Great! Note it does not build with Java 7 (using docker run -it maven:3-jdk-7):
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-javadoc-plugin:2.10.3:jar (attach-javadocs) on project taverna-baclava-language: MavenReportException: Error while generating Javadoc: [ERROR] Exit code: 1 - javadoc: error - invalid flag: -Xdoclint:none I think because the -Xdoclint option is not recognized. However we don't claim it would BUILD with Java 7 - so that's OK. (it works with -Dmaven.javadoc.skip=true) But I guess also then our dependencies then can't be Java 8 in the Android profile.. for instance jena.version is set to 3.1.0 which requires JDK 8: root@fc2a5ed3ebd6:~/.m2/repository# file org/apache/jena/web/DatasetGraphAccessorBasic.class org/apache/jena/web/DatasetGraphAccessorBasic.class: compiled Java class data, version 52.0 On 23 September 2016 at 13:00, Ian Dunlop <[email protected]> wrote: > Hello, > > taverna-language pom profile added for android. Another default profile had > to be added as wel which you get if you do a normal mvn installl. For the > Android Java7 profile use: > > mvn -P android clean install > > If we decide to use this in the app then maybe we should ban Java8+ > features from some of the modules > > Cheers, > > Ian > > On 15 September 2016 at 11:48, Stian Soiland-Reyes <[email protected]> wrote: > >> I think you won't get the annotation content for the mimetype without also >> using >> https://taverna.incubator.apache.org/javadoc/taverna- >> language/org/apache/taverna/scufl2/annotation/AnnotationTools.html >> >> but that would add dependency on Jena, which latest versions require >> Java 7 and I'm not sure if it works well on Android. >> >> >> Perhaps using just the XSD mapping from taverna-scufl2-t2flow would be >> a bit easier? You still need to trundle through the annotations which >> in .t2flow were serialized in a perhaps awkward way (an annotation >> chain which then contains a set of revisioned annotations). >> >> >> >> On 15 September 2016 at 11:29, Ian Dunlop <[email protected]> wrote: >> > Hello, >> > >> > @sagar did you use the maven profile idea? If so could you send a pull >> > request so that we can keep this for the future. >> > >> > I've never used the scufl2-api. I did find >> > https://taverna.incubator.apache.org/javadoc/taverna- >> language/org/apache/taverna/scufl2/api/core/Workflow.html#getInputPorts-- >> > which has >> > https://taverna.incubator.apache.org/javadoc/taverna- >> language/org/apache/taverna/scufl2/api/common/Named.html#getName-- >> > I remember from way back that the mime types were hidden inside an >> > annotation on the port. So maybe try >> > https://taverna.incubator.apache.org/javadoc/taverna- >> language/org/apache/taverna/scufl2/api/common/AbstractNamed.html# >> getAnnotations-- >> > and have a look at what is there. >> > >> > Cheers, >> > >> > Ian >> > >> > On 15 September 2016 at 10:36, Sagar <[email protected]> wrote: >> > >> >> Hi, >> >> >> >> I have build taverna-scufl2-api as jar using java 7 . >> >> >> >> Can you tell me how to use it to get all input and output MIME type and >> >> their name? >> >> >> >> >> >> On Mon, Sep 12, 2016 at 6:05 PM, Stian Soiland-Reyes <[email protected]> >> >> wrote: >> >> >> >> > Thanks - from this I would say Taverna Mobile can target KitKat (API >> >> > level 19), get 80% share - which would rise by the time we release the >> >> > app. >> >> > >> >> > But that still grounds us on Java 6 features - and even in latest >> >> > Android SDK API the package java.nio.file is not there - so robundle >> >> > would not work anyway. >> >> > >> >> > On 8 September 2016 at 19:24, Gale Naylor < >> [email protected]> >> >> > wrote: >> >> > > Here is the distribution of Android API levels in use as of Aug 1: >> >> > > https://developer.android.com/about/dashboards/index.html >> >> > > >> >> > > According to this, only 15% of all Android devices are running API >> 23. >> >> > > >> >> > > >> >> > > On Thu, Sep 8, 2016 at 6:29 AM Ian Dunlop <[email protected]> >> >> wrote: >> >> > > >> >> > >> Hello, >> >> > >> >> >> > >> That page is typically clear as mud! I think it is implying that >> jdk 7 >> >> > is >> >> > >> fine for all API levels but for jdk 8 you need API 23 and (if >> special >> >> > >> language features required) a different compiler. So as long as we >> >> don't >> >> > >> use jdk 8 features we will be ok (maybe). I guess that means >> >> > >> taverna-language can be used (until we go all lambda crazy). >> >> > >> >> >> > >> Cheers, >> >> > >> >> >> > >> Ian >> >> > >> >> >> > >> On 8 September 2016 at 14:24, Stian Soiland-Reyes < >> [email protected]> >> >> > >> wrote: >> >> > >> >> >> > >> > I don't think we use any Java 8 features in taverna-language >> (e.g. >> >> > >> > Stream or lambdas) - but taverna-robundle use java.nio.Path from >> >> Java >> >> > >> > 7. I think it should be possible to make a subset of >> >> Taverna-language >> >> > >> > you need compile for JAva 6 (e.g. taverna-scufl2-api, >> >> > >> > taverna-scufl2-t2flow and taverna-scufl2-ucfpackage) - perhaps >> as a >> >> > >> > Maven profile? >> >> > >> > >> >> > >> > https://developer.android.com/guide/platform/j8-jack.html says >> you >> >> > can >> >> > >> > use Java 7/8 features from API level 23-24. >> >> > >> > >> >> > >> > How do we decide which Android API level we want to support..? >> >> > >> > >> >> > >> > On 8 September 2016 at 10:56, Sagar <[email protected]> >> >> > wrote: >> >> > >> > > Hi, >> >> > >> > > >> >> > >> > > I was reading the readme and I found Taverna-language-API will >> >> only >> >> > >> work >> >> > >> > > with JAVA 8 and newer. >> >> > >> > > We can't use in taverna-mobile because Android API 16 works >> with >> >> > JAVA >> >> > >> 6. >> >> > >> > > >> >> > >> > > So, Now provide me with the schema of the .t2flow file. >> >> > >> > > >> >> > >> > > Thanks >> >> > >> > > >> >> > >> > > On Thu, Sep 8, 2016 at 2:13 PM, Sagar < >> [email protected]> >> >> > >> wrote: >> >> > >> > > >> >> > >> > >> Hi, >> >> > >> > >> >> >> > >> > >> How can I use the taverna-language API to know what will the >> >> inputs >> >> > >> and >> >> > >> > >> what will the outputs of workflow? >> >> > >> > >> >> >> > >> > >> I don't get any proper guide or code. >> >> > >> > >> >> >> > >> > >> Thanks >> >> > >> > >> >> >> > >> > >> On Fri, Sep 2, 2016 at 6:37 PM, Stian Soiland-Reyes < >> >> > [email protected] >> >> > >> > >> >> > >> > >> wrote: >> >> > >> > >> >> >> > >> > >>> Yes, you should use taverna-language to load the .t2flow and >> >> > inspect >> >> > >> > it. >> >> > >> > >>> >> >> > >> > >>> You should not really need to make any Java beans for it as >> the >> >> > >> > >>> workflow wouldn't be constructed on the phone (although you >> >> could >> >> > do >> >> > >> > >>> that with the Taverna Language API), but loaded from >> $somewhere >> >> as >> >> > >> > >>> previously saved from the Taverna Workbench or downloaded >> from >> >> > >> > >>> myExperiment - however you can use the API to inspect the >> >> > workflow, >> >> > >> > >>> e.g. list the input port names of the main workflow. >> >> > >> > >>> >> >> > >> > >>> >> >> > >> > >>> See: >> >> > >> > >>> >> >> > >> > >>> https://taverna.incubator.apache.org/download/language/ >> >> > >> > >>> >> >> > >> > >>> Javadoc: >> >> > >> > >>> https://taverna.incubator.apache.org/javadoc/taverna-languag >> >> > >> > >>> e/org/apache/taverna/scufl2/api/package-summary.html >> >> > >> > >>> >> >> > >> > >>> Example: >> >> > >> > >>> https://github.com/apache/incubator-taverna-language/blob/ >> >> > >> > >>> master/taverna-scufl2-examples/src/main/java/org/apache/ >> >> > >> > >>> taverna/examples/ProcessorNames.java >> >> > >> > >>> >> >> > >> > >>> On 29 August 2016 at 14:39, Ian Dunlop <[email protected] >> > >> >> > wrote: >> >> > >> > >>> > Hello, >> >> > >> > >>> > >> >> > >> > >>> > There is an xsd for t2flow available in the >> taverna-language >> >> > module >> >> > >> > >>> > https://github.com/apache/incubator-taverna-language/blob/ >> >> > >> > >>> master/taverna-scufl2-t2flow/src/main/resources/org/apache/ >> >> > >> > >>> taverna/scufl2/translator/t2flow/xsd/t2flow.xsd >> >> > >> > >>> > You should be able to re-use taverna-language to parse >> t2flow >> >> > >> rather >> >> > >> > >>> than >> >> > >> > >>> > build your own parser. Perhaps using >> >> > >> > >>> > https://github.com/apache/incubator-taverna-language/tree/ >> >> > >> > >>> master/taverna-scufl2-t2flow. >> >> > >> > >>> > No readme though. Maybe some other devs can advise how to >> use >> >> > it. >> >> > >> > >>> > >> >> > >> > >>> > Cheers, >> >> > >> > >>> > >> >> > >> > >>> > Ian >> >> > >> > >>> > >> >> > >> > >>> > On 28 August 2016 at 18:23, Sagar < >> [email protected]> >> >> > >> wrote: >> >> > >> > >>> > >> >> > >> > >>> >> Hi, >> >> > >> > >>> >> >> >> > >> > >>> >> Is there any predefined tree structure for t2flow xml >> file ? >> >> > >> > >>> >> >> >> > >> > >>> >> if yes, then provide me so that I am able to create java >> >> beans >> >> > for >> >> > >> > it. >> >> > >> > >>> >> otherwise, I will create it according to any t2flow xml >> file. >> >> > >> > >>> >> >> >> > >> > >>> >> Please revert ASAP. >> >> > >> > >>> >> >> >> > >> > >>> >> Thanks >> >> > >> > >>> >> >> >> > >> > >>> >> On Fri, Aug 26, 2016 at 3:54 PM, Finn Bacall < >> >> > >> > >>> [email protected] >> >> > >> > >>> >> > >> >> > >> > >>> >> wrote: >> >> > >> > >>> >> >> >> > >> > >>> >> > This wouldn't be that hard to implement, you can get the >> >> > unique >> >> > >> ID >> >> > >> > >>> for >> >> > >> > >>> >> the >> >> > >> > >>> >> > workflow from the parser gem, see: >> >> > >> > >>> >> > >> >> > >> > >>> >> > https://github.com/myExperiment/workflow_parser- >> >> t2flow/blob/ >> >> > >> > >>> >> > master/lib/t2flow/model.rb#L136 >> >> > >> > >>> >> > >> >> > >> > >>> >> > Then you'd just need to extract it in the parsing >> method: >> >> > >> > >>> >> > >> >> > >> > >>> >> > https://github.com/myGrid/taverna-player-portal/blob/ >> >> master/ >> >> > >> > >>> >> > app/models/workflow.rb#L40 >> >> > >> > >>> >> > >> >> > >> > >>> >> > and store it in a new field in the database. >> >> > >> > >>> >> > >> >> > >> > >>> >> > Cheers, >> >> > >> > >>> >> > >> >> > >> > >>> >> > Finn >> >> > >> > >>> >> > >> >> > >> > >>> >> > >> >> > >> > >>> >> > On 26/08/2016 09:32, Ian Dunlop wrote: >> >> > >> > >>> >> > >> >> > >> > >>> >> >> Hello, >> >> > >> > >>> >> >> >> >> > >> > >>> >> >> I think you are pretty much spot on with your >> diagnosis. I >> >> > >> agree >> >> > >> > it >> >> > >> > >>> is a >> >> > >> > >>> >> >> bit of a pain that the workflow ids are different. >> >> However, >> >> > >> each >> >> > >> > >>> >> workflow >> >> > >> > >>> >> >> does have a unique uuid internally (with t2flow >> anyway) so >> >> > that >> >> > >> > >>> could be >> >> > >> > >>> >> >> used to check if a workflow on myexperiment and the >> portal >> >> > are >> >> > >> > the >> >> > >> > >>> same. >> >> > >> > >>> >> >> Look for the element <dataflow >> >> id="0f5e83c1-bbb5-42e7-9ba3- >> >> > >> > >>> >> 438f645d3d17" >> >> > >> > >>> >> >> role="top"> in a t2flow file. This probably means that >> the >> >> > >> portal >> >> > >> > >>> would >> >> > >> > >>> >> >> need an extension to search by workflow uuid. For now I >> >> > would >> >> > >> > just >> >> > >> > >>> treat >> >> > >> > >>> >> >> each run as having a unique workflow and we can always >> >> > improve >> >> > >> it >> >> > >> > >>> later. >> >> > >> > >>> >> >> >> >> > >> > >>> >> >> Cheers, >> >> > >> > >>> >> >> >> >> > >> > >>> >> >> Ian >> >> > >> > >>> >> >> >> >> > >> > >>> >> >> On 26 August 2016 at 08:02, Sagar < >> >> > [email protected]> >> >> > >> > >>> wrote: >> >> > >> > >>> >> >> >> >> > >> > >>> >> >> Hello, >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> Thank you for providing code. Now, I am working on it. >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> Currently, I have understood that I need following >> steps >> >> to >> >> > >> run >> >> > >> > a >> >> > >> > >>> >> >>> workflow >> >> > >> > >>> >> >>> on taverna player portal >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> 1) Download workflow content. >> >> > >> > >>> >> >>> 2) Upload it to taverna player portal. >> >> > >> > >>> >> >>> 3) Run it on taverna player portal. >> >> > >> > >>> >> >>> 4) Show output of the complete workflow's run. >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> I have also understood that there is no link between >> >> > >> > myExperiment >> >> > >> > >>> >> >>> workflow >> >> > >> > >>> >> >>> and Taverna Player workflow that's why I can't retain >> >> > >> > >>> myExperiment's >> >> > >> > >>> >> >>> workflow running history on Taverna player portal and >> >> also >> >> > I >> >> > >> > can't >> >> > >> > >>> >> search >> >> > >> > >>> >> >>> the same workflow in taverna player portal. For each >> new >> >> > run, >> >> > >> I >> >> > >> > >>> have to >> >> > >> > >>> >> >>> upload it again. >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> If I have understood correct then Please revert back . >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> If not then, Please correct me. >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> Thanks >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> On Wed, Aug 24, 2016 at 8:48 PM, Ian Dunlop < >> >> > >> > [email protected]> >> >> > >> > >>> >> >>> wrote: >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> Hello, >> >> > >> > >>> >> >>>> >> >> > >> > >>> >> >>>> This is where the upload code is in the current >> mobile >> >> > code >> >> > >> > >>> >> >>>> https://github.com/apache/ >> >> incubator-taverna-mobile/blob/ >> >> > >> > >>> >> >>>> 4daa91d3f42b5a4474303fd39c7a7e >> >> > c1483cebff/app/src/main/java/ >> >> > >> > >>> >> >>>> org/apache/taverna/mobile/fragments/workflowdetails/ >> >> > >> > >>> >> >>>> WorkflowdetailFragment.java#L655 >> >> > >> > >>> >> >>>> >> >> > >> > >>> >> >>>> Cheers, >> >> > >> > >>> >> >>>> >> >> > >> > >>> >> >>>> Ian >> >> > >> > >>> >> >>>> >> >> > >> > >>> >> >>>> On 24 August 2016 at 14:40, Ian Dunlop < >> >> > [email protected] >> >> > >> > >> >> > >> > >>> wrote: >> >> > >> > >>> >> >>>> >> >> > >> > >>> >> >>>> Hello, >> >> > >> > >>> >> >>>>> >> >> > >> > >>> >> >>>>> That upload code should already be available in the >> >> > mobile >> >> > >> > app. >> >> > >> > >>> >> Larry, >> >> > >> > >>> >> >>>>> myself and Finn spent a few hours figuring all that >> >> stuff >> >> > >> out >> >> > >> > >>> last >> >> > >> > >>> >> time >> >> > >> > >>> >> >>>>> round. >> >> > >> > >>> >> >>>>> I have added an API call in the >> taverna-player-portal >> >> to >> >> > get >> >> > >> > the >> >> > >> > >>> runs >> >> > >> > >>> >> >>>>> >> >> > >> > >>> >> >>>> for >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>>> a user eg /users/1/runs. Pull request waiting in >> github >> >> > (hint >> >> > >> > hint >> >> > >> > >>> >> >>>>> >> >> > >> > >>> >> >>>> Finn). I >> >> > >> > >>> >> >>>> >> >> > >> > >>> >> >>>>> even added some tests. >> >> > >> > >>> >> >>>>> >> >> > >> > >>> >> >>>>> Cheers, >> >> > >> > >>> >> >>>>> >> >> > >> > >>> >> >>>>> Ian >> >> > >> > >>> >> >>>>> >> >> > >> > >>> >> >>>>> On 24 August 2016 at 10:57, Finn Bacall < >> >> > >> > >>> >> [email