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Posted to dev@taverna.apache.org by Dmitry <re...@list.ru> on 2015/03/27 17:52:13 UTC
incubating...
Hello everybody,
I did my best trying to refactor taverna-workbench to the org.taverna.*
packages.
There are many issues mainly with external code.
1. "*.workbench.models.graph.dot" package is missing
2. baclava
no "org.apache.taverna.baclava.factory.DataThingXMLFactory" in
taverna-baclava-language-0.15.0-incubating-SNAPSHOT.jar
(taverna-reference-ui fails)
3. provenance
as far as I understand the problem is with external LGPL(?) library.
4. there is a code with SUN TreeTable which must be removed...
... etc.
Cheers,
Dmitry
Re: incubating...
Posted by Stian Soiland-Reyes <st...@apache.org>.
Found it - they were autogenerated from
https://github.com/apache/incubator-taverna-workbench/tree/master/taverna-graph-model/src/main/jjtree
.. which said still net.sf.taverna....
I have fixed them, so now mvn generate-sources should give:
target/generated-sources/javacc/org/apache/taverna/workbench/models/graph/dot/DOTParser.java
target/generated-sources/javacc/org/apache/taverna/workbench/models/graph/dot/SimpleCharStream.java
target/generated-sources/javacc/org/apache/taverna/workbench/models/graph/dot/DOTParserConstants.java
target/generated-sources/javacc/org/apache/taverna/workbench/models/graph/dot/DOTParserTokenManager.java
target/generated-sources/javacc/org/apache/taverna/workbench/models/graph/dot/TokenMgrError.java
target/generated-sources/javacc/org/apache/taverna/workbench/models/graph/dot/ParseException.java
target/generated-sources/javacc/org/apache/taverna/workbench/models/graph/dot/Token.java
target/generated-sources/javacc/org/apache/taverna/workbench/models/graph/dot/NamedNode.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/ASTStatement.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/Node.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/ASTSubgraph.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/ASTStatementList.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/ASTAttributeStatement.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/JJTDOTParserState.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/ASTParse.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/ASTEdgeRHS.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/ASTAttributeList.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/ASTNodeId.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/DOTParserTreeConstants.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/ASTEdgeStatement.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/ASTNodeStatement.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/SimpleNode.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/ASTAList.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/ASTGraph.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/ASTPort.java
target/generated-sources/jjtree/org/apache/taverna/workbench/models/graph/dot/DOTParserVisitor.java
parsers.. more or less fun than copyright issues? :)
(I also get this problem with batik-osgi not being found - investigating that)
On 31 March 2015 at 17:13, Dmitry <re...@list.ru> wrote:
>> the workbench.models.graph.dot should be built by Maven
>> generate-sources -- in Eclipse do a right click and Maven -> Update
>> Project to find it in target/generated-sources
>
>
> the org.apache.taverna.workbench.models.graph.dot package has only one
> class:
> GraphLayout
>
> The "old" taverna graph-model had much more classes in
> net.sf.taverna.t2.workbench.models.graph.dot
> some classes are missing
>
>
> On 3/31/2015 5:43 PM, Stian Soiland-Reyes wrote:
>>
>> the workbench.models.graph.dot should be built by Maven
>> generate-sources -- in Eclipse do a right click and Maven -> Update
>> Project to find it in target/generated-sources
>>
>>
>> DataThingXMLFactory thing should probably not be used - do we want to
>> expose baclava in the UI anymore? Probably not until we get a
>> converter.
>>
>>
>> The provenance is not a LGPL issue - it is that the mechanism for
>> provenance has changed in Taverna 3 to use the run bundles and run
>> reports instead of the database, but lots of code in the UI (that I
>> believe is not displayed anymore) still refer to the old
>> provenanceconnector classes that access the database.
>>
>>
>> The workbench code is unfortunately still in a bit of flux - I updated
>> all the poms to have probably the right org.apache.taverna
>> dependencies - but there are a few compilation errors here and there
>> that needs sorting - someone like Alan might have the right eye to
>> determine what should be ripped out (Taverna 2 only leftovers) or what
>> must be updated.
>>
>>
>>
>> On 27 March 2015 at 16:52, Dmitry <re...@list.ru> wrote:
>>>
>>> Hello everybody,
>>>
>>> I did my best trying to refactor taverna-workbench to the org.taverna.*
>>> packages.
>>> There are many issues mainly with external code.
