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Posted to users@jena.apache.org by Diptendu Dutta <du...@gmail.com> on 2020/03/03 14:01:42 UTC
Exception in writing RDF from model
I am getting java.lang.StringIndexOutOfBoundsException while writing
RDF from a model (model.write()). I have tried with other mechanisms
such as RDFWriter, RDFDataMgr but I get exactly the same error.
Here is the code:
static public String getRDF(String corpus_file_id) {
String rdfString = null;
Model model = null;
dataset.begin(ReadWrite.READ) ;
try {
model = dataset.getNamedModel(corpus_file_id);
model.write(System.out, "RDF/XML");
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}finally {
model.close();
dataset.end();
}
return rdfString;
}
java.lang.StringIndexOutOfBoundsException: String index out of range: 46
at java.lang.String.charAt(String.java:658)
at org.apache.jena.atlas.lib.StrUtils.decodeHex(StrUtils.java:212)
at org.apache.jena.tdb.store.nodetable.NodecSSE.decode(NodecSSE.java:121)
at org.apache.jena.tdb.lib.NodeLib.decode(NodeLib.java:120)
at org.apache.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:97)
at
org.apache.jena.tdb.store.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:182)
at
org.apache.jena.tdb.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:108)
at
org.apache.jena.tdb.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:67)
at
org.apache.jena.tdb.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:128)
at
org.apache.jena.tdb.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:82)
at
org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:50)
at
org.apache.jena.tdb.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67)
at org.apache.jena.tdb.lib.TupleLib.quad(TupleLib.java:126)
at org.apache.jena.tdb.lib.TupleLib.quad(TupleLib.java:120)
at
org.apache.jena.tdb.lib.TupleLib.lambda$convertToQuads$3(TupleLib.java:59)
at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352)
at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352)
at org.apache.jena.atlas.iterator.Iter.next(Iter.java:1072)
at
org.apache.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94)
at org.apache.jena.util.iterator.Map1Iterator.next(Map1Iterator.java:46)
at org.apache.jena.util.iterator.NiceIterator.asSet(NiceIterator.java:208)
at org.apache.jena.util.iterator.NiceIterator.toSet(NiceIterator.java:199)
at org.apache.jena.graph.GraphUtil.listPredicates(GraphUtil.java:66)
at org.apache.jena.rdf.model.impl.ModelCom.listPredicates(ModelCom.java:999)
at
org.apache.jena.rdf.model.impl.ModelCom.listNameSpaces(ModelCom.java:1012)
at
org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.addNameSpaces(BaseXMLWriter.java:219)
at
org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.setupNamespaces(BaseXMLWriter.java:488)
at
org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.write(BaseXMLWriter.java:470)
at
org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.write(BaseXMLWriter.java:460)
at
org.apache.jena.riot.adapters.AdapterRDFWriter.write(AdapterRDFWriter.java:64)
at org.apache.jena.riot.RDFWriter.write$(RDFWriter.java:202)
at org.apache.jena.riot.RDFWriter.output(RDFWriter.java:161)
at org.apache.jena.riot.RDFWriter.output(RDFWriter.java:112)
at org.apache.jena.riot.RDFWriterBuilder.output(RDFWriterBuilder.java:205)
at org.apache.jena.riot.adapters.RDFWriterRIOT.write(RDFWriterRIOT.java:86)
at org.apache.jena.rdf.model.impl.ModelCom.write(ModelCom.java:379)
at knowledgegraph.JenaProcessor.getRDF(JenaProcessor.java:89)
Re: Exception in writing RDF from model
Posted by Diptendu Dutta <du...@gmail.com>.
I found the problem: spaces in the triple components
What would be a reasonable way to encode the triple strings?
On Tue 3 Mar, 2020 10:01 pm Andy Seaborne, <an...@apache.org> wrote:
> That codes OK - it uses transactions.
>
> Are you starting with a fresh database or an existing one with some data?
>
> Andy
>
> On 03/03/2020 14:45, Diptendu Dutta wrote:
> > The code that is used to populate the database is given below.
> > It is called in side a FOR loop. Why is the database getting corrupted?
