini.ttl 0.06s (Avg: 232)
13:50:54 INFO  loader               :: Data: /srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl: 50 mm-rdf.ttl 0.01s (Avg: 6,250)
13:50:55 INFO  loader               :: Finish - index SPO
13:50:55 INFO  loader               :: Start replay index SPO
13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS, SPO->OSP
13:50:55 INFO  loader               :: Index set:  SPO => SPO->POS, SPO->OSP [63 items, 0.0 seconds]
13:50:55 INFO  loader               :: Finish - index POS
13:50:55 INFO  loader               :: Finish - index OSP
$ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar:/srv/linked_data_store/apache-jena-3.8.0/lib/* jena.spatialindexer --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/srv/linked_data_store/fuseki-server/fuseki-server.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/srv/linked_data_store/apache-jena-3.8.0/lib/slf4j-log4j12-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
org.apache.jena.dboe.transaction.txn.TransactionException: Not in a transaction
	at org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
	at org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
	at org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
	at org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
	at org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
	at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
	at org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
	at org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
	at org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
	at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
	at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
	at jena.spatialindexer.exec(spatialindexer.java:110)
	at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
	at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
	at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
	at jena.spatialindexer.main(spatialindexer.java:53)

I can get rid of the SLF4J warnings:
$ java -cp /srv/linked_data_store/fuseki-server/fuseki-server.jar jena.spatialindexer --desc=/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
org.apache.jena.dboe.transaction.txn.TransactionException: Not in a transaction
	at org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
	at org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
	at org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
	at org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
	at org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
	at org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
	at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
	at org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
	at org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
	at org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
	at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
	at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
	at jena.spatialindexer.exec(spatialindexer.java:110)
	at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
	at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
	at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
	at jena.spatialindexer.main(spatialindexer.java:53)

There is no other java instance running at the time when I run those commands.
All paths are fully qualified and double checked. The destination directory and the Lucene directory were cleared just before.

The server does start and serve the data without errors or warnings in the log, but spatial queries do not work.

Does anyone see a reason for the TransactionException?
Thanks and best regards
Markus

Attachments:
/srv/linked_data_store/rdf_python_connector/turtle_files/mm-rdf.ttl:
@prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . 
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#>
@prefix mm: <http://rdf.meteomatics.com/mm/> .

<http://rdf.meteomatics.com/mm/>
    dcterms:publisher <http://api.meteomatics.com/Imprint.html> ;
    dcterms:title "Meteomatics RDF Vocabulary"@en .
    
mm:location a rdf:Property ;
    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
    rdfs:label "location" ;
    dcterms:description "Location of a measurement"@en .

mm:elevation a rdf:Property ;
    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
    rdfs:label "elevation" ;
    dcterms:description "Elevation of a location"@en .

mm:validdate a rdf:Property ;
    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
    rdfs:label "validdate" ;
    dcterms:description "Temporal information describing when a Measurement is/was valid"@en .

mm:value a rdf:Property ;
    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
    rdfs:label "value" ;
    dcterms:description "The (observed or predicted) value of a Measurement"@en .

mm:parameter a rdf:Property ;
    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
    rdfs:label "parameter" ;
    dcterms:description "what was measured"@en .

mm:station_name a rdf:Property ;
    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
    rdfs:label "station_name" ;
    dcterms:description "Name of a station"@en .

mm:abbreviation a rdf:Property ;
    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
    rdfs:label "abbreviation" ;
    dcterms:description "Abbreviation of a station name"@en .

mm:didok_id a rdf:Property ;
    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
    rdfs:label "didok_id" ;
    dcterms:description "didok id of a station"@en .

mm:unit_symbol a rdf:Property ;
    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
    rdfs:label "unit symbol" ;
    dcterms:description "unit symbol of a parameter"@en .

mm:Measurement a rdf:Class ;
    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
    rdfs:label "Measurement" ;
    dcterms:description "Measurement of a specific weather parameter at specific location at a specific date (both future or past)" .

mm:Location a rdf:Class ;
    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
    rdfs:label "Location" ;
    dcterms:description "A Point on the globe where we observe weather"@en .

mm:Parameter a rdf:Class ;
    rdfs:isDefinedBy <http://rdf.meteomatics.com/mm/> ;
    rdfs:label "Parameter" ;
    dcterms:description "A parameter describing an observable aspect of the weather"@en .

/srv/linked_data_store/rdf_python_connector/turtle_files/mm-loc-mini.ttl
@prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
@prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix mm: <http://rdf.meteomatics.com/mm/> .
@prefix mm-measurements: <http://rdf.meteomatics.com/mm/measurements/> .
@prefix mm-locations: <http://rdf.meteomatics.com/mm/locations/> .


mm-locations:8500015 a mm:Location ;
    a geosparql:Geometry ;
    mm:didok_id 8500015 ;
    geo:lat 47.54259 ;
    geo:long 7.61574 ;
    mm:elevation 273 .


mm-locations:8504238 a mm:Location ;
    a geosparql:Geometry ;
    geosparql:asWKT "POINT(6.86466645231 47.0840196485)"^^geosparql:wktLiteral ;
    mm:didok_id 8504238 ;
    geo:lat 47.08402 ;
    geo:long 6.86467 ;
    mm:elevation 1086 .

/srv/linked_data_store/fuseki-server/run/configuration/mm.ttl
@prefix :      <http://base/#> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
@prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix fuseki: <http://jena.apache.org/fuseki#> .
@prefix spatial: <http://jena.apache.org/spatial#> .
@prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
@prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
# Spatial
#[] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
#spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
#spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .

:service_tdb_all  a                   fuseki:Service ;
        rdfs:label                    "TDB2 mm" ;
        fuseki:dataset                :spatial_dataset ;
        fuseki:name                   "mm" ;
        fuseki:serviceQuery           "query" , "sparql" ;
        fuseki:serviceReadGraphStore  "get" ;
        fuseki:serviceReadWriteGraphStore
                "data" ;
        fuseki:serviceUpdate          "update" ;
        fuseki:serviceUpload          "upload" .

:spatial_dataset a spatial:SpatialDataset ;
    spatial:dataset   :tdb_dataset_readwrite ;
    spatial:index     <#indexLucene> ;
    .

<#indexLucene> a spatial:SpatialIndexLucene ;
    spatial:directory <file:Lucene> ;
    #spatial:directory "mem" ;
    spatial:definition <#definition> ;
    .

<#definition> a spatial:EntityDefinition ;
    spatial:entityField      "uri" ;
    spatial:geoField     "geo" ;
    # custom geo predicates for 1) Latitude/Longitude Format
    spatial:hasSpatialPredicatePairs (
         [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
         ) ;
    # custom geo predicates for 2) Well Known Text (WKT) Literal
    spatial:hasWKTPredicates (geosparql:asWKT) ;
    #spatial:spatialContextFactory
#         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
#	"org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
    .

:tdb_dataset_readwrite
        a              tdb2:DatasetTDB2 ;
        tdb2:location  "/srv/linked_data_store/fuseki-server/run/databases/mm" .


