I've added the wfbundle parser TAVERNA-71 workaround in master - see
https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/WorkflowBundleParser.java#L136
Do you think you could try out the latest SNAPSHOT?
<dependency>
<groupId>org.apache.taverna.language</groupId>
<artifactId>taverna-scufl2-wfbundle</artifactId>
<version>0.15.2-incubating-SNAPSHOT</version>
</dependency>
<repositories>
<repositories>
<repository>
<id>apache.snapshots</id>
<name>Apache Snapshot Repository</name>
<url>http://repository.apache.org/snapshots</url>
<releases>
<enabled>false</enabled>
</releases>
</repository>
</repositories>
(If this works, then you don't need your own version of parseAnnotations() )
On 4 May 2016 at 11:21, Stian Soiland-Reyes <[email protected]> wrote:
> My apologies - you are right - I realize now that if you open a
> wfbundle (as opposed to a .t2flow) - then getAnnotations() is always
> empty.
>
> It should work if you open a .t2flow as the T2flow parser populates
> wfbundle.getAnnotations().
>
>
> The reason is that the annotation links in wfbundle.getAnnotations()
> are not stored in the wfbundle manifest (and not parsed).
>
> some preliminary code for this was at:
>
> https://github.com/apache/incubator-taverna-language/blob/0.15.1-incubating/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLSerializer.java#L549
>
> To put it blunt - the t2flow parsed adds
> <annotation/02a6e877-a4f0-44f9-9730-6b60a55092a6.ttl> that describes
> <workflow/Workflow1/in/DataSetPath> - however the link between
> <workflow/Workflow1/in/DataSetPath> and
> <annotation/02a6e877-a4f0-44f9-9730-6b60a55092a6.ttl> is not
> serialized - and so the only way to find annotation/ now is to go
> through the annotation/ folder.
>
>
> I think this relates to
> https://issues.apache.org/jira/browse/TAVERNA-965 as the UCFPackage or
> WorkflowBundle didn't have a mechanism to serialize which annotations
> exist (it would basically need to replicate
> https://w3id.org/bundle/#manifest-annotations ) - and so there would
> not be any point in not moving to taverna-robundle for managing the
> bundle and the annotations.
>
> This bug was already tracked at
> https://issues.apache.org/jira/browse/TAVERNA-71 - I've promoted this
> to be Fix For Language 0.16.0.
>
> I've shown you a workaround in
> https://github.com/enridaga/taverna-sandbox/pull/1
> to parse the wfbundle annotations
> and I'm testing to add this to taverna-scufl2-wfbundle as a workaround.
>
>
>
>
> On 3 May 2016 at 11:19, Enrico Daga (enridaga) <[email protected]> wrote:
>> Hi Stian,
>>
>> I tried with the latest release but I am still struggling on getting this
>> work.
>>
>> I prepared a minimal project to test the issue [1], which contains a single
>> test using a workflow downloaded from my experiment (and converted to
>> wfbundle) [2].
>>
>> This wf contains a set of annotations, particularly from input ports. I can
>> see them unpacking the bundle [3].
>>
>> However, I cannot access them in the way you suggested (replicated here [4]).
>>
>> Best,
>>
>> Enrico
>>
>>
>>
>> [1] https://github.com/enridaga/taverna-sandbox
>> <https://github.com/enridaga/taverna-sandbox>
>> [2] http://www.myexperiment.org/workflows/4303.html
>> <http://www.myexperiment.org/workflows/4303.html>
>> [3]
>> https://github.com/enridaga/taverna-sandbox/tree/master/src/test/resources/bundles/3Drec-v1/annotation
>>
>> <https://github.com/enridaga/taverna-sandbox/tree/master/src/test/resources/bundles/3Drec-v1/annotation>
>> [4]
>> https://github.com/enridaga/taverna-sandbox/blob/master/src/test/java/enridaga/AppTest.java
>>
>> <https://github.com/enridaga/taverna-sandbox/blob/master/src/test/java/enridaga/AppTest.java>
>>
>> —
>> Enrico Daga (enridaga)
>> http://www.enridaga.net <http://www.enridaga.net/>
>> Il budda e’ nel parco.
>>
>>
>>
>>
>>
>>> On 3 May 2016, at 09:01, Enrico Daga (enridaga) <[email protected]>
>>> wrote:
>>>
>>> Thank you Stian, this is gold.
>>>
>>> Will try the new release as well.
>>>
>>> It's good to have Taverna at Apache!
>>>
>>> Best,
>>> Enrico
>>>
>>>
>>> —
>>> Enrico Daga (enridaga)
>>> http://www.enridaga.net <http://www.enridaga.net/>
>>> Il budda e’ nel parco.
>>>
>>>
>>>
>>>
>>>
>>>> On 2 May 2016, at 17:19, Stian Soiland-Reyes <[email protected]
>>>> <mailto:[email protected]>> wrote:
>>>>
>>>> BTW - another alternative - if you convert to wfdesc with tavlang convert
>>>> - see
>>>> https://github.com/apache/incubator-taverna-language/tree/master/taverna-tavlang-tool
>>>>
>>>> <https://github.com/apache/incubator-taverna-language/tree/master/taverna-tavlang-tool>
>>>>
>>>> then you should also get all the annotations across the workflow - but
>>>> you will loose the information about when it was made as it comes back
>>>> as a single Triple file.
>>>>
>>>> On 28 April 2016 at 16:25, Enrico Daga (enridaga) <[email protected]
>>>> <mailto:[email protected]>> wrote:
>>>>> Hi,
>>>>>
>>>>> I am using the taverna API to explore workflows downloaded from
>>>>> MyExperiment.
>>>>> At the moment, I converted the files to the .wfbundle format using the
>>>>> taverna command line tools. Everything looks fine.
>>>>> Unzipping a wfbundle I can read a set of .ttl files in the annotations/
>>>>> folder, but I am not able to do that through the Java API.
>>>>> In the simplest form, my code is as follows:
>>>>>
>>>>> WorkflowBundleIO io = new WorkflowBundleIO();
>>>>> final WorkflowBundle wb =
>>>>> io.readBundle(__f(“file.wfbundle"), null);
>>>>> System.out.println("Annotations: " +
>>>>> wb.getAnnotations().size());
>>>>>
>>>>> What is the recommended way to get:
>>>>> - The description of a workflow (as I can see it on the myexperiment
>>>>> portal)
>>>>> - All the annotations in a bundle
>>>>> - The annotations of a given WorkflowBean element
>>>>> - To access/modify/extend the annotations
>>>>>
>>>>> I am using release 0.15.0-incubating.
>>>>>
>>>>> Thank you in advance for your help,
>>>>>
>>>>> Enrico
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> —
>>>>> Enrico Daga (enridaga)
>>>>> http://www.enridaga.net <http://www.enridaga.net/>
>>>>> <http://www.enridaga.net/ <http://www.enridaga.net/>>
>>>>> Il budda e’ nel parco.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Stian Soiland-Reyes
>>>> Apache Taverna (incubating), Apache Commons RDF (incubating)
>>>> http://orcid.org/0000-0001-9842-9718 <http://orcid.org/0000-0001-9842-9718>
>>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