>>>
>>> 1. "*.workbench.models.graph.dot" package is missing
>>>
>>> 2. baclava
>>> no "org.apache.taverna.baclava.factory.DataThingXMLFactory" in
>>> taverna-baclava-language-0.15.0-incubating-SNAPSHOT.jar
>>> (taverna-reference-ui fails)
>>>
>>> 3. provenance
>>> as far as I understand the problem is with external LGPL(?) library.
>>>
>>> 4. there is a code with SUN TreeTable which must be removed...
>>>
>>> ... etc.
>>>
>>> Cheers,
>>>
>>> Dmitry
>>>
>>
>>
>
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: incubating...
Posted by Dmitry <re...@list.ru>.
> the workbench.models.graph.dot should be built by Maven
> generate-sources -- in Eclipse do a right click and Maven -> Update
> Project to find it in target/generated-sources
the org.apache.taverna.workbench.models.graph.dot package has only one
class:
GraphLayout
The "old" taverna graph-model had much more classes in
net.sf.taverna.t2.workbench.models.graph.dot
some classes are missing
On 3/31/2015 5:43 PM, Stian Soiland-Reyes wrote:
> the workbench.models.graph.dot should be built by Maven
> generate-sources -- in Eclipse do a right click and Maven -> Update
> Project to find it in target/generated-sources
>
>
> DataThingXMLFactory thing should probably not be used - do we want to
> expose baclava in the UI anymore? Probably not until we get a
> converter.
>
>
> The provenance is not a LGPL issue - it is that the mechanism for
> provenance has changed in Taverna 3 to use the run bundles and run
> reports instead of the database, but lots of code in the UI (that I
> believe is not displayed anymore) still refer to the old
> provenanceconnector classes that access the database.
>
>
> The workbench code is unfortunately still in a bit of flux - I updated
> all the poms to have probably the right org.apache.taverna
> dependencies - but there are a few compilation errors here and there
> that needs sorting - someone like Alan might have the right eye to
> determine what should be ripped out (Taverna 2 only leftovers) or what
> must be updated.
>
>
>
> On 27 March 2015 at 16:52, Dmitry <re...@list.ru> wrote:
>> Hello everybody,
>>
>> I did my best trying to refactor taverna-workbench to the org.taverna.*
>> packages.
>> There are many issues mainly with external code.
>>
>> 1. "*.workbench.models.graph.dot" package is missing
>>
>> 2. baclava
>> no "org.apache.taverna.baclava.factory.DataThingXMLFactory" in
>> taverna-baclava-language-0.15.0-incubating-SNAPSHOT.jar
>> (taverna-reference-ui fails)
>>
>> 3. provenance
>> as far as I understand the problem is with external LGPL(?) library.
>>
>> 4. there is a code with SUN TreeTable which must be removed...
>>
>> ... etc.
>>
>> Cheers,
>>
>> Dmitry
>>
>
>
Re: incubating...
Posted by Stian Soiland-Reyes <st...@apache.org>.
the workbench.models.graph.dot should be built by Maven
generate-sources -- in Eclipse do a right click and Maven -> Update
Project to find it in target/generated-sources
DataThingXMLFactory thing should probably not be used - do we want to
expose baclava in the UI anymore? Probably not until we get a
converter.
The provenance is not a LGPL issue - it is that the mechanism for
provenance has changed in Taverna 3 to use the run bundles and run
reports instead of the database, but lots of code in the UI (that I
believe is not displayed anymore) still refer to the old
provenanceconnector classes that access the database.
The workbench code is unfortunately still in a bit of flux - I updated
all the poms to have probably the right org.apache.taverna
dependencies - but there are a few compilation errors here and there
that needs sorting - someone like Alan might have the right eye to
determine what should be ripped out (Taverna 2 only leftovers) or what
must be updated.
On 27 March 2015 at 16:52, Dmitry <re...@list.ru> wrote:
> Hello everybody,
>
> I did my best trying to refactor taverna-workbench to the org.taverna.*
> packages.
> There are many issues mainly with external code.
>
> 1. "*.workbench.models.graph.dot" package is missing
>
> 2. baclava
> no "org.apache.taverna.baclava.factory.DataThingXMLFactory" in
> taverna-baclava-language-0.15.0-incubating-SNAPSHOT.jar
> (taverna-reference-ui fails)
>
> 3. provenance
> as far as I understand the problem is with external LGPL(?) library.
>
> 4. there is a code with SUN TreeTable which must be removed...
>
> ... etc.
>
> Cheers,
>
> Dmitry
>
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: incubating...
Posted by alaninmcr <al...@googlemail.com>.