> Am 17.09.2018 um 15:15 schrieb ajs6f <aj...@apache.org>:
> 
> I think you might have misunderstood the use of $JENA_HOME, or perhaps the Java classpath. $JENA_HOME, which should generally be an absolute filepath, allows the Jena scripts to find their libraries at runtime. Internally, the scripts use $JENA_HOME to set up the classpaths with which to start running Java code. But in this case, you're not using the scripts. You're calling a Java class directly, which means you have to give it all the libraries directly, using the classpath flag directly. For example, your second attempt:
> 
> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer --desc=fuseki-server/run/configuration/mm.ttl
> Error: Could not find or load main class apache-jena-3.8.0.lib.commons-cli-1.4.jar
> 
> may have failed because whatever directory you are in probably doesn't happen to have a Jena distribution in it called "apache-jena-3.8.0". Perhaps try:
> 
> java -cp $JENA_HOME/lib/* jena.spatialindexer --desc=fuseki-server/run/configuration/mm.ttl
> 
> Your first example looks like it might be misusing the -cp flag [1]. You probably don't want the *.jar, just *, like
> 
> java -cp lib/* jena.spatialindexer --desc=../fuseki-server/run/configuration/mm.ttl
> 
> especially if you happen to be using Windows. [2] That might not be the entire story, but you can at least try those invocations and see if you get anything different/better.
> 
> ajs6f
> 
> [1] https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762 <https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762>
> [2] https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath <https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath>
> 
> 
>> On Sep 17, 2018, at 7:07 AM, Markus Neumann <mneumann@meteomatics.com <ma...@meteomatics.com>> wrote:
>> 
>> Ok, that's exactly what I did here:
>> $ java -cp lib/*.jar jena.spatialindexer --desc=../fuseki-server/run/configuration/mm.ttl
>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>> 
>> Or from outside JENA_HOME:
>> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer --desc=fuseki-server/run/configuration/mm.ttl
>> Error: Could not find or load main class apache-jena-3.8.0.lib.commons-cli-1.4.jar
>> 
>> Or did I missunderstand something?
>> 
>>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <ma...@gmail.com>:
>>> 
>>> don't worry it's a common problem and frequent source of confusion not only
>>> with jena but java projects. try to simply inlcude all the jars.
>>> 
>>> I presume you run this on a linux box with OpenJDK 8. correct?
>>> 
>>> now once you have set up jena just add the following
>>> {replace_with_your_path}/apache-jena-3.8.0/lib/*
>>> 
>>> 
>>> 
>>> 
>>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>
>>> wrote:
>>> 
>>>> This is embarrassing but I don't get it.
>>>> 
>>>> I've configured $JENA_HOME and adjusted the PATH.
>>>> 
>>>> Now what classpath should I include when invoking the indexer?
>>>> What I've tried so far:
>>>> 
>>>> $ cd $JENA_HOME
>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>> Error: Could not find or load main class jena.spatialindexer
>>>> $ java -cp lib/*.jar jena.spatialindexer
>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>>>> 
>>>> Thanks for your patience
>>>> 
>>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <marco.neumann@gmail.com <ma...@gmail.com>>:
>>>>> 
>>>>> yes correct, this looks good. now include the classpath during invocation
>>>>> of the spatialindexer
>>>>> 
>>>>> in addition it's always a good idea to properly configure jena along your
>>>>> java runtime environment settings to avoid jdk / lib conflicts during
>>>>> execution.
>>>>> 
>>>>> https://jena.apache.org/documentation/tools/index.html <https://jena.apache.org/documentation/tools/index.html> <
>>>> https://jena.apache.org/documentation/tools/index.html <https://jena.apache.org/documentation/tools/index.html> <https://jena.apache.org/documentation/tools/index.html <https://jena.apache.org/documentation/tools/index.html>>>
>>>>> 
>>>>> 
>>>>> 
>>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>
>>>>> wrote:
>>>>> 
>>>>>> 1.: what do you mean by indexer?
>>>>>> Probably my biggest problem is, that I have no clue how to find out,
>>>> where
>>>>>> the jena.spatialindexer could be located except for asking here.
>>>>>> 
>>>>>> Here is the content of the apache jena I downloaded:
>>>>>> $ ls -lh ../apache-jena-3.8.0/lib
>>>>>> total 17M
>>>>>> -rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
>>>>>> -rw-r--r-- 1 process process  53K Oct 26  2017 commons-cli-1.4.jar
>>>>>> -rw-r--r-- 1 process process 328K Mar  5  2018 commons-codec-1.11.jar
>>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59 commons-compress-1.17.jar
>>>>>> -rw-r--r-- 1 process process  41K Mar  5  2018 commons-csv-1.5.jar
>>>>>> -rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
>>>>>> -rw-r--r-- 1 process process 425K Oct 26  2017 commons-lang3-3.4.jar
>>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01 httpclient-4.5.5.jar
>>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
>>>> httpclient-cache-4.5.5.jar
>>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
>>>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
>>>>>> jackson-annotations-2.9.0.jar
>>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01 jackson-core-2.9.5.jar
>>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
>>>> jackson-databind-2.9.5.jar
>>>>>> -rw-r--r-- 1 process process  17K Oct 26  2017 jcl-over-slf4j-1.7.25.jar
>>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
>>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01 jena-base-3.8.0.jar
>>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07 jena-cmds-3.8.0.jar
>>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02 jena-core-3.8.0.jar
>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05 jena-dboe-base-3.8.0.jar
>>>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05 jena-dboe-index-3.8.0.jar
>>>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
>>>>>> jena-dboe-transaction-3.8.0.jar
>>>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
>>>>>> jena-dboe-trans-data-3.8.0.jar
>>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
>>>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
>>>> jena-rdfconnection-3.8.0.jar
>>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
>>>> jena-shaded-guava-3.8.0.jar
>>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06 jena-tdb2-3.8.0.jar
>>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
>>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01 jsonld-java-0.12.0.jar
>>>>>> -rw-r--r-- 1 process process 232K Mar  5  2018 libthrift-0.10.0.jar
>>>>>> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
>>>>>> -rw-r--r-- 1 process process  41K Oct 26  2017 slf4j-api-1.7.25.jar
>>>>>> -rw-r--r-- 1 process process  12K Oct 26  2017 slf4j-log4j12-1.7.25.jar
>>>>>> 
>>>>>> 2.: Turns out, I don't need the jts. after commenting out the affected
>>>>>> lines, the server still runs fine. (But still without spatial index)
>>>>>> 
>>>>>> Best Markus
>>>>>> 
>>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <marco.neumann@gmail.com <ma...@gmail.com> <mailto:marco.neumann@gmail.com <ma...@gmail.com>>
>>>>> :
>>>>>>> 
>>>>>>> Ok let's take a look at this.
>>>>>>> 
>>>>>>> 1. please include in the indexer in the classpath. It's part of the
>>>>>> current
>>>>>>> jena distribution.
>>>>>>> 
>>>>>>> 2. do you need jts? it's a package that allows you to index multi point
>>>>>>> geometries. here a sample query would be helpful. If single point
>>>>>>> geometries are indexed and used in conjunction with MBR range queries.
>>>>>>> there is no need for jts.
>>>>>>> 
>>>>>>> 
>>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
>>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>
>>>>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>>
>>>>>>> wrote:
>>>>>>> 
>>>>>>>> Hi,
>>>>>>>> (sorry for the long post)
>>>>>>>> 
>>>>>>>> I've been struggling with the spatial index for a while now.
>>>>>>>> I've read
>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>>> <
>>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>>>> and
>>>>>>>> skipped through about every spatial related thread here on the list.
>>>>>>>> I managed to get an in-memory version up and running at some point
>>>>>>>> following this
>>>>>>>> 
>>>>>>>> 
>>>>>> 
>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>> <
>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>> 
>>>>>> <
>>>>>> 
>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>> <
>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>> 
>>>>>>> 
>>>>>>>> <
>>>>>>>> 
>>>>>> 
>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>> <
>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>> 
>>>>>> <
>>>>>> 
>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>> <
>>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066><https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>>
>>>>> 
>>>>>>> 
>>>>>>>>> 
>>>>>>>> and this
>>>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>>
>>>> <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>>>>>>>> 
>>>>>>>> But that was on a small dataset that I uploaded via the web-interface
>>>> of
>>>>>>>> Fuseki.
>>>>>>>> 
>>>>>>>> Now the story is a bit different. I'm building the database using
>>>>>>>> tdbloader2 and would like to create the spatial index upfront.
>>>>>>>> 
>>>>>>>> java -cp jena-spatial.jar jena.spatialindexer --desc=assembler_file
>>>>>>>> I could not figure out, how to get this line to work. I have the
>>>>>> following
>>>>>>>> possible scenarios:
>>>>>>>> 
>>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in the
>>>>>> classpath:
>>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>>>> Error: Could not find or load main class jena.spatialindexer
>>>>>>>> 
>>>>>>>> 2. I use the fuseki-server jar:
>>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
>>>>>>>> --desc=./run/configuration/mm.ttl
>>>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
>>>>>>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>>>>>>> transaction
>>>>>>>> 
>>>>>>>> I managed to eliminate the warning about jts by including that in the
>>>>>>>> classpath, but the error remains the same (with full trace):
>>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
>>>>>>>> --desc=./run/configuration/mm.ttl
>>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>>>>>>> transaction
>>>>>>>>    at
>>>>>>>> 
>>>>>> 
>>>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>>>>>>    at
>>>>>>>> 
>>>>>> 
>>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>>>>>>    at
>>>>>>>> 
>>>>>> 
>>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>>>>>>    at
>>>>>>>> 
>>>>>> 
>>>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>>>>>>    at
>>>>>>>> 
>>>>>> 
>>>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>>>>>>    at
>>>>>>>> 
>>>>>> 
>>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>>>>>>    at
>>>>>>>> 
>>>>>> 
>>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>>>>>>    at
>>>>>>>> 
>>>>>> 
>>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>>>>>>    at
>>>>>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>>>>>>    at
>>>>>>>> 
>>>>>> 
>>>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>>>>>>    at
>>>>>>>> 
>>>>>> 
>>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>>>>>>    at
>>>>>>>> 
>>>>>> 
>>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>>>>>>    at
>>>>>>>> 
>>>>>> 
>>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>>>    at
>>>>>>>> 
>>>>>> 
>>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>>>    at jena.spatialindexer.exec(spatialindexer.java:110)
>>>>>>>>    at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>>>>>>    at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>>>>>>    at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>>>>>>    at jena.spatialindexer.main(spatialindexer.java:53)
>>>>>>>> 
>>>>>>>> My configuration is the following:
>>>>>>>> @prefix :      <http://base/#> .
>>>>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>>>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>>>>>>> # Spatial
>>>>>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>>>>>>>> 
>>>>>>>> :service_tdb_all  a                   fuseki:Service ;
>>>>>>>>    rdfs:label                    "TDB2 mm" ;
>>>>>>>>    fuseki:dataset                :spatial_dataset ;
>>>>>>>>    fuseki:name                   "mm" ;
>>>>>>>>    fuseki:serviceQuery           "query" , "sparql" ;
>>>>>>>>    fuseki:serviceReadGraphStore  "get" ;
>>>>>>>>    fuseki:serviceReadWriteGraphStore
>>>>>>>>            "data" ;
>>>>>>>>    fuseki:serviceUpdate          "update" ;
>>>>>>>>    fuseki:serviceUpload          "upload" .
>>>>>>>> 
>>>>>>>> :spatial_dataset a spatial:SpatialDataset ;
>>>>>>>> spatial:dataset   :tdb_dataset_readwrite ;
>>>>>>>> spatial:index     <#indexLucene> ;
>>>>>>>> .
>>>>>>>> 
>>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>>>>>>> spatial:directory <file:Lucene> ;
>>>>>>>> #spatial:directory "mem" ;
>>>>>>>> spatial:definition <#definition> ;
>>>>>>>> .
>>>>>>>> 
>>>>>>>> <#definition> a spatial:EntityDefinition ;
>>>>>>>> spatial:entityField      "uri" ;
>>>>>>>> spatial:geoField     "geo" ;
>>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format
>>>>>>>> spatial:hasSpatialPredicatePairs (
>>>>>>>>     [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>>>>>>>     ) ;
>>>>>>>> # custom geo predicates for 2) Well Known Text (WKT) Literal
>>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ;
>>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT) Literal
>>>>>>>> spatial:spatialContextFactory
>>>>>>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>>>>>>> 
>>>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>>>>>>> .
>>>>>>>> 
>>>>>>>> :tdb_dataset_readwrite
>>>>>>>>    a              tdb2:DatasetTDB2 ;
>>>>>>>>    tdb2:location
>>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>>>>>>> 
>>>>>>>> And I've changed the fuseki script to include the jts jar:
>>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
>>>>>>>> 
>>>>>>>> I see no errors or warnings in the server log, when starting with that
>>>>>>>> configuration, the Lucene folder is created and populated with
>>>>>> something:
>>>>>>>> $ ll run/configuration/Lucene/
>>>>>>>> total 4
>>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
>>>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
>>>>>>>> 
>>>>>>>> But any spatial query does not return any results.
>>>>>>>> Any help on how to tackle this would be highly appreciated.
>>>>>>>> 
>>>>>>>> Best
>>>>>>>> Markus Neumann
>>>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>>>> --
>>>>>>> 
>>>>>>> 
>>>>>>> ---
>>>>>>> Marco Neumann
>>>>>>> KONA
>>>>>> 
>>>>>> 
>>>>> 
>>>>> --
>>>>> 
>>>>> 
>>>>> ---
>>>>> Marco Neumann
>>>>> KONA
>>>> 
>>>> 
>>> 
>>> -- 
>>> 
>>> 
>>> ---
>>> Marco Neumann
>>> KONA

Re: Building a spatial index with jena/fuseki

Posted by ajs6f <aj...@apache.org>.
I think you might have misunderstood the use of $JENA_HOME, or perhaps the Java classpath. $JENA_HOME, which should generally be an absolute filepath, allows the Jena scripts to find their libraries at runtime. Internally, the scripts use $JENA_HOME to set up the classpaths with which to start running Java code. But in this case, you're not using the scripts. You're calling a Java class directly, which means you have to give it all the libraries directly, using the classpath flag directly. For example, your second attempt:

$ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer --desc=fuseki-server/run/configuration/mm.ttl
Error: Could not find or load main class apache-jena-3.8.0.lib.commons-cli-1.4.jar

may have failed because whatever directory you are in probably doesn't happen to have a Jena distribution in it called "apache-jena-3.8.0". Perhaps try:

java -cp $JENA_HOME/lib/* jena.spatialindexer --desc=fuseki-server/run/configuration/mm.ttl

Your first example looks like it might be misusing the -cp flag [1]. You probably don't want the *.jar, just *, like

java -cp lib/* jena.spatialindexer --desc=../fuseki-server/run/configuration/mm.ttl

especially if you happen to be using Windows. [2] That might not be the entire story, but you can at least try those invocations and see if you get anything different/better.

ajs6f

[1] https://docs.oracle.com/javase/8/docs/technotes/tools/windows/classpath.html#A1100762
[2] https://stackoverflow.com/questions/219585/including-all-the-jars-in-a-directory-within-the-java-classpath


