Great! If you find the SNAPSHOT fixes things for you, we can look at bringing out a patch release soonish.
(We want to get the Command line out first but we are waiting for legal clearance) On 10 May 2016 at 10:16, Enrico Daga (enridaga) <[email protected]> wrote: > Dear Stian, > > (sorry for this late reply, I’ve been away for few days) > > I understand the problem from your explanation. I really appreciate you > integrated the workaround in the current master. > I am OK on using the SNAPSHOT release for the time being, and happy to report > any issues I might find. > > Again, thank you for the help. > > Best > > Enrico > > > — > Enrico Daga (enridaga) > http://www.enridaga.net <http://www.enridaga.net/> > Il budda e’ nel parco. > > > > > >> On 4 May 2016, at 12:04, Stian Soiland-Reyes <[email protected]> wrote: >> >> 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 > -- Stian Soiland-Reyes Apache Taverna (incubating), Apache Commons RDF (incubating) http://orcid.org/0000-0001-9842-9718