> >
> > static public void writeTriple(String corpus_file_id, String subject,
> > String predicate, String object) {
> >
> > dataset.begin(ReadWrite.WRITE) ;
> > Model model = null;
> >
> > try {
> >
> > model = dataset.getNamedModel(corpus_file_id);
> >
> > Resource subjectResource =
> model.createResource(ns.concat(subject));
> >
> > Property property = model.createProperty(ns.concat(predicate));
> >
> > Resource objectResource =
> model.createResource(ns.concat(object));
> >
> > model.add(subjectResource, property, objectResource);
> > Statement statement = model.createStatement(subjectResource,
> > property, objectResource);
> > model.add(statement);
> > model.close();
> > dataset.commit();
> > }
> > catch(Exception ex) {
> > ex.printStackTrace();
> > }
> > finally {
> > dataset.end();
> > }
> >
> > }
> >
> > I can see that the database has been created:
> >
> > image.png
> >
> >
> > On Tue, Mar 3, 2020 at 7:40 PM Andy Seaborne <andy@apache.org
> > <ma...@apache.org>> wrote:
> >
> > It looks like previously you were using the database withotu
> > transactions and didn't shutdown cleanly.
> >
> > The database has been corrupted. You'll need to rebuild it.
> >
> > The code below is fine - the problem happened beforehand and is only
> > now
> > showing up.
> >
> > Andy
> >
> > On 03/03/2020 14:01, Diptendu Dutta wrote:
> > > I am getting java.lang.StringIndexOutOfBoundsException while
> writing
> > > RDF from a model (model.write()). I have tried with other
> mechanisms
> > > such as RDFWriter, RDFDataMgr but I get exactly the same error.
> > > Here is the code:
> > >
> > > static public String getRDF(String corpus_file_id) {
> > >
> > > String rdfString = null;
> > >
> > > Model model = null;
> > >
> > > dataset.begin(ReadWrite.READ) ;
> > >
> > > try {
> > > model = dataset.getNamedModel(corpus_file_id);
> > > model.write(System.out, "RDF/XML");
> > > } catch (Exception e) {
> > > // TODO Auto-generated catch block
> > > e.printStackTrace();
> > > }finally {
> > > model.close();
> > > dataset.end();
> > > }
> > > return rdfString;
> > > }
> > >
> > > java.lang.StringIndexOutOfBoundsException: String index out of
> > range: 46
> > > at java.lang.String.charAt(String.java:658)
> > > at org.apache.jena.atlas.lib.StrUtils.decodeHex(StrUtils.java:212)
> > > at
> >
> org.apache.jena.tdb.store.nodetable.NodecSSE.decode(NodecSSE.java:121)
> > > at org.apache.jena.tdb.lib.NodeLib.decode(NodeLib.java:120)
> > > at org.apache.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:97)
> > > at
> > >
> >
> org.apache.jena.tdb.store.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:182)
> > > at
> > >
> >
> org.apache.jena.tdb.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:108)
> > > at
> > >
> >
> org.apache.jena.tdb.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:67)
> > > at
> > >
> >
> org.apache.jena.tdb.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:128)
> > > at
> > >
> >
> org.apache.jena.tdb.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:82)
> > > at
> > >
> >
> org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:50)
> > > at
> > >
> >
> org.apache.jena.tdb.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67)
> > > at org.apache.jena.tdb.lib.TupleLib.quad(TupleLib.java:126)
> > > at org.apache.jena.tdb.lib.TupleLib.quad(TupleLib.java:120)
> > > at
> > >
> >
> org.apache.jena.tdb.lib.TupleLib.lambda$convertToQuads$3(TupleLib.java:59)
> > > at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352)
> > > at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352)