> On Sep 17, 2018, at 7:07 AM, Markus Neumann <mn...@meteomatics.com> wrote:
> 
> Ok, that's exactly what I did here:
> $ java -cp lib/*.jar jena.spatialindexer --desc=../fuseki-server/run/configuration/mm.ttl
> Error: Could not find or load main class lib.commons-cli-1.4.jar
> 
> Or from outside JENA_HOME:
> $ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer --desc=fuseki-server/run/configuration/mm.ttl
> Error: Could not find or load main class apache-jena-3.8.0.lib.commons-cli-1.4.jar
> 
> Or did I missunderstand something?
> 
>> Am 17.09.2018 um 12:02 schrieb Marco Neumann <ma...@gmail.com>:
>> 
>> don't worry it's a common problem and frequent source of confusion not only
>> with jena but java projects. try to simply inlcude all the jars.
>> 
>> I presume you run this on a linux box with OpenJDK 8. correct?
>> 
>> now once you have set up jena just add the following
>> {replace_with_your_path}/apache-jena-3.8.0/lib/*
>> 
>> 
>> 
>> 
>> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <mneumann@meteomatics.com <ma...@meteomatics.com>>
>> wrote:
>> 
>>> This is embarrassing but I don't get it.
>>> 
>>> I've configured $JENA_HOME and adjusted the PATH.
>>> 
>>> Now what classpath should I include when invoking the indexer?
>>> What I've tried so far:
>>> 
>>> $ cd $JENA_HOME
>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>> Error: Could not find or load main class jena.spatialindexer
>>> $ java -cp lib/*.jar jena.spatialindexer
>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>>> 
>>> Thanks for your patience
>>> 
>>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <ma...@gmail.com>:
>>>> 
>>>> yes correct, this looks good. now include the classpath during invocation
>>>> of the spatialindexer
>>>> 
>>>> in addition it's always a good idea to properly configure jena along your
>>>> java runtime environment settings to avoid jdk / lib conflicts during
>>>> execution.
>>>> 
>>>> https://jena.apache.org/documentation/tools/index.html <
>>> https://jena.apache.org/documentation/tools/index.html <https://jena.apache.org/documentation/tools/index.html>>
>>>> 
>>>> 
>>>> 
>>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
>>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>
>>>> wrote:
>>>> 
>>>>> 1.: what do you mean by indexer?
>>>>> Probably my biggest problem is, that I have no clue how to find out,
>>> where
>>>>> the jena.spatialindexer could be located except for asking here.
>>>>> 
>>>>> Here is the content of the apache jena I downloaded:
>>>>> $ ls -lh ../apache-jena-3.8.0/lib
>>>>> total 17M
>>>>> -rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
>>>>> -rw-r--r-- 1 process process  53K Oct 26  2017 commons-cli-1.4.jar
>>>>> -rw-r--r-- 1 process process 328K Mar  5  2018 commons-codec-1.11.jar
>>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59 commons-compress-1.17.jar
>>>>> -rw-r--r-- 1 process process  41K Mar  5  2018 commons-csv-1.5.jar
>>>>> -rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
>>>>> -rw-r--r-- 1 process process 425K Oct 26  2017 commons-lang3-3.4.jar
>>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01 httpclient-4.5.5.jar
>>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
>>> httpclient-cache-4.5.5.jar
>>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
>>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
>>>>> jackson-annotations-2.9.0.jar
>>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01 jackson-core-2.9.5.jar
>>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
>>> jackson-databind-2.9.5.jar
>>>>> -rw-r--r-- 1 process process  17K Oct 26  2017 jcl-over-slf4j-1.7.25.jar
>>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
>>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01 jena-base-3.8.0.jar
>>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07 jena-cmds-3.8.0.jar
>>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02 jena-core-3.8.0.jar
>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05 jena-dboe-base-3.8.0.jar
>>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05 jena-dboe-index-3.8.0.jar
>>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
>>>>> jena-dboe-transaction-3.8.0.jar
>>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
>>>>> jena-dboe-trans-data-3.8.0.jar
>>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
>>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
>>> jena-rdfconnection-3.8.0.jar
>>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
>>> jena-shaded-guava-3.8.0.jar
>>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06 jena-tdb2-3.8.0.jar
>>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
>>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01 jsonld-java-0.12.0.jar
>>>>> -rw-r--r-- 1 process process 232K Mar  5  2018 libthrift-0.10.0.jar
>>>>> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
>>>>> -rw-r--r-- 1 process process  41K Oct 26  2017 slf4j-api-1.7.25.jar
>>>>> -rw-r--r-- 1 process process  12K Oct 26  2017 slf4j-log4j12-1.7.25.jar
>>>>> 
>>>>> 2.: Turns out, I don't need the jts. after commenting out the affected
>>>>> lines, the server still runs fine. (But still without spatial index)
>>>>> 
>>>>> Best Markus
>>>>> 
>>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <marco.neumann@gmail.com <ma...@gmail.com>
>>>> :
>>>>>> 
>>>>>> Ok let's take a look at this.
>>>>>> 
>>>>>> 1. please include in the indexer in the classpath. It's part of the
>>>>> current
>>>>>> jena distribution.
>>>>>> 
>>>>>> 2. do you need jts? it's a package that allows you to index multi point
>>>>>> geometries. here a sample query would be helpful. If single point
>>>>>> geometries are indexed and used in conjunction with MBR range queries.
>>>>>> there is no need for jts.
>>>>>> 
>>>>>> 
>>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
>>> mneumann@meteomatics.com <ma...@meteomatics.com>
>>>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>
>>>>>> wrote:
>>>>>> 
>>>>>>> Hi,
>>>>>>> (sorry for the long post)
>>>>>>> 
>>>>>>> I've been struggling with the spatial index for a while now.
>>>>>>> I've read
>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <
>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <
>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <
>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <
>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>>> and
>>>>>>> skipped through about every spatial related thread here on the list.
>>>>>>> I managed to get an in-memory version up and running at some point
>>>>>>> following this
>>>>>>> 
>>>>>>> 
>>>>> 
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>> <
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>>> 
>>>>> <
>>>>> 
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>> <
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>>> 
>>>>>> 
>>>>>>> <
>>>>>>> 
>>>>> 
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>> <
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>>> 
>>>>> <
>>>>> 
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>> <
>>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>>> 
>>>>>> 
>>>>>>>> 
>>>>>>> and this
>>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>>> <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>>>>>>> 
>>>>>>> But that was on a small dataset that I uploaded via the web-interface
>>> of
>>>>>>> Fuseki.
>>>>>>> 
>>>>>>> Now the story is a bit different. I'm building the database using
>>>>>>> tdbloader2 and would like to create the spatial index upfront.
>>>>>>> 
>>>>>>> java -cp jena-spatial.jar jena.spatialindexer --desc=assembler_file
>>>>>>> I could not figure out, how to get this line to work. I have the
>>>>> following
>>>>>>> possible scenarios:
>>>>>>> 
>>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in the
>>>>> classpath:
>>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>>> Error: Could not find or load main class jena.spatialindexer
>>>>>>> 
>>>>>>> 2. I use the fuseki-server jar:
>>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
>>>>>>> --desc=./run/configuration/mm.ttl
>>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
>>>>>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>>>>>> transaction
>>>>>>> 
>>>>>>> I managed to eliminate the warning about jts by including that in the
>>>>>>> classpath, but the error remains the same (with full trace):
>>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
>>>>>>> --desc=./run/configuration/mm.ttl
>>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>>>>>> transaction
>>>>>>>     at
>>>>>>> 
>>>>> 
>>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>>>>>     at
>>>>>>> 
>>>>> 
>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>>>>>     at
>>>>>>> 
>>>>> 
>>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>>>>>     at
>>>>>>> 
>>>>> 
>>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>>>>>     at
>>>>>>> 
>>>>> 
>>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>>>>>     at
>>>>>>> 
>>>>> 
>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>>>>>     at
>>>>>>> 
>>>>> 
>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>>>>>     at
>>>>>>> 
>>>>> 
>>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>>>>>     at
>>>>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>>>>>     at
>>>>>>> 
>>>>> 
>>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>>>>>     at
>>>>>>> 
>>>>> 
>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>>>>>     at
>>>>>>> 
>>>>> 
>>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>>>>>     at
>>>>>>> 
>>>>> 
>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>>     at
>>>>>>> 
>>>>> 
>>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>>     at jena.spatialindexer.exec(spatialindexer.java:110)
>>>>>>>     at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>>>>>     at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>>>>>     at jena.spatialindexer.main(spatialindexer.java:53)
>>>>>>> 
>>>>>>> My configuration is the following:
>>>>>>> @prefix :      <http://base/#> .
>>>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>>>>>> # Spatial
>>>>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>>>>>>> 
>>>>>>> :service_tdb_all  a                   fuseki:Service ;
>>>>>>>     rdfs:label                    "TDB2 mm" ;
>>>>>>>     fuseki:dataset                :spatial_dataset ;
>>>>>>>     fuseki:name                   "mm" ;
>>>>>>>     fuseki:serviceQuery           "query" , "sparql" ;
>>>>>>>     fuseki:serviceReadGraphStore  "get" ;
>>>>>>>     fuseki:serviceReadWriteGraphStore
>>>>>>>             "data" ;
>>>>>>>     fuseki:serviceUpdate          "update" ;
>>>>>>>     fuseki:serviceUpload          "upload" .
>>>>>>> 
>>>>>>> :spatial_dataset a spatial:SpatialDataset ;
>>>>>>> spatial:dataset   :tdb_dataset_readwrite ;
>>>>>>> spatial:index     <#indexLucene> ;
>>>>>>> .
>>>>>>> 
>>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>>>>>> spatial:directory <file:Lucene> ;
>>>>>>> #spatial:directory "mem" ;
>>>>>>> spatial:definition <#definition> ;
>>>>>>> .
>>>>>>> 
>>>>>>> <#definition> a spatial:EntityDefinition ;
>>>>>>> spatial:entityField      "uri" ;
>>>>>>> spatial:geoField     "geo" ;
>>>>>>> # custom geo predicates for 1) Latitude/Longitude Format
>>>>>>> spatial:hasSpatialPredicatePairs (
>>>>>>>      [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>>>>>>      ) ;
>>>>>>> # custom geo predicates for 2) Well Known Text (WKT) Literal
>>>>>>> spatial:hasWKTPredicates (geosparql:asWKT) ;
>>>>>>> # custom SpatialContextFactory for 2) Well Known Text (WKT) Literal
>>>>>>> spatial:spatialContextFactory
>>>>>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>>>>>> 
>>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>>>>>> .
>>>>>>> 
>>>>>>> :tdb_dataset_readwrite
>>>>>>>     a              tdb2:DatasetTDB2 ;
>>>>>>>     tdb2:location
>>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>>>>>> 
>>>>>>> And I've changed the fuseki script to include the jts jar:
>>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
>>>>>>> 
>>>>>>> I see no errors or warnings in the server log, when starting with that
>>>>>>> configuration, the Lucene folder is created and populated with
>>>>> something:
>>>>>>> $ ll run/configuration/Lucene/
>>>>>>> total 4
>>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
>>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
>>>>>>> 
>>>>>>> But any spatial query does not return any results.
>>>>>>> Any help on how to tackle this would be highly appreciated.
>>>>>>> 
>>>>>>> Best
>>>>>>> Markus Neumann
>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>>> --
>>>>>> 
>>>>>> 
>>>>>> ---
>>>>>> Marco Neumann
>>>>>> KONA
>>>>> 
>>>>> 
>>>> 
>>>> --
>>>> 
>>>> 
>>>> ---
>>>> Marco Neumann
>>>> KONA
>>> 
>>> 
>> 
>> -- 
>> 
>> 
>> ---
>> Marco Neumann
>> KONA
>

Re: Building a spatial index with jena/fuseki

Posted by Markus Neumann <mn...@meteomatics.com>.
Ok, that's exactly what I did here:
$ java -cp lib/*.jar jena.spatialindexer --desc=../fuseki-server/run/configuration/mm.ttl
Error: Could not find or load main class lib.commons-cli-1.4.jar

Or from outside JENA_HOME:
$ java -cp apache-jena-3.8.0/lib/* jena.spatialindexer --desc=fuseki-server/run/configuration/mm.ttl
Error: Could not find or load main class apache-jena-3.8.0.lib.commons-cli-1.4.jar

Or did I missunderstand something?