protected]> >> >> > >> > >>> >> >>>>> wrote: >> >> > >> > >>> >> >>>>> >> >> > >> > >>> >> >>>>> On 23/08/2016 11:38, Sagar wrote: >> >> > >> > >>> >> >>>>>> >> >> > >> > >>> >> >>>>>> Hi, >> >> > >> > >>> >> >>>>>>> >> >> > >> > >>> >> >>>>>>> I think there is some problem as mention below >> >> > >> > >>> >> >>>>>>> >> >> > >> > >>> >> >>>>>>> 1) How can I upload a workflow using API ? >> >> > >> > >>> >> >>>>>>> >> >> > >> > >>> >> >>>>>>> here's a gist of some Java code someone wrote to >> >> > upload a >> >> > >> > >>> workflow >> >> > >> > >>> >> to >> >> > >> > >>> >> >>>>>> >> >> > >> > >>> >> >>>>> the >> >> > >> > >>> >> >>>> >> >> > >> > >>> >> >>>>> portal: >> >> > >> > >>> >> >>>>>> https://gist.github.com/larrytech7/ >> >> 957cc61a3bdd82e3e030 >> >> > >> > >>> >> >>>>>> >> >> > >> > >>> >> >>>>>> Basically the format is: >> >> > >> > >>> >> >>>>>> >> >> > >> > >>> >> >>>>>> { "workflow" : { "document" : >> >> > "data:application/octet- >> >> > >> > >>> >> >>>>>> >> >> > >> > >>> >> >>>>> stream;base64,<<<Insert >> >> > >> > >>> >> >>>> >> >> > >> > >>> >> >>>>> base64 encoded workflow here>>>" } } >> >> > >> > >>> >> >>>>>> >> >> > >> > >>> >> >>>>>> Finn >> >> > >> > >>> >> >>>>>> >> >> > >> > >>> >> >>>>>> >> >> > >> > >>> >> >>>>> >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> -- >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> *With warm regards * >> >> > >> > >>> >> >>> *Sincerely yours* >> >> > >> > >>> >> >>> Sagar >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> *Student ,(7th Semester )B.Tech IT and mathematical >> >> > >> innovation* >> >> > >> > >>> >> >>> *Cluster Innovation Centre* >> >> > >> > >>> >> >>> *University of Delhi * >> >> > >> > >>> >> >>> >> >> > >> > >>> >> >>> >> >> > >> > >>> >> > >> >> > >> > >>> >> >> >> > >> > >>> >> >> >> > >> > >>> >> -- >> >> > >> > >>> >> >> >> > >> > >>> >> *With warm regards * >> >> > >> > >>> >> *Sincerely yours* >> >> > >> > >>> >> Sagar >> >> > >> > >>> >> >> >> > >> > >>> >> >> >> > >> > >>> >> *Student ,(7th Semester )B.Tech IT and mathematical >> >> innovation* >> >> > >> > >>> >> *Cluster Innovation Centre* >> >> > >> > >>> >> *University of Delhi * >> >> > >> > >>> >> >> >> > >> > >>> >> >> > >> > >>> >> >> > >> > >>> >> >> > >> > >>> -- >> >> > >> > >>> Stian Soiland-Reyes >> >> > >> > >>> Apache Taverna (incubating), Apache Commons >> >> > >> > >>> http://orcid.org/0000-0001-9842-9718 >> >> > >> > >>> >> >> > >> > >> >> >> > >> > >> >> >> > >> > >> >> >> > >> > >> -- >> >> > >> > >> >> >> > >> > >> *With warm regards * >> >> > >> > >> *Sincerely yours* >> >> > >> > >> Sagar >> >> > >> > >> >> >> > >> > >> >> >> > >> > >> *Student ,(7th Semester )B.Tech IT and mathematical >> innovation* >> >> > >> > >> *Cluster Innovation Centre* >> >> > >> > >> *University of Delhi * >> >> > >> > >> >> >> > >> > >> >> >> > >> > > >> >> > >> > > >> >> > >> > > -- >> >> > >> > > >> >> > >> > > *With warm regards * >> >> > >> > > *Sincerely yours* >> >> > >> > > Sagar >> >> > >> > > >> >> > >> > > >> >> > >> > > *Student ,(7th Semester )B.Tech IT and mathematical innovation* >> >> > >> > > *Cluster Innovation Centre* >> >> > >> > > *University of Delhi * >> >> > >> > >> >> > >> > >> >> > >> > >> >> > >> > -- >> >> > >> > Stian Soiland-Reyes >> >> > >> > http://orcid.org/0000-0001-9842-9718 >> >> > >> > >> >> > >> >> >> > >> >> > >> >> > >> >> > -- >> >> > Stian Soiland-Reyes >> >> > http://orcid.org/0000-0001-9842-9718 >> >> > >> >> >> >> >> >> >> >> -- >> >> >> >> *With warm regards * >> >> *Sincerely yours* >> >> Sagar >> >> >> >> >> >> *Student ,(7th Semester )B.Tech IT and mathematical innovation* >> >> *Cluster Innovation Centre* >> >> *University of Delhi * >> >> >> >> >> >> -- >> Stian Soiland-Reyes >> http://orcid.org/0000-0001-9842-9718 >> -- Stian Soiland-Reyes http://orcid.org/0000-0001-9842-9718