> > > at org.apache.jena.atlas.iterator.Iter.next(Iter.java:1072)
> > > at
> > >
> >
> org.apache.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94)
> > > at
> > org.apache.jena.util.iterator.Map1Iterator.next(Map1Iterator.java:46)
> > > at
> >
> org.apache.jena.util.iterator.NiceIterator.asSet(NiceIterator.java:208)
> > > at
> >
> org.apache.jena.util.iterator.NiceIterator.toSet(NiceIterator.java:199)
> > > at
> org.apache.jena.graph.GraphUtil.listPredicates(GraphUtil.java:66)
> > > at
> >
> org.apache.jena.rdf.model.impl.ModelCom.listPredicates(ModelCom.java:999)
> > > at
> > >
> >
> org.apache.jena.rdf.model.impl.ModelCom.listNameSpaces(ModelCom.java:1012)
> > > at
> > >
> >
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.addNameSpaces(BaseXMLWriter.java:219)
> > > at
> > >
> >
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.setupNamespaces(BaseXMLWriter.java:488)
> > > at
> > >
> >
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.write(BaseXMLWriter.java:470)
> > > at
> > >
> >
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.write(BaseXMLWriter.java:460)
> > > at
> > >
> >
> org.apache.jena.riot.adapters.AdapterRDFWriter.write(AdapterRDFWriter.java:64)
> > > at org.apache.jena.riot.RDFWriter.write$(RDFWriter.java:202)
> > > at org.apache.jena.riot.RDFWriter.output(RDFWriter.java:161)
> > > at org.apache.jena.riot.RDFWriter.output(RDFWriter.java:112)
> > > at
> >
> org.apache.jena.riot.RDFWriterBuilder.output(RDFWriterBuilder.java:205)
> > > at
> >
> org.apache.jena.riot.adapters.RDFWriterRIOT.write(RDFWriterRIOT.java:86)
> > > at
> org.apache.jena.rdf.model.impl.ModelCom.write(ModelCom.java:379)
> > > at knowledgegraph.JenaProcessor.getRDF(JenaProcessor.java:89)
> > >
> >
>
Re: Exception in writing RDF from model
Posted by Andy Seaborne <an...@apache.org>.
That codes OK - it uses transactions.
Are you starting with a fresh database or an existing one with some data?
Andy
On 03/03/2020 14:45, Diptendu Dutta wrote:
> The code that is used to populate the database is given below.
> It is called in side a FOR loop. Why is the database getting corrupted?
>
> static public void writeTriple(String corpus_file_id, String subject,
> String predicate, String object) {
>
> dataset.begin(ReadWrite.WRITE) ;
> Model model = null;
>
> try {
>
> model = dataset.getNamedModel(corpus_file_id);
>
> Resource subjectResource = model.createResource(ns.concat(subject));
>
> Property property = model.createProperty(ns.concat(predicate));
>
> Resource objectResource = model.createResource(ns.concat(object));
>
> model.add(subjectResource, property, objectResource);
> Statement statement = model.createStatement(subjectResource,
> property, objectResource);
> model.add(statement);
> model.close();
> dataset.commit();
> }
> catch(Exception ex) {
> ex.printStackTrace();
> }
> finally {
> dataset.end();
> }
>
> }
>
> I can see that the database has been created:
>
> image.png
>
>
> On Tue, Mar 3, 2020 at 7:40 PM Andy Seaborne <andy@apache.org
> <ma...@apache.org>> wrote:
>
> It looks like previously you were using the database withotu
> transactions and didn't shutdown cleanly.
>
> The database has been corrupted. You'll need to rebuild it.
>
> The code below is fine - the problem happened beforehand and is only
> now
> showing up.
>
> Andy
>
> On 03/03/2020 14:01, Diptendu Dutta wrote:
> > I am getting java.lang.StringIndexOutOfBoundsException while writing
> > RDF from a model (model.write()). I have tried with other mechanisms
> > such as RDFWriter, RDFDataMgr but I get exactly the same error.