> Am 17.09.2018 um 12:02 schrieb Marco Neumann <ma...@gmail.com>:
> 
> don't worry it's a common problem and frequent source of confusion not only
> with jena but java projects. try to simply inlcude all the jars.
> 
> I presume you run this on a linux box with OpenJDK 8. correct?
> 
> now once you have set up jena just add the following
> {replace_with_your_path}/apache-jena-3.8.0/lib/*
> 
> 
> 
> 
> On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <mneumann@meteomatics.com <ma...@meteomatics.com>>
> wrote:
> 
>> This is embarrassing but I don't get it.
>> 
>> I've configured $JENA_HOME and adjusted the PATH.
>> 
>> Now what classpath should I include when invoking the indexer?
>> What I've tried so far:
>> 
>> $ cd $JENA_HOME
>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>> --desc=../fuseki-server/run/configuration/mm.ttl
>> Error: Could not find or load main class jena.spatialindexer
>> $ java -cp lib/*.jar jena.spatialindexer
>> --desc=../fuseki-server/run/configuration/mm.ttl
>> Error: Could not find or load main class lib.commons-cli-1.4.jar
>> 
>> Thanks for your patience
>> 
>>> Am 17.09.2018 um 11:38 schrieb Marco Neumann <ma...@gmail.com>:
>>> 
>>> yes correct, this looks good. now include the classpath during invocation
>>> of the spatialindexer
>>> 
>>> in addition it's always a good idea to properly configure jena along your
>>> java runtime environment settings to avoid jdk / lib conflicts during
>>> execution.
>>> 
>>> https://jena.apache.org/documentation/tools/index.html <
>> https://jena.apache.org/documentation/tools/index.html <https://jena.apache.org/documentation/tools/index.html>>
>>> 
>>> 
>>> 
>>> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
>> mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>
>>> wrote:
>>> 
>>>> 1.: what do you mean by indexer?
>>>> Probably my biggest problem is, that I have no clue how to find out,
>> where
>>>> the jena.spatialindexer could be located except for asking here.
>>>> 
>>>> Here is the content of the apache jena I downloaded:
>>>> $ ls -lh ../apache-jena-3.8.0/lib
>>>> total 17M
>>>> -rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
>>>> -rw-r--r-- 1 process process  53K Oct 26  2017 commons-cli-1.4.jar
>>>> -rw-r--r-- 1 process process 328K Mar  5  2018 commons-codec-1.11.jar
>>>> -rw-r--r-- 1 process process 576K Jun 25 09:59 commons-compress-1.17.jar
>>>> -rw-r--r-- 1 process process  41K Mar  5  2018 commons-csv-1.5.jar
>>>> -rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
>>>> -rw-r--r-- 1 process process 425K Oct 26  2017 commons-lang3-3.4.jar
>>>> -rw-r--r-- 1 process process 749K Jun 25 10:01 httpclient-4.5.5.jar
>>>> -rw-r--r-- 1 process process 158K Jun 25 10:01
>> httpclient-cache-4.5.5.jar
>>>> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
>>>> -rw-r--r-- 1 process process  65K Oct 26  2017
>>>> jackson-annotations-2.9.0.jar
>>>> -rw-r--r-- 1 process process 315K Jun 25 10:01 jackson-core-2.9.5.jar
>>>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
>> jackson-databind-2.9.5.jar
>>>> -rw-r--r-- 1 process process  17K Oct 26  2017 jcl-over-slf4j-1.7.25.jar
>>>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
>>>> -rw-r--r-- 1 process process 211K Jun 25 11:01 jena-base-3.8.0.jar
>>>> -rw-r--r-- 1 process process 259K Jun 25 11:07 jena-cmds-3.8.0.jar
>>>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02 jena-core-3.8.0.jar
>>>> -rw-r--r-- 1 process process 135K Jun 25 11:05 jena-dboe-base-3.8.0.jar
>>>> -rw-r--r-- 1 process process  21K Jun 25 11:05 jena-dboe-index-3.8.0.jar
>>>> -rw-r--r-- 1 process process  74K Jun 25 11:05
>>>> jena-dboe-transaction-3.8.0.jar
>>>> -rw-r--r-- 1 process process  95K Jun 25 11:06
>>>> jena-dboe-trans-data-3.8.0.jar
>>>> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
>>>> -rw-r--r-- 1 process process  49K Jun 25 11:04
>> jena-rdfconnection-3.8.0.jar
>>>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
>> jena-shaded-guava-3.8.0.jar
>>>> -rw-r--r-- 1 process process 264K Jun 25 11:06 jena-tdb2-3.8.0.jar
>>>> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
>>>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01 jsonld-java-0.12.0.jar
>>>> -rw-r--r-- 1 process process 232K Mar  5  2018 libthrift-0.10.0.jar
>>>> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
>>>> -rw-r--r-- 1 process process  41K Oct 26  2017 slf4j-api-1.7.25.jar
>>>> -rw-r--r-- 1 process process  12K Oct 26  2017 slf4j-log4j12-1.7.25.jar
>>>> 
>>>> 2.: Turns out, I don't need the jts. after commenting out the affected
>>>> lines, the server still runs fine. (But still without spatial index)
>>>> 
>>>> Best Markus
>>>> 
>>>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <marco.neumann@gmail.com <ma...@gmail.com>
>>> :
>>>>> 
>>>>> Ok let's take a look at this.
>>>>> 
>>>>> 1. please include in the indexer in the classpath. It's part of the
>>>> current
>>>>> jena distribution.
>>>>> 
>>>>> 2. do you need jts? it's a package that allows you to index multi point
>>>>> geometries. here a sample query would be helpful. If single point
>>>>> geometries are indexed and used in conjunction with MBR range queries.
>>>>> there is no need for jts.
>>>>> 
>>>>> 
>>>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
>> mneumann@meteomatics.com <ma...@meteomatics.com>
>>>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>>
>>>>> wrote:
>>>>> 
>>>>>> Hi,
>>>>>> (sorry for the long post)
>>>>>> 
>>>>>> I've been struggling with the spatial index for a while now.
>>>>>> I've read
>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>> <
>>>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>>> and
>>>>>> skipped through about every spatial related thread here on the list.
>>>>>> I managed to get an in-memory version up and running at some point
>>>>>> following this
>>>>>> 
>>>>>> 
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>> 
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>> 
>>>>> 
>>>>>> <
>>>>>> 
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>> 
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>> 
>>>>> 
>>>>>>> 
>>>>>> and this
>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>> <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>>>>>> 
>>>>>> But that was on a small dataset that I uploaded via the web-interface
>> of
>>>>>> Fuseki.
>>>>>> 
>>>>>> Now the story is a bit different. I'm building the database using
>>>>>> tdbloader2 and would like to create the spatial index upfront.
>>>>>> 
>>>>>> java -cp jena-spatial.jar jena.spatialindexer --desc=assembler_file
>>>>>> I could not figure out, how to get this line to work. I have the
>>>> following
>>>>>> possible scenarios:
>>>>>> 
>>>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in the
>>>> classpath:
>>>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>>>> Error: Could not find or load main class jena.spatialindexer
>>>>>> 
>>>>>> 2. I use the fuseki-server jar:
>>>>>> $ java -cp fuseki-server.jar jena.spatialindexer
>>>>>> --desc=./run/configuration/mm.ttl
>>>>>> WARN  Custom SpatialContextFactory lib is not ready in
>>>>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>>>>> transaction
>>>>>> 
>>>>>> I managed to eliminate the warning about jts by including that in the
>>>>>> classpath, but the error remains the same (with full trace):
>>>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
>>>>>> --desc=./run/configuration/mm.ttl
>>>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>>>>> transaction
>>>>>>      at
>>>>>> 
>>>> 
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>>>>      at
>>>>>> 
>>>> 
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>>>>      at
>>>>>> 
>>>> 
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>>>>      at
>>>>>> 
>>>> 
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>>>>      at
>>>>>> 
>>>> 
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>>>>      at
>>>>>> 
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>>>>      at
>>>>>> 
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>>>>      at
>>>>>> 
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>>>>      at
>>>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>>>>      at
>>>>>> 
>>>> 
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>>>>      at
>>>>>> 
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>>>>      at
>>>>>> 
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>>>>      at
>>>>>> 
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>      at
>>>>>> 
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>>>      at jena.spatialindexer.exec(spatialindexer.java:110)
>>>>>>      at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>>>>      at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>>>>      at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>>>>      at jena.spatialindexer.main(spatialindexer.java:53)
>>>>>> 
>>>>>> My configuration is the following:
>>>>>> @prefix :      <http://base/#> .
>>>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>>>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>>>>> # Spatial
>>>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>>>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>>>>> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>>>>>> 
>>>>>> :service_tdb_all  a                   fuseki:Service ;
>>>>>>      rdfs:label                    "TDB2 mm" ;
>>>>>>      fuseki:dataset                :spatial_dataset ;
>>>>>>      fuseki:name                   "mm" ;
>>>>>>      fuseki:serviceQuery           "query" , "sparql" ;
>>>>>>      fuseki:serviceReadGraphStore  "get" ;
>>>>>>      fuseki:serviceReadWriteGraphStore
>>>>>>              "data" ;
>>>>>>      fuseki:serviceUpdate          "update" ;
>>>>>>      fuseki:serviceUpload          "upload" .
>>>>>> 
>>>>>> :spatial_dataset a spatial:SpatialDataset ;
>>>>>>  spatial:dataset   :tdb_dataset_readwrite ;
>>>>>>  spatial:index     <#indexLucene> ;
>>>>>>  .
>>>>>> 
>>>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>>>>>  spatial:directory <file:Lucene> ;
>>>>>>  #spatial:directory "mem" ;
>>>>>>  spatial:definition <#definition> ;
>>>>>>  .
>>>>>> 
>>>>>> <#definition> a spatial:EntityDefinition ;
>>>>>>  spatial:entityField      "uri" ;
>>>>>>  spatial:geoField     "geo" ;
>>>>>>  # custom geo predicates for 1) Latitude/Longitude Format
>>>>>>  spatial:hasSpatialPredicatePairs (
>>>>>>       [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>>>>>       ) ;
>>>>>>  # custom geo predicates for 2) Well Known Text (WKT) Literal
>>>>>>  spatial:hasWKTPredicates (geosparql:asWKT) ;
>>>>>>  # custom SpatialContextFactory for 2) Well Known Text (WKT) Literal
>>>>>>  spatial:spatialContextFactory
>>>>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>>>>> 
>> "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>>>>>  .
>>>>>> 
>>>>>> :tdb_dataset_readwrite
>>>>>>      a              tdb2:DatasetTDB2 ;
>>>>>>      tdb2:location
>>>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>>>>> 
>>>>>> And I've changed the fuseki script to include the jts jar:
>>>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
>>>>>> 
>>>>>> I see no errors or warnings in the server log, when starting with that
>>>>>> configuration, the Lucene folder is created and populated with
>>>> something:
>>>>>> $ ll run/configuration/Lucene/
>>>>>> total 4
>>>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
>>>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
>>>>>> 
>>>>>> But any spatial query does not return any results.
>>>>>> Any help on how to tackle this would be highly appreciated.
>>>>>> 
>>>>>> Best
>>>>>> Markus Neumann
>>>>>> 
>>>>>> 
>>>>> 
>>>>> --
>>>>> 
>>>>> 
>>>>> ---
>>>>> Marco Neumann
>>>>> KONA
>>>> 
>>>> 
>>> 
>>> --
>>> 
>>> 
>>> ---
>>> Marco Neumann
>>> KONA
>> 
>> 
> 
> -- 
> 
> 
> ---
> Marco Neumann
> KONA

Re: Building a spatial index with jena/fuseki

Posted by Marco Neumann <ma...@gmail.com>.
don't worry it's a common problem and frequent source of confusion not only
with jena but java projects. try to simply inlcude all the jars.

I presume you run this on a linux box with OpenJDK 8. correct?

now once you have set up jena just add the following
{replace_with_your_path}/apache-jena-3.8.0/lib/*




On Mon, Sep 17, 2018 at 10:56 AM Markus Neumann <mn...@meteomatics.com>
wrote:

> This is embarrassing but I don't get it.
>
> I've configured $JENA_HOME and adjusted the PATH.
>
> Now what classpath should I include when invoking the indexer?
> What I've tried so far:
>
> $ cd $JENA_HOME
> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> --desc=../fuseki-server/run/configuration/mm.ttl
> Error: Could not find or load main class jena.spatialindexer
> $ java -cp lib/*.jar jena.spatialindexer
> --desc=../fuseki-server/run/configuration/mm.ttl
> Error: Could not find or load main class lib.commons-cli-1.4.jar
>
> Thanks for your patience
>
> > Am 17.09.2018 um 11:38 schrieb Marco Neumann <ma...@gmail.com>:
> >
> > yes correct, this looks good. now include the classpath during invocation
> > of the spatialindexer
> >
> > in addition it's always a good idea to properly configure jena along your
> > java runtime environment settings to avoid jdk / lib conflicts during
> > execution.
> >
> > https://jena.apache.org/documentation/tools/index.html <
> https://jena.apache.org/documentation/tools/index.html>
> >
> >
> >
> > On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <
> mneumann@meteomatics.com <ma...@meteomatics.com>>
> > wrote:
> >
> >> 1.: what do you mean by indexer?
> >> Probably my biggest problem is, that I have no clue how to find out,
> where
> >> the jena.spatialindexer could be located except for asking here.
> >>
> >> Here is the content of the apache jena I downloaded:
> >> $ ls -lh ../apache-jena-3.8.0/lib
> >> total 17M
> >> -rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
> >> -rw-r--r-- 1 process process  53K Oct 26  2017 commons-cli-1.4.jar
> >> -rw-r--r-- 1 process process 328K Mar  5  2018 commons-codec-1.11.jar
> >> -rw-r--r-- 1 process process 576K Jun 25 09:59 commons-compress-1.17.jar
> >> -rw-r--r-- 1 process process  41K Mar  5  2018 commons-csv-1.5.jar
> >> -rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
> >> -rw-r--r-- 1 process process 425K Oct 26  2017 commons-lang3-3.4.jar
> >> -rw-r--r-- 1 process process 749K Jun 25 10:01 httpclient-4.5.5.jar
> >> -rw-r--r-- 1 process process 158K Jun 25 10:01
> httpclient-cache-4.5.5.jar
> >> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
> >> -rw-r--r-- 1 process process  65K Oct 26  2017
> >> jackson-annotations-2.9.0.jar
> >> -rw-r--r-- 1 process process 315K Jun 25 10:01 jackson-core-2.9.5.jar
> >> -rw-r--r-- 1 process process 1.3M Jun 25 10:01
> jackson-databind-2.9.5.jar
> >> -rw-r--r-- 1 process process  17K Oct 26  2017 jcl-over-slf4j-1.7.25.jar
> >> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
> >> -rw-r--r-- 1 process process 211K Jun 25 11:01 jena-base-3.8.0.jar
> >> -rw-r--r-- 1 process process 259K Jun 25 11:07 jena-cmds-3.8.0.jar
> >> -rw-r--r-- 1 process process 1.7M Jun 25 11:02 jena-core-3.8.0.jar
> >> -rw-r--r-- 1 process process 135K Jun 25 11:05 jena-dboe-base-3.8.0.jar
> >> -rw-r--r-- 1 process process  21K Jun 25 11:05 jena-dboe-index-3.8.0.jar
> >> -rw-r--r-- 1 process process  74K Jun 25 11:05
> >> jena-dboe-transaction-3.8.0.jar
> >> -rw-r--r-- 1 process process  95K Jun 25 11:06
> >> jena-dboe-trans-data-3.8.0.jar
> >> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
> >> -rw-r--r-- 1 process process  49K Jun 25 11:04
> jena-rdfconnection-3.8.0.jar
> >> -rw-r--r-- 1 process process 2.8M Jun 25 11:01
> jena-shaded-guava-3.8.0.jar
> >> -rw-r--r-- 1 process process 264K Jun 25 11:06 jena-tdb2-3.8.0.jar
> >> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
> >> -rw-r--r-- 1 process process 1.6M Jun 25 10:01 jsonld-java-0.12.0.jar
> >> -rw-r--r-- 1 process process 232K Mar  5  2018 libthrift-0.10.0.jar
> >> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
> >> -rw-r--r-- 1 process process  41K Oct 26  2017 slf4j-api-1.7.25.jar
> >> -rw-r--r-- 1 process process  12K Oct 26  2017 slf4j-log4j12-1.7.25.jar
> >>
> >> 2.: Turns out, I don't need the jts. after commenting out the affected
> >> lines, the server still runs fine. (But still without spatial index)
> >>
> >> Best Markus
> >>
> >>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <marco.neumann@gmail.com
> >:
> >>>
> >>> Ok let's take a look at this.
> >>>
> >>> 1. please include in the indexer in the classpath. It's part of the
> >> current
> >>> jena distribution.
> >>>
> >>> 2. do you need jts? it's a package that allows you to index multi point
> >>> geometries. here a sample query would be helpful. If single point
> >>> geometries are indexed and used in conjunction with MBR range queries.
> >>> there is no need for jts.
> >>>
> >>>
> >>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <
> mneumann@meteomatics.com
> >> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>
> >>> wrote:
> >>>
> >>>> Hi,
> >>>> (sorry for the long post)
> >>>>
> >>>> I've been struggling with the spatial index for a while now.
> >>>> I've read
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>> <
> >>>> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>>> and
> >>>> skipped through about every spatial related thread here on the list.
> >>>> I managed to get an in-memory version up and running at some point
> >>>> following this
> >>>>
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >
> >>>
> >>>> <
> >>>>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >
> >>>
> >>>>>
> >>>> and this
> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/
> <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> >>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
> >>>>
> >>>> But that was on a small dataset that I uploaded via the web-interface
> of
> >>>> Fuseki.
> >>>>
> >>>> Now the story is a bit different. I'm building the database using
> >>>> tdbloader2 and would like to create the spatial index upfront.
> >>>>
> >>>> java -cp jena-spatial.jar jena.spatialindexer --desc=assembler_file
> >>>> I could not figure out, how to get this line to work. I have the
> >> following
> >>>> possible scenarios:
> >>>>
> >>>> 1. I download the jena-spatial-3.8.0.jar and specify that in the
> >> classpath:
> >>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> >>>> --desc=../fuseki-server/run/configuration/mm.ttl
> >>>> Error: Could not find or load main class jena.spatialindexer
> >>>>
> >>>> 2. I use the fuseki-server jar:
> >>>> $ java -cp fuseki-server.jar jena.spatialindexer
> >>>> --desc=./run/configuration/mm.ttl
> >>>> WARN  Custom SpatialContextFactory lib is not ready in
> >>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
> >>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> >>>> transaction
> >>>>
> >>>> I managed to eliminate the warning about jts by including that in the
> >>>> classpath, but the error remains the same (with full trace):
> >>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
> >>>> --desc=./run/configuration/mm.ttl
> >>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> >>>> transaction
> >>>>       at
> >>>>
> >>
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>>>       at
> >>>>
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>>>       at
> >>>>
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>>>       at
> >>>>
> >>
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>>>       at
> >>>>
> >>
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>>>       at
> >>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>>>       at
> >>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>>>       at
> >>>>
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>>>       at
> >> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>>>       at
> >>>>
> >>
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>>>       at
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>>>       at
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>>>       at
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>       at
> >>>>
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>>>       at jena.spatialindexer.exec(spatialindexer.java:110)
> >>>>       at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>>>       at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>>>       at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>>>       at jena.spatialindexer.main(spatialindexer.java:53)
> >>>>
> >>>> My configuration is the following:
> >>>> @prefix :      <http://base/#> .
> >>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> >>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> >>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> >>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
> >>>> @prefix spatial: <http://jena.apache.org/spatial#> .
> >>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >>>> # Spatial
> >>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
> >>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> >>>> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
> >>>>
> >>>> :service_tdb_all  a                   fuseki:Service ;
> >>>>       rdfs:label                    "TDB2 mm" ;
> >>>>       fuseki:dataset                :spatial_dataset ;
> >>>>       fuseki:name                   "mm" ;
> >>>>       fuseki:serviceQuery           "query" , "sparql" ;
> >>>>       fuseki:serviceReadGraphStore  "get" ;
> >>>>       fuseki:serviceReadWriteGraphStore
> >>>>               "data" ;
> >>>>       fuseki:serviceUpdate          "update" ;
> >>>>       fuseki:serviceUpload          "upload" .
> >>>>
> >>>> :spatial_dataset a spatial:SpatialDataset ;
> >>>>   spatial:dataset   :tdb_dataset_readwrite ;
> >>>>   spatial:index     <#indexLucene> ;
> >>>>   .
> >>>>
> >>>> <#indexLucene> a spatial:SpatialIndexLucene ;
> >>>>   spatial:directory <file:Lucene> ;
> >>>>   #spatial:directory "mem" ;
> >>>>   spatial:definition <#definition> ;
> >>>>   .
> >>>>
> >>>> <#definition> a spatial:EntityDefinition ;
> >>>>   spatial:entityField      "uri" ;
> >>>>   spatial:geoField     "geo" ;
> >>>>   # custom geo predicates for 1) Latitude/Longitude Format
> >>>>   spatial:hasSpatialPredicatePairs (
> >>>>        [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
> >>>>        ) ;
> >>>>   # custom geo predicates for 2) Well Known Text (WKT) Literal
> >>>>   spatial:hasWKTPredicates (geosparql:asWKT) ;
> >>>>   # custom SpatialContextFactory for 2) Well Known Text (WKT) Literal
> >>>>   spatial:spatialContextFactory
> >>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
> >>>>
>  "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
> >>>>   .
> >>>>
> >>>> :tdb_dataset_readwrite
> >>>>       a              tdb2:DatasetTDB2 ;
> >>>>       tdb2:location
> >>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
> >>>>
> >>>> And I've changed the fuseki script to include the jts jar:
> >>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
> >>>>
> >>>> I see no errors or warnings in the server log, when starting with that
> >>>> configuration, the Lucene folder is created and populated with
> >> something:
> >>>> $ ll run/configuration/Lucene/
> >>>> total 4
> >>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
> >>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
> >>>>
> >>>> But any spatial query does not return any results.
> >>>> Any help on how to tackle this would be highly appreciated.
> >>>>
> >>>> Best
> >>>> Markus Neumann
> >>>>
> >>>>
> >>>
> >>> --
> >>>
> >>>
> >>> ---
> >>> Marco Neumann
> >>> KONA
> >>
> >>
> >
> > --
> >
> >
> > ---
> > Marco Neumann
> > KONA
>
>