On 30/03/2015 14:42, Dmitry wrote:
> Hello Alan,
>
> The org.apache.taverna.workbench.ui.impl.LoggerStream is from JBoss (LGPL)
> *************************************
> ...
> //FIXME Replace this class entirely
> class LoggerStream extends PrintStream
> ...
> *************************************
Looking at
http://stackoverflow.com/questions/11187461/redirect-system-out-and-system-err-to-slf4j
we should be able to use Apache's LoggingOutputStream.
> There are some modules that do not compile.
> I understand that some of them, probably, are not supposed to be
> included in T3.
> For instance Taverna plug-in manager GUI is based on Raven (???)
As the plugin mechanism will change, I think the plugin manager will
have be rewritten.
> BioCatalogue should be updated to T3 also.
That depends if we want to keep having a Service Catalogue perspective.
For a long time, I have argued that Taverna should not try to include
poor versions of external websites. Instead, we should re-think how we
talk with websites.
> engine:
> <module>taverna-provenanceconnector</module>
> is commented, but some workbench modules depend on it.
>
> Note that there are some dependencies on
> org.openprovenance and org.tupeloproject
>
> Dmitry
>
> P.S. is Apache Taverna JIRA already working?
I am not sure. Stian will know.
Alan
Re: incubating...
Posted by Dmitry <re...@list.ru>.
Hello Alan,
The org.apache.taverna.workbench.ui.impl.LoggerStream is from JBoss (LGPL)
*************************************
...
//FIXME Replace this class entirely
class LoggerStream extends PrintStream
...
*************************************
There are some modules that do not compile.
I understand that some of them, probably, are not supposed to be
included in T3.
For instance Taverna plug-in manager GUI is based on Raven (???)
BioCatalogue should be updated to T3 also.
engine:
<module>taverna-provenanceconnector</module>
is commented, but some workbench modules depend on it.
Note that there are some dependencies on
org.openprovenance and org.tupeloproject
Dmitry
P.S. is Apache Taverna JIRA already working?
On 3/30/2015 2:20 PM, alaninmcr wrote:
> On 27/03/2015 16:52, Dmitry wrote:
>> Hello everybody,
>>
>> I did my best trying to refactor taverna-workbench to the org.taverna.*
>> packages.
>
> Great.
>
>> There are many issues mainly with external code.
>
> Do you have a list of these issues so they can be added into Jira?
>
>> 1. "*.workbench.models.graph.dot" package is missing
>>
>> 2. baclava
>> no "org.apache.taverna.baclava.factory.DataThingXMLFactory" in
>> taverna-baclava-language-0.15.0-incubating-SNAPSHOT.jar
>> (taverna-reference-ui fails)
>
> That is not surprising. We need to decide if the T3 workbench should
> do anything with baclava. If it does, then probably the new baclava
> package will need some new methods, and the code that calls it will
> need to be updated.
>
> I think the default position should be that the T3 workbench should be
> using databundles instead of baclava.
>
>> 3. provenance
>> as far as I understand the problem is with external LGPL(?) library.
>
> Which part of provenance?
>
>> 4. there is a code with SUN TreeTable which must be removed...
>
> This is the JTreeTable in (what used to be)
> net.sf.taverna.t2.lang.ui.treetable ?
>
>> ... etc.
>
> Can you share the "etc." ?
>
>> Cheers,
>>
>> Dmitry
>
> Alan
>
>
Re: incubating...
Posted by alaninmcr <al...@googlemail.com>.
On 27/03/2015 16:52, Dmitry wrote:
> Hello everybody,
>
> I did my best trying to refactor taverna-workbench to the org.taverna.*
> packages.
Great.
> There are many issues mainly with external code.
Do you have a list of these issues so they can be added into Jira?
> 1. "*.workbench.models.graph.dot" package is missing
>
> 2. baclava
> no "org.apache.taverna.baclava.factory.DataThingXMLFactory" in
> taverna-baclava-language-0.15.0-incubating-SNAPSHOT.jar
> (taverna-reference-ui fails)
That is not surprising. We need to decide if the T3 workbench should do
anything with baclava. If it does, then probably the new baclava package
will need some new methods, and the code that calls it will need to be
updated.
I think the default position should be that the T3 workbench should be
using databundles instead of baclava.
> 3. provenance
> as far as I understand the problem is with external LGPL(?) library.
Which part of provenance?
> 4. there is a code with SUN TreeTable which must be removed...
This is the JTreeTable in (what used to be)
net.sf.taverna.t2.lang.ui.treetable ?
> ... etc.
Can you share the "etc." ?
> Cheers,
>
> Dmitry
Alan