> > Here is the code:
> >
> > static public String getRDF(String corpus_file_id) {
> >
> > String rdfString = null;
> >
> > Model model = null;
> >
> > dataset.begin(ReadWrite.READ) ;
> >
> > try {
> > model = dataset.getNamedModel(corpus_file_id);
> > model.write(System.out, "RDF/XML");
> > } catch (Exception e) {
> > // TODO Auto-generated catch block
> > e.printStackTrace();
> > }finally {
> > model.close();
> > dataset.end();
> > }
> > return rdfString;
> > }
> >
> > java.lang.StringIndexOutOfBoundsException: String index out of
> range: 46
> > at java.lang.String.charAt(String.java:658)
> > at org.apache.jena.atlas.lib.StrUtils.decodeHex(StrUtils.java:212)
> > at
> org.apache.jena.tdb.store.nodetable.NodecSSE.decode(NodecSSE.java:121)
> > at org.apache.jena.tdb.lib.NodeLib.decode(NodeLib.java:120)
> > at org.apache.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:97)
> > at
> >
> org.apache.jena.tdb.store.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:182)
> > at
> >
> org.apache.jena.tdb.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:108)
> > at
> >
> org.apache.jena.tdb.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:67)
> > at
> >
> org.apache.jena.tdb.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:128)
> > at
> >
> org.apache.jena.tdb.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:82)
> > at
> >
> org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:50)
> > at
> >
> org.apache.jena.tdb.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67)
> > at org.apache.jena.tdb.lib.TupleLib.quad(TupleLib.java:126)
> > at org.apache.jena.tdb.lib.TupleLib.quad(TupleLib.java:120)
> > at
> >
> org.apache.jena.tdb.lib.TupleLib.lambda$convertToQuads$3(TupleLib.java:59)
> > at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352)
> > at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352)
> > at org.apache.jena.atlas.iterator.Iter.next(Iter.java:1072)
> > at
> >
> org.apache.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94)
> > at
> org.apache.jena.util.iterator.Map1Iterator.next(Map1Iterator.java:46)
> > at
> org.apache.jena.util.iterator.NiceIterator.asSet(NiceIterator.java:208)
> > at
> org.apache.jena.util.iterator.NiceIterator.toSet(NiceIterator.java:199)
> > at org.apache.jena.graph.GraphUtil.listPredicates(GraphUtil.java:66)
> > at
> org.apache.jena.rdf.model.impl.ModelCom.listPredicates(ModelCom.java:999)
> > at
> >
> org.apache.jena.rdf.model.impl.ModelCom.listNameSpaces(ModelCom.java:1012)
> > at
> >
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.addNameSpaces(BaseXMLWriter.java:219)
> > at
> >
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.setupNamespaces(BaseXMLWriter.java:488)
> > at
> >
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.write(BaseXMLWriter.java:470)
> > at
> >
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.write(BaseXMLWriter.java:460)
> > at
> >
> org.apache.jena.riot.adapters.AdapterRDFWriter.write(AdapterRDFWriter.java:64)
> > at org.apache.jena.riot.RDFWriter.write$(RDFWriter.java:202)
> > at org.apache.jena.riot.RDFWriter.output(RDFWriter.java:161)
> > at org.apache.jena.riot.RDFWriter.output(RDFWriter.java:112)
> > at
> org.apache.jena.riot.RDFWriterBuilder.output(RDFWriterBuilder.java:205)
> > at
> org.apache.jena.riot.adapters.RDFWriterRIOT.write(RDFWriterRIOT.java:86)
> > at org.apache.jena.rdf.model.impl.ModelCom.write(ModelCom.java:379)
> > at knowledgegraph.JenaProcessor.getRDF(JenaProcessor.java:89)
> >
>
Re: Exception in writing RDF from model
Posted by Diptendu Dutta <du...@gmail.com>.
The code that is used to populate the database is given below.
It is called in side a FOR loop. Why is the database getting corrupted?
static public void writeTriple(String corpus_file_id, String subject,
String predicate, String object) {
dataset.begin(ReadWrite.WRITE) ;
Model model = null;
try {
model = dataset.getNamedModel(corpus_file_id);
Resource subjectResource = model.createResource(ns.concat(subject));
Property property = model.createProperty(ns.concat(predicate));
Resource objectResource = model.createResource(ns.concat(object));
model.add(subjectResource, property, objectResource);
Statement statement = model.createStatement(subjectResource,
property, objectResource);
model.add(statement);
model.close();
dataset.commit();
}
catch(Exception ex) {
ex.printStackTrace();
}
finally {
dataset.end();
}
}
I can see that the database has been created:
[image: image.png]
On Tue, Mar 3, 2020 at 7:40 PM Andy Seaborne <an...@apache.org> wrote:
> It looks like previously you were using the database withotu
> transactions and didn't shutdown cleanly.