-- 


---
Marco Neumann
KONA

Re: Building a spatial index with jena/fuseki

Posted by Markus Neumann <mn...@meteomatics.com>.
This is embarrassing but I don't get it.

I've configured $JENA_HOME and adjusted the PATH.

Now what classpath should I include when invoking the indexer?
What I've tried so far:

$ cd $JENA_HOME
$ java -cp jena-spatial-3.8.0.jar jena.spatialindexer --desc=../fuseki-server/run/configuration/mm.ttl
Error: Could not find or load main class jena.spatialindexer
$ java -cp lib/*.jar jena.spatialindexer --desc=../fuseki-server/run/configuration/mm.ttl
Error: Could not find or load main class lib.commons-cli-1.4.jar

Thanks for your patience

> Am 17.09.2018 um 11:38 schrieb Marco Neumann <ma...@gmail.com>:
> 
> yes correct, this looks good. now include the classpath during invocation
> of the spatialindexer
> 
> in addition it's always a good idea to properly configure jena along your
> java runtime environment settings to avoid jdk / lib conflicts during
> execution.
> 
> https://jena.apache.org/documentation/tools/index.html <https://jena.apache.org/documentation/tools/index.html>
> 
> 
> 
> On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <mneumann@meteomatics.com <ma...@meteomatics.com>>
> wrote:
> 
>> 1.: what do you mean by indexer?
>> Probably my biggest problem is, that I have no clue how to find out, where
>> the jena.spatialindexer could be located except for asking here.
>> 
>> Here is the content of the apache jena I downloaded:
>> $ ls -lh ../apache-jena-3.8.0/lib
>> total 17M
>> -rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
>> -rw-r--r-- 1 process process  53K Oct 26  2017 commons-cli-1.4.jar
>> -rw-r--r-- 1 process process 328K Mar  5  2018 commons-codec-1.11.jar
>> -rw-r--r-- 1 process process 576K Jun 25 09:59 commons-compress-1.17.jar
>> -rw-r--r-- 1 process process  41K Mar  5  2018 commons-csv-1.5.jar
>> -rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
>> -rw-r--r-- 1 process process 425K Oct 26  2017 commons-lang3-3.4.jar
>> -rw-r--r-- 1 process process 749K Jun 25 10:01 httpclient-4.5.5.jar
>> -rw-r--r-- 1 process process 158K Jun 25 10:01 httpclient-cache-4.5.5.jar
>> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
>> -rw-r--r-- 1 process process  65K Oct 26  2017
>> jackson-annotations-2.9.0.jar
>> -rw-r--r-- 1 process process 315K Jun 25 10:01 jackson-core-2.9.5.jar
>> -rw-r--r-- 1 process process 1.3M Jun 25 10:01 jackson-databind-2.9.5.jar
>> -rw-r--r-- 1 process process  17K Oct 26  2017 jcl-over-slf4j-1.7.25.jar
>> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
>> -rw-r--r-- 1 process process 211K Jun 25 11:01 jena-base-3.8.0.jar
>> -rw-r--r-- 1 process process 259K Jun 25 11:07 jena-cmds-3.8.0.jar
>> -rw-r--r-- 1 process process 1.7M Jun 25 11:02 jena-core-3.8.0.jar
>> -rw-r--r-- 1 process process 135K Jun 25 11:05 jena-dboe-base-3.8.0.jar
>> -rw-r--r-- 1 process process  21K Jun 25 11:05 jena-dboe-index-3.8.0.jar
>> -rw-r--r-- 1 process process  74K Jun 25 11:05
>> jena-dboe-transaction-3.8.0.jar
>> -rw-r--r-- 1 process process  95K Jun 25 11:06
>> jena-dboe-trans-data-3.8.0.jar
>> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
>> -rw-r--r-- 1 process process  49K Jun 25 11:04 jena-rdfconnection-3.8.0.jar
>> -rw-r--r-- 1 process process 2.8M Jun 25 11:01 jena-shaded-guava-3.8.0.jar
>> -rw-r--r-- 1 process process 264K Jun 25 11:06 jena-tdb2-3.8.0.jar
>> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
>> -rw-r--r-- 1 process process 1.6M Jun 25 10:01 jsonld-java-0.12.0.jar
>> -rw-r--r-- 1 process process 232K Mar  5  2018 libthrift-0.10.0.jar
>> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
>> -rw-r--r-- 1 process process  41K Oct 26  2017 slf4j-api-1.7.25.jar
>> -rw-r--r-- 1 process process  12K Oct 26  2017 slf4j-log4j12-1.7.25.jar
>> 
>> 2.: Turns out, I don't need the jts. after commenting out the affected
>> lines, the server still runs fine. (But still without spatial index)
>> 
>> Best Markus
>> 
>>> Am 17.09.2018 um 11:14 schrieb Marco Neumann <ma...@gmail.com>:
>>> 
>>> Ok let's take a look at this.
>>> 
>>> 1. please include in the indexer in the classpath. It's part of the
>> current
>>> jena distribution.
>>> 
>>> 2. do you need jts? it's a package that allows you to index multi point
>>> geometries. here a sample query would be helpful. If single point
>>> geometries are indexed and used in conjunction with MBR range queries.
>>> there is no need for jts.
>>> 
>>> 
>>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <mneumann@meteomatics.com
>> <mailto:mneumann@meteomatics.com <ma...@meteomatics.com>>>
>>> wrote:
>>> 
>>>> Hi,
>>>> (sorry for the long post)
>>>> 
>>>> I've been struggling with the spatial index for a while now.
>>>> I've read
>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> <
>>>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>>> and
>>>> skipped through about every spatial related thread here on the list.
>>>> I managed to get an in-memory version up and running at some point
>>>> following this
>>>> 
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>> 
>>>> <
>>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>> 
>>>>> 
>>>> and this
>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>>>> 
>>>> But that was on a small dataset that I uploaded via the web-interface of
>>>> Fuseki.
>>>> 
>>>> Now the story is a bit different. I'm building the database using
>>>> tdbloader2 and would like to create the spatial index upfront.
>>>> 
>>>> java -cp jena-spatial.jar jena.spatialindexer --desc=assembler_file
>>>> I could not figure out, how to get this line to work. I have the
>> following
>>>> possible scenarios:
>>>> 
>>>> 1. I download the jena-spatial-3.8.0.jar and specify that in the
>> classpath:
>>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>>> Error: Could not find or load main class jena.spatialindexer
>>>> 
>>>> 2. I use the fuseki-server jar:
>>>> $ java -cp fuseki-server.jar jena.spatialindexer
>>>> --desc=./run/configuration/mm.ttl
>>>> WARN  Custom SpatialContextFactory lib is not ready in
>>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>>> transaction
>>>> 
>>>> I managed to eliminate the warning about jts by including that in the
>>>> classpath, but the error remains the same (with full trace):
>>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
>>>> --desc=./run/configuration/mm.ttl
>>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>>> transaction
>>>>       at
>>>> 
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>>       at
>>>> 
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>>       at
>>>> 
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>>       at
>>>> 
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>>       at
>>>> 
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>>       at
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>>       at
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>>       at
>>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>>       at
>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>>       at
>>>> 
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>>       at
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>>       at
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>>       at
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>       at
>>>> 
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>>       at jena.spatialindexer.exec(spatialindexer.java:110)
>>>>       at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>>       at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>>       at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>>       at jena.spatialindexer.main(spatialindexer.java:53)
>>>> 
>>>> My configuration is the following:
>>>> @prefix :      <http://base/#> .
>>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>>> # Spatial
>>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>>> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>>>> 
>>>> :service_tdb_all  a                   fuseki:Service ;
>>>>       rdfs:label                    "TDB2 mm" ;
>>>>       fuseki:dataset                :spatial_dataset ;
>>>>       fuseki:name                   "mm" ;
>>>>       fuseki:serviceQuery           "query" , "sparql" ;
>>>>       fuseki:serviceReadGraphStore  "get" ;
>>>>       fuseki:serviceReadWriteGraphStore
>>>>               "data" ;
>>>>       fuseki:serviceUpdate          "update" ;
>>>>       fuseki:serviceUpload          "upload" .
>>>> 
>>>> :spatial_dataset a spatial:SpatialDataset ;
>>>>   spatial:dataset   :tdb_dataset_readwrite ;
>>>>   spatial:index     <#indexLucene> ;
>>>>   .
>>>> 
>>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>>>   spatial:directory <file:Lucene> ;
>>>>   #spatial:directory "mem" ;
>>>>   spatial:definition <#definition> ;
>>>>   .
>>>> 
>>>> <#definition> a spatial:EntityDefinition ;
>>>>   spatial:entityField      "uri" ;
>>>>   spatial:geoField     "geo" ;
>>>>   # custom geo predicates for 1) Latitude/Longitude Format
>>>>   spatial:hasSpatialPredicatePairs (
>>>>        [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>>>        ) ;
>>>>   # custom geo predicates for 2) Well Known Text (WKT) Literal
>>>>   spatial:hasWKTPredicates (geosparql:asWKT) ;
>>>>   # custom SpatialContextFactory for 2) Well Known Text (WKT) Literal
>>>>   spatial:spatialContextFactory
>>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>>>       "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>>>   .
>>>> 
>>>> :tdb_dataset_readwrite
>>>>       a              tdb2:DatasetTDB2 ;
>>>>       tdb2:location
>>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>>> 
>>>> And I've changed the fuseki script to include the jts jar:
>>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
>>>> 
>>>> I see no errors or warnings in the server log, when starting with that
>>>> configuration, the Lucene folder is created and populated with
>> something:
>>>> $ ll run/configuration/Lucene/
>>>> total 4
>>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
>>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
>>>> 
>>>> But any spatial query does not return any results.
>>>> Any help on how to tackle this would be highly appreciated.
>>>> 
>>>> Best
>>>> Markus Neumann
>>>> 
>>>> 
>>> 
>>> --
>>> 
>>> 
>>> ---
>>> Marco Neumann
>>> KONA
>> 
>> 
> 
> -- 
> 
> 
> ---
> Marco Neumann
> KONA

Re: Building a spatial index with jena/fuseki

Posted by Marco Neumann <ma...@gmail.com>.
yes correct, this looks good. now include the classpath during invocation
of the spatialindexer

in addition it's always a good idea to properly configure jena along your
java runtime environment settings to avoid jdk / lib conflicts during
execution.

https://jena.apache.org/documentation/tools/index.html



On Mon, Sep 17, 2018 at 10:28 AM Markus Neumann <mn...@meteomatics.com>
wrote:

> 1.: what do you mean by indexer?
> Probably my biggest problem is, that I have no clue how to find out, where
> the jena.spatialindexer could be located except for asking here.
>
> Here is the content of the apache jena I downloaded:
> $ ls -lh ../apache-jena-3.8.0/lib
> total 17M
> -rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
> -rw-r--r-- 1 process process  53K Oct 26  2017 commons-cli-1.4.jar
> -rw-r--r-- 1 process process 328K Mar  5  2018 commons-codec-1.11.jar
> -rw-r--r-- 1 process process 576K Jun 25 09:59 commons-compress-1.17.jar
> -rw-r--r-- 1 process process  41K Mar  5  2018 commons-csv-1.5.jar
> -rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
> -rw-r--r-- 1 process process 425K Oct 26  2017 commons-lang3-3.4.jar
> -rw-r--r-- 1 process process 749K Jun 25 10:01 httpclient-4.5.5.jar
> -rw-r--r-- 1 process process 158K Jun 25 10:01 httpclient-cache-4.5.5.jar
> -rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
> -rw-r--r-- 1 process process  65K Oct 26  2017
> jackson-annotations-2.9.0.jar
> -rw-r--r-- 1 process process 315K Jun 25 10:01 jackson-core-2.9.5.jar
> -rw-r--r-- 1 process process 1.3M Jun 25 10:01 jackson-databind-2.9.5.jar
> -rw-r--r-- 1 process process  17K Oct 26  2017 jcl-over-slf4j-1.7.25.jar
> -rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
> -rw-r--r-- 1 process process 211K Jun 25 11:01 jena-base-3.8.0.jar
> -rw-r--r-- 1 process process 259K Jun 25 11:07 jena-cmds-3.8.0.jar
> -rw-r--r-- 1 process process 1.7M Jun 25 11:02 jena-core-3.8.0.jar
> -rw-r--r-- 1 process process 135K Jun 25 11:05 jena-dboe-base-3.8.0.jar
> -rw-r--r-- 1 process process  21K Jun 25 11:05 jena-dboe-index-3.8.0.jar
> -rw-r--r-- 1 process process  74K Jun 25 11:05
> jena-dboe-transaction-3.8.0.jar
> -rw-r--r-- 1 process process  95K Jun 25 11:06
> jena-dboe-trans-data-3.8.0.jar
> -rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
> -rw-r--r-- 1 process process  49K Jun 25 11:04 jena-rdfconnection-3.8.0.jar
> -rw-r--r-- 1 process process 2.8M Jun 25 11:01 jena-shaded-guava-3.8.0.jar
> -rw-r--r-- 1 process process 264K Jun 25 11:06 jena-tdb2-3.8.0.jar
> -rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
> -rw-r--r-- 1 process process 1.6M Jun 25 10:01 jsonld-java-0.12.0.jar
> -rw-r--r-- 1 process process 232K Mar  5  2018 libthrift-0.10.0.jar
> -rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
> -rw-r--r-- 1 process process  41K Oct 26  2017 slf4j-api-1.7.25.jar
> -rw-r--r-- 1 process process  12K Oct 26  2017 slf4j-log4j12-1.7.25.jar
>
> 2.: Turns out, I don't need the jts. after commenting out the affected
> lines, the server still runs fine. (But still without spatial index)
>
> Best Markus
>
> > Am 17.09.2018 um 11:14 schrieb Marco Neumann <ma...@gmail.com>:
> >
> > Ok let's take a look at this.
> >
> > 1. please include in the indexer in the classpath. It's part of the
> current
> > jena distribution.
> >
> > 2. do you need jts? it's a package that allows you to index multi point
> > geometries. here a sample query would be helpful. If single point
> > geometries are indexed and used in conjunction with MBR range queries.
> > there is no need for jts.
> >
> >
> > On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <mneumann@meteomatics.com
> <ma...@meteomatics.com>>
> > wrote:
> >
> >> Hi,
> >> (sorry for the long post)
> >>
> >> I've been struggling with the spatial index for a while now.
> >> I've read
> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> <
> >> https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html>> and
> >> skipped through about every spatial related thread here on the list.
> >> I managed to get an in-memory version up and running at some point
> >> following this
> >>
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >
> >> <
> >>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >
> >>>
> >> and this
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
> >> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
> >>
> >> But that was on a small dataset that I uploaded via the web-interface of
> >> Fuseki.
> >>
> >> Now the story is a bit different. I'm building the database using
> >> tdbloader2 and would like to create the spatial index upfront.
> >>
> >> java -cp jena-spatial.jar jena.spatialindexer --desc=assembler_file
> >> I could not figure out, how to get this line to work. I have the
> following
> >> possible scenarios:
> >>
> >> 1. I download the jena-spatial-3.8.0.jar and specify that in the
> classpath:
> >> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> >> --desc=../fuseki-server/run/configuration/mm.ttl
> >> Error: Could not find or load main class jena.spatialindexer
> >>
> >> 2. I use the fuseki-server jar:
> >> $ java -cp fuseki-server.jar jena.spatialindexer
> >> --desc=./run/configuration/mm.ttl
> >> WARN  Custom SpatialContextFactory lib is not ready in
> >> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
> >> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> >> transaction
> >>
> >> I managed to eliminate the warning about jts by including that in the
> >> classpath, but the error remains the same (with full trace):
> >> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
> >> --desc=./run/configuration/mm.ttl
> >> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> >> transaction
> >>        at
> >>
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >>        at
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >>        at
> >>
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >>        at
> >>
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >>        at
> >>
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >>        at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >>        at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >>        at
> >>
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >>        at
> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >>        at
> >>
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >>        at
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >>        at
> >>
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >>        at
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>        at
> >>
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >>        at jena.spatialindexer.exec(spatialindexer.java:110)
> >>        at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >>        at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >>        at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >>        at jena.spatialindexer.main(spatialindexer.java:53)
> >>
> >> My configuration is the following:
> >> @prefix :      <http://base/#> .
> >> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> >> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> >> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> >> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> >> @prefix fuseki: <http://jena.apache.org/fuseki#> .
> >> @prefix spatial: <http://jena.apache.org/spatial#> .
> >> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> >> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> >> # Spatial
> >> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
> >> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> >> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
> >>
> >> :service_tdb_all  a                   fuseki:Service ;
> >>        rdfs:label                    "TDB2 mm" ;
> >>        fuseki:dataset                :spatial_dataset ;
> >>        fuseki:name                   "mm" ;
> >>        fuseki:serviceQuery           "query" , "sparql" ;
> >>        fuseki:serviceReadGraphStore  "get" ;
> >>        fuseki:serviceReadWriteGraphStore
> >>                "data" ;
> >>        fuseki:serviceUpdate          "update" ;
> >>        fuseki:serviceUpload          "upload" .
> >>
> >> :spatial_dataset a spatial:SpatialDataset ;
> >>    spatial:dataset   :tdb_dataset_readwrite ;
> >>    spatial:index     <#indexLucene> ;
> >>    .
> >>
> >> <#indexLucene> a spatial:SpatialIndexLucene ;
> >>    spatial:directory <file:Lucene> ;
> >>    #spatial:directory "mem" ;
> >>    spatial:definition <#definition> ;
> >>    .
> >>
> >> <#definition> a spatial:EntityDefinition ;
> >>    spatial:entityField      "uri" ;
> >>    spatial:geoField     "geo" ;
> >>    # custom geo predicates for 1) Latitude/Longitude Format
> >>    spatial:hasSpatialPredicatePairs (
> >>         [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
> >>         ) ;
> >>    # custom geo predicates for 2) Well Known Text (WKT) Literal
> >>    spatial:hasWKTPredicates (geosparql:asWKT) ;
> >>    # custom SpatialContextFactory for 2) Well Known Text (WKT) Literal
> >>    spatial:spatialContextFactory
> >> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
> >>        "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
> >>    .
> >>
> >> :tdb_dataset_readwrite
> >>        a              tdb2:DatasetTDB2 ;
> >>        tdb2:location
> >> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
> >>
> >> And I've changed the fuseki script to include the jts jar:
> >> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
> >>
> >> I see no errors or warnings in the server log, when starting with that
> >> configuration, the Lucene folder is created and populated with
> something:
> >> $ ll run/configuration/Lucene/
> >> total 4
> >> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
> >> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
> >>
> >> But any spatial query does not return any results.
> >> Any help on how to tackle this would be highly appreciated.
> >>
> >> Best
> >> Markus Neumann
> >>
> >>
> >
> > --
> >
> >
> > ---
> > Marco Neumann
> > KONA
>
>

-- 


---
Marco Neumann
KONA

Re: Building a spatial index with jena/fuseki

Posted by Markus Neumann <mn...@meteomatics.com>.
1.: what do you mean by indexer?
Probably my biggest problem is, that I have no clue how to find out, where the jena.spatialindexer could be located except for asking here.

Here is the content of the apache jena I downloaded:
$ ls -lh ../apache-jena-3.8.0/lib
total 17M
-rw-r--r-- 1 process process 162K Oct 26  2017 collection-0.7.jar
-rw-r--r-- 1 process process  53K Oct 26  2017 commons-cli-1.4.jar
-rw-r--r-- 1 process process 328K Mar  5  2018 commons-codec-1.11.jar
-rw-r--r-- 1 process process 576K Jun 25 09:59 commons-compress-1.17.jar
-rw-r--r-- 1 process process  41K Mar  5  2018 commons-csv-1.5.jar
-rw-r--r-- 1 process process 210K Mar  5  2018 commons-io-2.6.jar
-rw-r--r-- 1 process process 425K Oct 26  2017 commons-lang3-3.4.jar
-rw-r--r-- 1 process process 749K Jun 25 10:01 httpclient-4.5.5.jar
-rw-r--r-- 1 process process 158K Jun 25 10:01 httpclient-cache-4.5.5.jar
-rw-r--r-- 1 process process 318K Jun 25 10:01 httpcore-4.4.9.jar
-rw-r--r-- 1 process process  65K Oct 26  2017 jackson-annotations-2.9.0.jar
-rw-r--r-- 1 process process 315K Jun 25 10:01 jackson-core-2.9.5.jar
-rw-r--r-- 1 process process 1.3M Jun 25 10:01 jackson-databind-2.9.5.jar
-rw-r--r-- 1 process process  17K Oct 26  2017 jcl-over-slf4j-1.7.25.jar
-rw-r--r-- 1 process process 2.9M Jun 25 11:03 jena-arq-3.8.0.jar
-rw-r--r-- 1 process process 211K Jun 25 11:01 jena-base-3.8.0.jar
-rw-r--r-- 1 process process 259K Jun 25 11:07 jena-cmds-3.8.0.jar
-rw-r--r-- 1 process process 1.7M Jun 25 11:02 jena-core-3.8.0.jar
-rw-r--r-- 1 process process 135K Jun 25 11:05 jena-dboe-base-3.8.0.jar
-rw-r--r-- 1 process process  21K Jun 25 11:05 jena-dboe-index-3.8.0.jar
-rw-r--r-- 1 process process  74K Jun 25 11:05 jena-dboe-transaction-3.8.0.jar
-rw-r--r-- 1 process process  95K Jun 25 11:06 jena-dboe-trans-data-3.8.0.jar
-rw-r--r-- 1 process process 135K Jun 25 11:01 jena-iri-3.8.0.jar
-rw-r--r-- 1 process process  49K Jun 25 11:04 jena-rdfconnection-3.8.0.jar
-rw-r--r-- 1 process process 2.8M Jun 25 11:01 jena-shaded-guava-3.8.0.jar
-rw-r--r-- 1 process process 264K Jun 25 11:06 jena-tdb2-3.8.0.jar
-rw-r--r-- 1 process process 512K Jun 25 11:04 jena-tdb-3.8.0.jar
-rw-r--r-- 1 process process 1.6M Jun 25 10:01 jsonld-java-0.12.0.jar
-rw-r--r-- 1 process process 232K Mar  5  2018 libthrift-0.10.0.jar
-rw-r--r-- 1 process process 479K Oct 26  2017 log4j-1.2.17.jar
-rw-r--r-- 1 process process  41K Oct 26  2017 slf4j-api-1.7.25.jar
-rw-r--r-- 1 process process  12K Oct 26  2017 slf4j-log4j12-1.7.25.jar