>
> The database has been corrupted. You'll need to rebuild it.
>
> The code below is fine - the problem happened beforehand and is only now
> showing up.
>
> Andy
>
> On 03/03/2020 14:01, Diptendu Dutta wrote:
> > I am getting java.lang.StringIndexOutOfBoundsException while writing
> > RDF from a model (model.write()). I have tried with other mechanisms
> > such as RDFWriter, RDFDataMgr but I get exactly the same error.
> > Here is the code:
> >
> > static public String getRDF(String corpus_file_id) {
> >
> > String rdfString = null;
> >
> > Model model = null;
> >
> > dataset.begin(ReadWrite.READ) ;
> >
> > try {
> > model = dataset.getNamedModel(corpus_file_id);
> > model.write(System.out, "RDF/XML");
> > } catch (Exception e) {
> > // TODO Auto-generated catch block
> > e.printStackTrace();
> > }finally {
> > model.close();
> > dataset.end();
> > }
> > return rdfString;
> > }
> >
> > java.lang.StringIndexOutOfBoundsException: String index out of range: 46
> > at java.lang.String.charAt(String.java:658)
> > at org.apache.jena.atlas.lib.StrUtils.decodeHex(StrUtils.java:212)
> > at org.apache.jena.tdb.store.nodetable.NodecSSE.decode(NodecSSE.java:121)
> > at org.apache.jena.tdb.lib.NodeLib.decode(NodeLib.java:120)
> > at org.apache.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:97)
> > at
> >
> org.apache.jena.tdb.store.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:182)
> > at
> >
> org.apache.jena.tdb.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:108)
> > at
> >
> org.apache.jena.tdb.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:67)
> > at
> >
> org.apache.jena.tdb.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:128)
> > at
> >
> org.apache.jena.tdb.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:82)
> > at
> >
> org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:50)
> > at
> >
> org.apache.jena.tdb.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67)
> > at org.apache.jena.tdb.lib.TupleLib.quad(TupleLib.java:126)
> > at org.apache.jena.tdb.lib.TupleLib.quad(TupleLib.java:120)
> > at
> >
> org.apache.jena.tdb.lib.TupleLib.lambda$convertToQuads$3(TupleLib.java:59)
> > at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352)
> > at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352)
> > at org.apache.jena.atlas.iterator.Iter.next(Iter.java:1072)
> > at
> >
> org.apache.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94)
> > at org.apache.jena.util.iterator.Map1Iterator.next(Map1Iterator.java:46)
> > at
> org.apache.jena.util.iterator.NiceIterator.asSet(NiceIterator.java:208)
> > at
> org.apache.jena.util.iterator.NiceIterator.toSet(NiceIterator.java:199)
> > at org.apache.jena.graph.GraphUtil.listPredicates(GraphUtil.java:66)
> > at
> org.apache.jena.rdf.model.impl.ModelCom.listPredicates(ModelCom.java:999)
> > at
> >
> org.apache.jena.rdf.model.impl.ModelCom.listNameSpaces(ModelCom.java:1012)
> > at
> >
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.addNameSpaces(BaseXMLWriter.java:219)
> > at
> >
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.setupNamespaces(BaseXMLWriter.java:488)
> > at
> >
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.write(BaseXMLWriter.java:470)
> > at
> >
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.write(BaseXMLWriter.java:460)
> > at
> >
> org.apache.jena.riot.adapters.AdapterRDFWriter.write(AdapterRDFWriter.java:64)
> > at org.apache.jena.riot.RDFWriter.write$(RDFWriter.java:202)
> > at org.apache.jena.riot.RDFWriter.output(RDFWriter.java:161)
> > at org.apache.jena.riot.RDFWriter.output(RDFWriter.java:112)
> > at
> org.apache.jena.riot.RDFWriterBuilder.output(RDFWriterBuilder.java:205)
> > at
> org.apache.jena.riot.adapters.RDFWriterRIOT.write(RDFWriterRIOT.java:86)
> > at org.apache.jena.rdf.model.impl.ModelCom.write(ModelCom.java:379)
> > at knowledgegraph.JenaProcessor.getRDF(JenaProcessor.java:89)
> >
>
Re: Exception in writing RDF from model
Posted by Andy Seaborne <an...@apache.org>.