2.: Turns out, I don't need the jts. after commenting out the affected lines, the server still runs fine. (But still without spatial index)

Best Markus

> Am 17.09.2018 um 11:14 schrieb Marco Neumann <ma...@gmail.com>:
> 
> Ok let's take a look at this.
> 
> 1. please include in the indexer in the classpath. It's part of the current
> jena distribution.
> 
> 2. do you need jts? it's a package that allows you to index multi point
> geometries. here a sample query would be helpful. If single point
> geometries are indexed and used in conjunction with MBR range queries.
> there is no need for jts.
> 
> 
> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <mneumann@meteomatics.com <ma...@meteomatics.com>>
> wrote:
> 
>> Hi,
>> (sorry for the long post)
>> 
>> I've been struggling with the spatial index for a while now.
>> I've read https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html> <
>> https://jena.apache.org/documentation/query/spatial-query.html <https://jena.apache.org/documentation/query/spatial-query.html>> and
>> skipped through about every spatial related thread here on the list.
>> I managed to get an in-memory version up and running at some point
>> following this
>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>> <
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066 <https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066>
>>> 
>> and this
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/> <
>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>> 
>> But that was on a small dataset that I uploaded via the web-interface of
>> Fuseki.
>> 
>> Now the story is a bit different. I'm building the database using
>> tdbloader2 and would like to create the spatial index upfront.
>> 
>> java -cp jena-spatial.jar jena.spatialindexer --desc=assembler_file
>> I could not figure out, how to get this line to work. I have the following
>> possible scenarios:
>> 
>> 1. I download the jena-spatial-3.8.0.jar and specify that in the classpath:
>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>> --desc=../fuseki-server/run/configuration/mm.ttl
>> Error: Could not find or load main class jena.spatialindexer
>> 
>> 2. I use the fuseki-server jar:
>> $ java -cp fuseki-server.jar jena.spatialindexer
>> --desc=./run/configuration/mm.ttl
>> WARN  Custom SpatialContextFactory lib is not ready in
>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>> transaction
>> 
>> I managed to eliminate the warning about jts by including that in the
>> classpath, but the error remains the same (with full trace):
>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
>> --desc=./run/configuration/mm.ttl
>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>> transaction
>>        at
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>        at
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>        at
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>        at
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>        at
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>        at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>        at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>        at
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>        at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>        at
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>        at
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>        at
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>        at
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>        at
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>        at jena.spatialindexer.exec(spatialindexer.java:110)
>>        at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>        at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>        at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>        at jena.spatialindexer.main(spatialindexer.java:53)
>> 
>> My configuration is the following:
>> @prefix :      <http://base/#> .
>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>> @prefix spatial: <http://jena.apache.org/spatial#> .
>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>> # Spatial
>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>> 
>> :service_tdb_all  a                   fuseki:Service ;
>>        rdfs:label                    "TDB2 mm" ;
>>        fuseki:dataset                :spatial_dataset ;
>>        fuseki:name                   "mm" ;
>>        fuseki:serviceQuery           "query" , "sparql" ;
>>        fuseki:serviceReadGraphStore  "get" ;
>>        fuseki:serviceReadWriteGraphStore
>>                "data" ;
>>        fuseki:serviceUpdate          "update" ;
>>        fuseki:serviceUpload          "upload" .
>> 
>> :spatial_dataset a spatial:SpatialDataset ;
>>    spatial:dataset   :tdb_dataset_readwrite ;
>>    spatial:index     <#indexLucene> ;
>>    .
>> 
>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>    spatial:directory <file:Lucene> ;
>>    #spatial:directory "mem" ;
>>    spatial:definition <#definition> ;
>>    .
>> 
>> <#definition> a spatial:EntityDefinition ;
>>    spatial:entityField      "uri" ;
>>    spatial:geoField     "geo" ;
>>    # custom geo predicates for 1) Latitude/Longitude Format
>>    spatial:hasSpatialPredicatePairs (
>>         [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>         ) ;
>>    # custom geo predicates for 2) Well Known Text (WKT) Literal
>>    spatial:hasWKTPredicates (geosparql:asWKT) ;
>>    # custom SpatialContextFactory for 2) Well Known Text (WKT) Literal
>>    spatial:spatialContextFactory
>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>        "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>    .
>> 
>> :tdb_dataset_readwrite
>>        a              tdb2:DatasetTDB2 ;
>>        tdb2:location
>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>> 
>> And I've changed the fuseki script to include the jts jar:
>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
>> 
>> I see no errors or warnings in the server log, when starting with that
>> configuration, the Lucene folder is created and populated with something:
>> $ ll run/configuration/Lucene/
>> total 4
>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
>> 
>> But any spatial query does not return any results.
>> Any help on how to tackle this would be highly appreciated.
>> 
>> Best
>> Markus Neumann
>> 
>> 
> 
> -- 
> 
> 
> ---
> Marco Neumann
> KONA

Re: Building a spatial index with jena/fuseki

Posted by Markus Neumann <mn...@meteomatics.com>.
Hi,

I tried that and it does not change anything in the behaviour.
Server starts fine but spatial queries don't work.

Best
Markus

> Am 17.09.2018 um 11:26 schrieb Øyvind Gjesdal <oy...@gmail.com>:
> 
> Looking at our very similar config (based on the fuseki examples) only
> difference I see (except from the additional library) is that our config
> uses TDB, and your config uses TDB2. I believe tdbloader2 generates tdb1
> data ( I could be wrong), since I remember using it pre tdb2 release, so
> there might be a mismatch in your config and built database.
> 
> :tdb_dataset_readwrite
>        a              tdb2:DatasetTDB2 ;
>        tdb2:location
> "/srv/linked_data_store/fuseki-server/run/databases/mm"
> 
> Does using
> :tdb_dataset_readwrite
>        a              tdb:DatasetTDB ;
>        tdb:location
> "/srv/linked_data_store/fuseki-server/run/databases/mm"
> 
> in your config help?
> 
> Best regards,
> Øyvind
> 
> 
> Den man. 17. sep. 2018 kl. 11:14 skrev Marco Neumann <
> marco.neumann@gmail.com>:
> 
>> Ok let's take a look at this.
>> 
>> 1. please include in the indexer in the classpath. It's part of the current
>> jena distribution.
>> 
>> 2. do you need jts? it's a package that allows you to index multi point
>> geometries. here a sample query would be helpful. If single point
>> geometries are indexed and used in conjunction with MBR range queries.
>> there is no need for jts.
>> 
>> 
>> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <mn...@meteomatics.com>
>> wrote:
>> 
>>> Hi,
>>> (sorry for the long post)
>>> 
>>> I've been struggling with the spatial index for a while now.
>>> I've read https://jena.apache.org/documentation/query/spatial-query.html
>> <
>>> https://jena.apache.org/documentation/query/spatial-query.html> and
>>> skipped through about every spatial related thread here on the list.
>>> I managed to get an in-memory version up and running at some point
>>> following this
>>> 
>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>> <
>>> 
>> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
>>>> 
>>> and this
>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
>>> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>>> 
>>> But that was on a small dataset that I uploaded via the web-interface of
>>> Fuseki.
>>> 
>>> Now the story is a bit different. I'm building the database using
>>> tdbloader2 and would like to create the spatial index upfront.
>>> 
>>> java -cp jena-spatial.jar jena.spatialindexer --desc=assembler_file
>>> I could not figure out, how to get this line to work. I have the
>> following
>>> possible scenarios:
>>> 
>>> 1. I download the jena-spatial-3.8.0.jar and specify that in the
>> classpath:
>>> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
>>> --desc=../fuseki-server/run/configuration/mm.ttl
>>> Error: Could not find or load main class jena.spatialindexer
>>> 
>>> 2. I use the fuseki-server jar:
>>> $ java -cp fuseki-server.jar jena.spatialindexer
>>> --desc=./run/configuration/mm.ttl
>>> WARN  Custom SpatialContextFactory lib is not ready in
>>> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>> transaction
>>> 
>>> I managed to eliminate the warning about jts by including that in the
>>> classpath, but the error remains the same (with full trace):
>>> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
>>> --desc=./run/configuration/mm.ttl
>>> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
>>> transaction
>>>        at
>>> 
>> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>>>        at
>>> 
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>>>        at
>>> 
>> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>>>        at
>>> 
>> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>>>        at
>>> 
>> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>>>        at
>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>>>        at
>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>>>        at
>>> 
>> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>>>        at
>> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>>>        at
>>> 
>> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>>>        at
>>> 
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>>>        at
>>> 
>> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>>>        at
>>> 
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>        at
>>> 
>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>>>        at jena.spatialindexer.exec(spatialindexer.java:110)
>>>        at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>>>        at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>>>        at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>>>        at jena.spatialindexer.main(spatialindexer.java:53)
>>> 
>>> My configuration is the following:
>>> @prefix :      <http://base/#> .
>>> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>>> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
>>> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
>>> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
>>> @prefix fuseki: <http://jena.apache.org/fuseki#> .
>>> @prefix spatial: <http://jena.apache.org/spatial#> .
>>> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
>>> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
>>> # Spatial
>>> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
>>> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
>>> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>>> 
>>> :service_tdb_all  a                   fuseki:Service ;
>>>        rdfs:label                    "TDB2 mm" ;
>>>        fuseki:dataset                :spatial_dataset ;
>>>        fuseki:name                   "mm" ;
>>>        fuseki:serviceQuery           "query" , "sparql" ;
>>>        fuseki:serviceReadGraphStore  "get" ;
>>>        fuseki:serviceReadWriteGraphStore
>>>                "data" ;
>>>        fuseki:serviceUpdate          "update" ;
>>>        fuseki:serviceUpload          "upload" .
>>> 
>>> :spatial_dataset a spatial:SpatialDataset ;
>>>    spatial:dataset   :tdb_dataset_readwrite ;
>>>    spatial:index     <#indexLucene> ;
>>>    .
>>> 
>>> <#indexLucene> a spatial:SpatialIndexLucene ;
>>>    spatial:directory <file:Lucene> ;
>>>    #spatial:directory "mem" ;
>>>    spatial:definition <#definition> ;
>>>    .
>>> 
>>> <#definition> a spatial:EntityDefinition ;
>>>    spatial:entityField      "uri" ;
>>>    spatial:geoField     "geo" ;
>>>    # custom geo predicates for 1) Latitude/Longitude Format
>>>    spatial:hasSpatialPredicatePairs (
>>>         [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>>>         ) ;
>>>    # custom geo predicates for 2) Well Known Text (WKT) Literal
>>>    spatial:hasWKTPredicates (geosparql:asWKT) ;
>>>    # custom SpatialContextFactory for 2) Well Known Text (WKT) Literal
>>>    spatial:spatialContextFactory
>>> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>>>        "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>>>    .
>>> 
>>> :tdb_dataset_readwrite
>>>        a              tdb2:DatasetTDB2 ;
>>>        tdb2:location
>>> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>>> 
>>> And I've changed the fuseki script to include the jts jar:
>>> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
>>> 
>>> I see no errors or warnings in the server log, when starting with that
>>> configuration, the Lucene folder is created and populated with something:
>>> $ ll run/configuration/Lucene/
>>> total 4
>>> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
>>> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
>>> 
>>> But any spatial query does not return any results.
>>> Any help on how to tackle this would be highly appreciated.
>>> 
>>> Best
>>> Markus Neumann
>>> 
>>> 
>> 
>> --
>> 
>> 
>> ---
>> Marco Neumann
>> KONA
>>

Re: Building a spatial index with jena/fuseki

Posted by Øyvind Gjesdal <oy...@gmail.com>.
Looking at our very similar config (based on the fuseki examples) only
difference I see (except from the additional library) is that our config
uses TDB, and your config uses TDB2. I believe tdbloader2 generates tdb1
data ( I could be wrong), since I remember using it pre tdb2 release, so
there might be a mismatch in your config and built database.

:tdb_dataset_readwrite
        a              tdb2:DatasetTDB2 ;
        tdb2:location
"/srv/linked_data_store/fuseki-server/run/databases/mm"

Does using
:tdb_dataset_readwrite
        a              tdb:DatasetTDB ;
        tdb:location
"/srv/linked_data_store/fuseki-server/run/databases/mm"

in your config help?

Best regards,
Øyvind


Den man. 17. sep. 2018 kl. 11:14 skrev Marco Neumann <
marco.neumann@gmail.com>:

> Ok let's take a look at this.
>
> 1. please include in the indexer in the classpath. It's part of the current
> jena distribution.
>
> 2. do you need jts? it's a package that allows you to index multi point
> geometries. here a sample query would be helpful. If single point
> geometries are indexed and used in conjunction with MBR range queries.
> there is no need for jts.
>
>
> On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <mn...@meteomatics.com>
> wrote:
>
> > Hi,
> > (sorry for the long post)
> >
> > I've been struggling with the spatial index for a while now.
> > I've read https://jena.apache.org/documentation/query/spatial-query.html
> <
> > https://jena.apache.org/documentation/query/spatial-query.html> and
> > skipped through about every spatial related thread here on the list.
> > I managed to get an in-memory version up and running at some point
> > following this
> >
> >
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> > <
> >
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> > >
> > and this
> > https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
> > https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
> >
> > But that was on a small dataset that I uploaded via the web-interface of
> > Fuseki.
> >
> > Now the story is a bit different. I'm building the database using
> > tdbloader2 and would like to create the spatial index upfront.
> >
> > java -cp jena-spatial.jar jena.spatialindexer --desc=assembler_file
> > I could not figure out, how to get this line to work. I have the
> following
> > possible scenarios:
> >
> > 1. I download the jena-spatial-3.8.0.jar and specify that in the
> classpath:
> > $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> > --desc=../fuseki-server/run/configuration/mm.ttl
> > Error: Could not find or load main class jena.spatialindexer
> >
> > 2. I use the fuseki-server jar:
> > $ java -cp fuseki-server.jar jena.spatialindexer
> > --desc=./run/configuration/mm.ttl
> > WARN  Custom SpatialContextFactory lib is not ready in
> > classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
> > org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> > transaction
> >
> > I managed to eliminate the warning about jts by including that in the
> > classpath, but the error remains the same (with full trace):
> > java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
> > --desc=./run/configuration/mm.ttl
> > org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> > transaction
> >         at
> >
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
> >         at
> >
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
> >         at
> >
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
> >         at
> >
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
> >         at
> >
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
> >         at
> >
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
> >         at
> >
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
> >         at
> >
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
> >         at
> org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
> >         at
> >
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
> >         at
> >
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
> >         at
> >
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
> >         at
> >
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >         at
> >
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
> >         at jena.spatialindexer.exec(spatialindexer.java:110)
> >         at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
> >         at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
> >         at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
> >         at jena.spatialindexer.main(spatialindexer.java:53)
> >
> > My configuration is the following:
> > @prefix :      <http://base/#> .
> > @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> > @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> > @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> > @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> > @prefix fuseki: <http://jena.apache.org/fuseki#> .
> > @prefix spatial: <http://jena.apache.org/spatial#> .
> > @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> > @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> > # Spatial
> > [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
> > spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> > spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
> >
> > :service_tdb_all  a                   fuseki:Service ;
> >         rdfs:label                    "TDB2 mm" ;
> >         fuseki:dataset                :spatial_dataset ;
> >         fuseki:name                   "mm" ;
> >         fuseki:serviceQuery           "query" , "sparql" ;
> >         fuseki:serviceReadGraphStore  "get" ;
> >         fuseki:serviceReadWriteGraphStore
> >                 "data" ;
> >         fuseki:serviceUpdate          "update" ;
> >         fuseki:serviceUpload          "upload" .
> >
> > :spatial_dataset a spatial:SpatialDataset ;
> >     spatial:dataset   :tdb_dataset_readwrite ;
> >     spatial:index     <#indexLucene> ;
> >     .
> >
> > <#indexLucene> a spatial:SpatialIndexLucene ;
> >     spatial:directory <file:Lucene> ;
> >     #spatial:directory "mem" ;
> >     spatial:definition <#definition> ;
> >     .
> >
> > <#definition> a spatial:EntityDefinition ;
> >     spatial:entityField      "uri" ;
> >     spatial:geoField     "geo" ;
> >     # custom geo predicates for 1) Latitude/Longitude Format
> >     spatial:hasSpatialPredicatePairs (
> >          [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
> >          ) ;
> >     # custom geo predicates for 2) Well Known Text (WKT) Literal
> >     spatial:hasWKTPredicates (geosparql:asWKT) ;
> >     # custom SpatialContextFactory for 2) Well Known Text (WKT) Literal
> >     spatial:spatialContextFactory
> > #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
> >         "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
> >     .
> >
> > :tdb_dataset_readwrite
> >         a              tdb2:DatasetTDB2 ;
> >         tdb2:location
> > "/srv/linked_data_store/fuseki-server/run/databases/mm" .
> >
> > And I've changed the fuseki script to include the jts jar:
> > FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
> >
> > I see no errors or warnings in the server log, when starting with that
> > configuration, the Lucene folder is created and populated with something:
> > $ ll run/configuration/Lucene/
> > total 4
> > -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
> > -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
> >
> > But any spatial query does not return any results.
> > Any help on how to tackle this would be highly appreciated.
> >
> > Best
> > Markus Neumann
> >
> >
>
> --
>
>
> ---
> Marco Neumann
> KONA
>

Re: Building a spatial index with jena/fuseki

Posted by Marco Neumann <ma...@gmail.com>.
Ok let's take a look at this.

1. please include in the indexer in the classpath. It's part of the current
jena distribution.

2. do you need jts? it's a package that allows you to index multi point
geometries. here a sample query would be helpful. If single point
geometries are indexed and used in conjunction with MBR range queries.
there is no need for jts.


On Mon, Sep 17, 2018 at 9:14 AM Markus Neumann <mn...@meteomatics.com>
wrote:

> Hi,
> (sorry for the long post)
>
> I've been struggling with the spatial index for a while now.
> I've read https://jena.apache.org/documentation/query/spatial-query.html <
> https://jena.apache.org/documentation/query/spatial-query.html> and
> skipped through about every spatial related thread here on the list.
> I managed to get an in-memory version up and running at some point
> following this
>
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> <
> https://stackoverflow.com/questions/45814956/building-geospatial-index-when-working-with-jena-fuseki/52099066#52099066
> >
> and this
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/ <
> https://ceyxstudios.com/2017/11/25/rdf-datenbank-mit-geo-funktionen/>
>
> But that was on a small dataset that I uploaded via the web-interface of
> Fuseki.
>
> Now the story is a bit different. I'm building the database using
> tdbloader2 and would like to create the spatial index upfront.
>
> java -cp jena-spatial.jar jena.spatialindexer --desc=assembler_file
> I could not figure out, how to get this line to work. I have the following
> possible scenarios:
>
> 1. I download the jena-spatial-3.8.0.jar and specify that in the classpath:
> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer
> --desc=../fuseki-server/run/configuration/mm.ttl
> Error: Could not find or load main class jena.spatialindexer
>
> 2. I use the fuseki-server jar:
> $ java -cp fuseki-server.jar jena.spatialindexer
> --desc=./run/configuration/mm.ttl
> WARN  Custom SpatialContextFactory lib is not ready in
> classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> transaction
>
> I managed to eliminate the warning about jts by including that in the
> classpath, but the error remains the same (with full trace):
> java -cp fuseki-server.jar:jts-1.13.jar jena.spatialindexer
> --desc=./run/configuration/mm.ttl
> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a
> transaction
>         at
> org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
>         at
> org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
>         at
> org.apache.jena.dboe.trans.bplustree.BPlusTree.iterator(BPlusTree.java:348)
>         at
> org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.all(TupleIndexRecord.java:251)
>         at
> org.apache.jena.tdb2.store.tupletable.TupleTable.find(TupleTable.java:148)
>         at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:161)
>         at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:150)
>         at
> org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:141)
>         at org.apache.jena.tdb2.store.TripleTable.find(TripleTable.java:64)
>         at
> org.apache.jena.tdb2.store.DatasetGraphTDB.findInDftGraph(DatasetGraphTDB.java:104)
>         at
> org.apache.jena.sparql.core.DatasetGraphBaseFind.findAny(DatasetGraphBaseFind.java:72)
>         at
> org.apache.jena.sparql.core.DatasetGraphBaseFind.find(DatasetGraphBaseFind.java:50)
>         at
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>         at
> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:152)
>         at jena.spatialindexer.exec(spatialindexer.java:110)
>         at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
>         at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
>         at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
>         at jena.spatialindexer.main(spatialindexer.java:53)
>
> My configuration is the following:
> @prefix :      <http://base/#> .
> @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> @prefix tdb2:  <http://jena.apache.org/2016/tdb#> .
> @prefix ja:    <http://jena.hpl.hp.com/2005/11/Assembler#> .
> @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
> @prefix fuseki: <http://jena.apache.org/fuseki#> .
> @prefix spatial: <http://jena.apache.org/spatial#> .
> @prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
> @prefix geosparql: <http://www.opengis.net/ont/geosparql#> .
> # Spatial
> [] ja:loadClass "org.apache.jena.query.spatial.SpatialQuery" .
> spatial:SpatialtDataset rdfs:subClassOf ja:RDFDataset .
> spatial:SpatialIndexLucene rdfs:subClassOf spatial:SpatialIndex .
>
> :service_tdb_all  a                   fuseki:Service ;
>         rdfs:label                    "TDB2 mm" ;
>         fuseki:dataset                :spatial_dataset ;
>         fuseki:name                   "mm" ;
>         fuseki:serviceQuery           "query" , "sparql" ;
>         fuseki:serviceReadGraphStore  "get" ;
>         fuseki:serviceReadWriteGraphStore
>                 "data" ;
>         fuseki:serviceUpdate          "update" ;
>         fuseki:serviceUpload          "upload" .
>
> :spatial_dataset a spatial:SpatialDataset ;
>     spatial:dataset   :tdb_dataset_readwrite ;
>     spatial:index     <#indexLucene> ;
>     .
>
> <#indexLucene> a spatial:SpatialIndexLucene ;
>     spatial:directory <file:Lucene> ;
>     #spatial:directory "mem" ;
>     spatial:definition <#definition> ;
>     .
>
> <#definition> a spatial:EntityDefinition ;
>     spatial:entityField      "uri" ;
>     spatial:geoField     "geo" ;
>     # custom geo predicates for 1) Latitude/Longitude Format
>     spatial:hasSpatialPredicatePairs (
>          [ spatial:latitude geo:lat ; spatial:longitude geo:long ]
>          ) ;
>     # custom geo predicates for 2) Well Known Text (WKT) Literal
>     spatial:hasWKTPredicates (geosparql:asWKT) ;
>     # custom SpatialContextFactory for 2) Well Known Text (WKT) Literal
>     spatial:spatialContextFactory
> #         "com.spatial4j.core.context.jts.JtsSpatialContextFactory"
>         "org.locationtech.spatial4j.context.jts.JtsSpatialContextFactory"
>     .
>
> :tdb_dataset_readwrite
>         a              tdb2:DatasetTDB2 ;
>         tdb2:location
> "/srv/linked_data_store/fuseki-server/run/databases/mm" .
>
> And I've changed the fuseki script to include the jts jar:
> FUSEKI_CLASSES=$FUSEKI_HOME/jts-1.13.jar
>
> I see no errors or warnings in the server log, when starting with that
> configuration, the Lucene folder is created and populated with something:
> $ ll run/configuration/Lucene/
> total 4
> -rw-rw-r-- 1 process process 71 Sep 14 09:28 segments_1
> -rw-rw-r-- 1 process process  0 Sep 14 09:28 write.lock
>
> But any spatial query does not return any results.
> Any help on how to tackle this would be highly appreciated.
>
> Best
> Markus Neumann
>
>

-- 


---
Marco Neumann
KONA

Re: Building a spatial index with jena/fuseki

Posted by "Lorenz B." <bu...@informatik.uni-leipzig.de>.
> 1. I download the jena-spatial-3.8.0.jar and specify that in the classpath:
> $ java -cp jena-spatial-3.8.0.jar jena.spatialindexer --desc=../fuseki-server/run/configuration/mm.ttl 
> Error: Could not find or load main class jena.spatialindexer
The documentation is a bit misleading I'd say. Just having
jena-spatial-3.8.0.jar in the classpath isn't enough and it fails -
indeed with a not helpful message - because other libs like jena-core,
jena-arq, etc are missing. Either you you add the Jena distribution libs
to the default classpath, or you just use the Fuseki server jar as you
already did

>
> 2. I use the fuseki-server jar:
> $ java -cp fuseki-server.jar jena.spatialindexer --desc=./run/configuration/mm.ttl
> WARN  Custom SpatialContextFactory lib is not ready in classpath:com/vividsolutions/jts/geom/CoordinateSequenceFactory
> org.apache.jena.dboe.transaction.txn.TransactionException: Not in a transaction
Well, Andy knows better. Maybe, the docs are a bit outdated or something
is different when using it in combination with TDB2. Lets wait for a
correct answer.

-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center