It looks like previously you were using the database withotu
transactions and didn't shutdown cleanly.
The database has been corrupted. You'll need to rebuild it.
The code below is fine - the problem happened beforehand and is only now
showing up.
Andy
On 03/03/2020 14:01, Diptendu Dutta wrote:
> I am getting java.lang.StringIndexOutOfBoundsException while writing
> RDF from a model (model.write()). I have tried with other mechanisms
> such as RDFWriter, RDFDataMgr but I get exactly the same error.
> Here is the code:
>
> static public String getRDF(String corpus_file_id) {
>
> String rdfString = null;
>
> Model model = null;
>
> dataset.begin(ReadWrite.READ) ;
>
> try {
> model = dataset.getNamedModel(corpus_file_id);
> model.write(System.out, "RDF/XML");
> } catch (Exception e) {
> // TODO Auto-generated catch block
> e.printStackTrace();
> }finally {
> model.close();
> dataset.end();
> }
> return rdfString;
> }
>
> java.lang.StringIndexOutOfBoundsException: String index out of range: 46
> at java.lang.String.charAt(String.java:658)
> at org.apache.jena.atlas.lib.StrUtils.decodeHex(StrUtils.java:212)
> at org.apache.jena.tdb.store.nodetable.NodecSSE.decode(NodecSSE.java:121)
> at org.apache.jena.tdb.lib.NodeLib.decode(NodeLib.java:120)
> at org.apache.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:97)
> at
> org.apache.jena.tdb.store.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:182)
> at
> org.apache.jena.tdb.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:108)
> at
> org.apache.jena.tdb.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:67)
> at
> org.apache.jena.tdb.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:128)
> at
> org.apache.jena.tdb.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:82)
> at
> org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:50)
> at
> org.apache.jena.tdb.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67)
> at org.apache.jena.tdb.lib.TupleLib.quad(TupleLib.java:126)
> at org.apache.jena.tdb.lib.TupleLib.quad(TupleLib.java:120)
> at
> org.apache.jena.tdb.lib.TupleLib.lambda$convertToQuads$3(TupleLib.java:59)
> at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352)
> at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352)
> at org.apache.jena.atlas.iterator.Iter.next(Iter.java:1072)
> at
> org.apache.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94)
> at org.apache.jena.util.iterator.Map1Iterator.next(Map1Iterator.java:46)
> at org.apache.jena.util.iterator.NiceIterator.asSet(NiceIterator.java:208)
> at org.apache.jena.util.iterator.NiceIterator.toSet(NiceIterator.java:199)
> at org.apache.jena.graph.GraphUtil.listPredicates(GraphUtil.java:66)
> at org.apache.jena.rdf.model.impl.ModelCom.listPredicates(ModelCom.java:999)
> at
> org.apache.jena.rdf.model.impl.ModelCom.listNameSpaces(ModelCom.java:1012)
> at
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.addNameSpaces(BaseXMLWriter.java:219)
> at
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.setupNamespaces(BaseXMLWriter.java:488)
> at
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.write(BaseXMLWriter.java:470)
> at
> org.apache.jena.rdfxml.xmloutput.impl.BaseXMLWriter.write(BaseXMLWriter.java:460)
> at
> org.apache.jena.riot.adapters.AdapterRDFWriter.write(AdapterRDFWriter.java:64)
> at org.apache.jena.riot.RDFWriter.write$(RDFWriter.java:202)
> at org.apache.jena.riot.RDFWriter.output(RDFWriter.java:161)
> at org.apache.jena.riot.RDFWriter.output(RDFWriter.java:112)
> at org.apache.jena.riot.RDFWriterBuilder.output(RDFWriterBuilder.java:205)
> at org.apache.jena.riot.adapters.RDFWriterRIOT.write(RDFWriterRIOT.java:86)
> at org.apache.jena.rdf.model.impl.ModelCom.write(ModelCom.java:379)
> at knowledgegraph.JenaProcessor.getRDF(JenaProcessor.java:89)
>