├── .gitignore ├── .travis.yml ├── DEPENDENCIES ├── DISCLAIMER ├── LICENSE ├── NOTICE ├── README.md ├── pom.xml ├── taverna-baclava-language ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── baclava │ │ │ ├── BaclavaReader.java │ │ │ └── BaclavaWriter.java │ └── resources │ │ └── xsd │ │ ├── baclava.xsd │ │ └── xscufl.xsd │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── baclava │ │ ├── TestExample1.java │ │ └── TestRoundTrip.java │ └── resources │ ├── example1.xml │ └── example2.xml ├── taverna-databundle ├── README.md ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── apache │ │ └── taverna │ │ └── databundle │ │ ├── DataBundles.java │ │ └── ErrorDocument.java │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── databundle │ │ ├── TestDataBundles.java │ │ └── TestExample.java │ └── resources │ └── full-example │ └── ebi-wfrun-2013-05-31 │ ├── Graphical_output.png │ ├── Workflow16_getStatus_output_status.txt │ ├── email.txt │ ├── getResult_3_output_output.xml │ ├── getResult_output_output.octet-stream │ ├── intermediates │ ├── 11 │ │ └── 111e5771-37b7-4ef8-9888-e50eadbc2a5c.txt │ ├── 13 │ │ └── 132a7e6c-1857-4ad6-8252-5f747f6f0feb.txt │ ├── 14 │ │ ├── 147eda4d-f40f-418b-bca2-dc12e19122de.txt │ │ └── 14b9027d-11bb-4586-bff7-89130856409b.txt │ ├── 18 │ │ └── 18d41521-e314-4122-a4ff-cb7718982935.txt │ ├── 21 │ │ └── 219626eb-a4fc-4c83-9132-67b2b40d5a68.txt │ ├── 26 │ │ └── 268a47b4-34aa-42d0-96ad-98b99601a4e5.txt │ ├── 28 │ │ └── 28ccca88-6e06-4d5a-a43e-93ad263c6abd.txt │ ├── 32 │ │ └── 321106aa-13f1-49e5-a10b-bf08693f7df6.txt │ ├── 37 │ │ └── 3792ebd6-6210-4af9-bc3f-74e3934a52ef.txt │ ├── 51 │ │ └── 51845ad9-e0a3-4094-8ce8-f2f5bd06e61e.txt │ ├── 67 │ │ └── 67958fa2-98dd-4f82-b9f6-96537cea9528.txt │ ├── 71 │ │ └── 71540c58-5ff6-4dee-a26e-f1360b135e54.txt │ ├── 73 │ │ └── 731b11bb-a3be-4054-b1e4-3331a8f3c0c0.txt │ ├── 77 │ │ └── 77ede682-e556-4d89-b429-219adfbe48be.txt │ ├── 86 │ │ ├── 8618bc0b-9852-457d-b0b7-16af5526faaf.txt │ │ └── 864a72a6-34b8-4d74-86f7-4b6ccfe91a1f.txt │ ├── 91 │ │ └── 91fdc8e6-159e-495e-842a-ef51fe3ec534.txt │ ├── 94 │ │ ├── 94a5377e-5752-433c-aa8b-c39bb461505f.txt │ │ └── 94d65aea-ed02-488c-aa38-d3b9840e4b65.txt │ ├── 00 │ │ └── 00548907-43e1-4484-9582-bfa8727d44ca.txt │ ├── 07 │ │ └── 079d289b-796e-45cf-a759-82f91a0aa3d5.txt │ ├── 0a │ │ └── 0a2b3aa2-5b11-433d-b48f-1009424bb486.txt │ ├── 0b │ │ └── 0bd05e27-46d6-4de5-b76b-0988638f9231.txt │ ├── 0c │ │ └── 0c29c209-b442-49c5-bee2-5b5efdacad0e.txt │ ├── 0f │ │ └── 0f93d00f-131b-42ec-bbba-22b50582903e.txt │ ├── 1f │ │ └── 1f536bcf-ba43-44ec-a983-b30a45f2b739.txt │ ├── 2a │ │ ├── 2a8831af-c11f-4d0e-be9d-d90c170c1002.txt │ │ └── 2a91a135-c649-4735-a02f-6db45b9c847e.txt │ ├── 3d │ │ └── 3df7b202-58f3-4425-b063-4f4f7ab4cd5a.txt │ ├── 4a │ │ └── 4acb798d-0fd2-4b9c-91e5-587e5aa8366a.txt │ ├── 5a │ │ └── 5aec892f-fad5-4f90-b1c1-8241b8917f8b.txt │ ├── 5b │ │ ├── 5b5357f1-3062-43ab-adab-e0f3e3721dcc.txt │ │ ├── 5b8444ec-0592-4154-8f02-638c79f4171a.txt │ │ └── 5bb72df1-fc1d-43d8-9206-dcab6ced0437.txt │ ├── 5d │ │ └── 5d572af1-f6fb-48a4-b338-a7ce140932ec.txt │ ├── 7c │ │ └── 7ceba67b-46e2-4c4b-9cec-e5f0e11c43e9.txt │ ├── 7e │ │ └── 7e7ee056-5a86-45a3-b4e6-e8de44679922.txt │ ├── 8c │ │ └── 8c50b1fe-e91e-4840-86af-ec99c2b04a67.txt │ ├── 8e │ │ └── 8ed106dd-7ada-4d61-a3f6-01740454cd76.txt │ ├── a2 │ │ └── a217d73f-1843-4162-9bae-a5b05541b538.txt │ ├── a5 │ │ └── a58b2fcd-fb4c-4445-be36-b5c00b96a813.txt │ ├── a7 │ │ ├── a746bcfc-5d24-48ae-a12f-e3d285ed3b4d.txt │ │ └── a7c9ef28-f3de-4566-aac6-90d5fa20318a.txt │ ├── a8 │ │ └── a8fba0e7-10a6-4fed-afd9-3a15fd24ba8e.txt │ ├── ad │ │ └── add43936-5cc3-4635-bc4e-dc64a6664dd8.txt │ ├── b0 │ │ └── b07b9f2f-e0c1-4ec0-ba83-102d18e3cf11.txt │ ├── b3 │ │ └── b3dd41e8-e94b-4e14-9080-1e44efa8ab66.txt │ ├── b5 │ │ └── b5a4997d-d390-4d62-820c-85018453186f.txt │ ├── b8 │ │ └── b8685135-065a-409c-9c11-1fedbd61bb90.txt │ ├── c4 │ │ └── c4776372-5fa1-4b05-92bc-585ccb4344af.txt │ ├── cc │ │ └── cc26451d-53c7-490d-8d9f-ac7a1f45e30e.txt │ ├── d3 │ │ └── d34be34f-e857-46ee-8ee2-5c3384e05655.txt │ ├── d6 │ │ └── d69fe838-97dd-43cc-9a08-567cfb842f1a.txt │ ├── da │ │ └── dac12490-1cbc-4607-a825-40f121f69fc4.txt │ ├── f2 │ │ └── f273b491-edd2-4e18-aba5-106279f491d8.txt │ └── f7 │ │ └── f7e2a950-6426-4e3f-b9f0-844bfae9ed96.txt │ ├── sequence.txt │ └── workflowrun.prov.ttl ├── taverna-ro-vocabs ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── ro │ │ └── vocabs │ │ ├── bundle.java │ │ ├── foaf.java │ │ ├── oa.java │ │ ├── ore.java │ │ ├── package-info.java │ │ ├── pav.java │ │ ├── prov.java │ │ ├── ro.java │ │ ├── roevo.java │ │ ├── roterms.java │ │ ├── wf4ever.java │ │ ├── wfdesc.java │ │ └── wfprov.java │ └── resources │ └── ontologies │ ├── bundle.owl │ ├── oa.rdf │ └── ore-owl.owl ├── taverna-robundle ├── README.md ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── robundle │ │ │ ├── Bundle.java │ │ │ ├── Bundles.java │ │ │ ├── fs │ │ │ ├── BundleFileStore.java │ │ │ ├── BundleFileSystem.java │ │ │ ├── BundleFileSystemProvider.java │ │ │ ├── BundleFileTypeDetector.java │ │ │ └── BundlePath.java │ │ │ ├── manifest │ │ │ ├── Agent.java │ │ │ ├── Manifest.java │ │ │ ├── PathAnnotation.java │ │ │ ├── PathMetadata.java │ │ │ ├── Proxy.java │ │ │ ├── RDFToManifest.java │ │ │ ├── combine │ │ │ │ └── CombineManifest.java │ │ │ └── odf │ │ │ │ ├── ODFJaxb.java │ │ │ │ └── ODFManifest.java │ │ │ ├── utils │ │ │ ├── PathHelper.java │ │ │ ├── RDFUtils.java │ │ │ ├── RecursiveCopyFileVisitor.java │ │ │ ├── RecursiveDeleteVisitor.java │ │ │ └── TemporaryFiles.java │ │ │ └── validator │ │ │ ├── RoValidator.java │ │ │ └── ValidationReport.java │ ├── resources │ │ ├── META-INF │ │ │ ├── LICENSE │ │ │ ├── LICENSE.w3c.19980720 │ │ │ ├── LICENSE.w3c.20021231 │ │ │ └── services │ │ │ │ ├── java.nio.file.spi.FileSystemProvider │ │ │ │ └── java.nio.file.spi.FileTypeDetector │ │ ├── contexts │ │ │ └── bundle.jsonld │ │ └── jarcache.json │ └── xsd │ │ ├── binding.xjb │ │ ├── combine.xsd │ │ ├── container.xsd │ │ ├── manifest.xsd │ │ ├── xenc-schema.xsd │ │ └── xmldsig-core-schema.xsd │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── robundle │ │ ├── TestBundles.java │ │ ├── TestExample.java │ │ ├── fs │ │ ├── Helper.java │ │ ├── MemoryEfficiencyIT.java │ │ ├── TestBundleFileSystem.java │ │ ├── TestBundleFileTypeDetector.java │ │ ├── TestBundlePaths.java │ │ ├── TestFileSystemProvider.java │ │ └── TestZipFS.java │ │ ├── manifest │ │ ├── TestManifest.java │ │ ├── TestManifestJSON.java │ │ ├── TestRDFToManifest.java │ │ ├── combine │ │ │ └── TestCombineManifest.java │ │ ├── odf │ │ │ └── TestODFManifest.java │ │ └── utils │ │ │ ├── TestRecursiveCopyFileVisitor.java │ │ │ ├── TestRecursiveCopyFileVisitorInBundle.java │ │ │ └── TestRecursiveCopyFileVisitorMultipleBundles.java │ │ └── validator │ │ └── ValidatorTest.java │ └── resources │ ├── bag-of-bags-manifest.json │ ├── combine │ ├── Boris-skeleton.omex │ ├── DirectoryMadness-skeleton.omex │ ├── DirectoryMadnessZipped-skeleton.omex │ ├── aslanidi_purkinje_model_skeleton.zip │ ├── jwsonline-broken-date.sedx │ └── jwsonline-fixed-date.sedx │ ├── document.odt │ ├── helloworld.wfbundle │ ├── manifest.json │ ├── win8.url │ └── workflowrun.bundle.zip ├── taverna-scufl2-annotation ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── apache │ │ └── taverna │ │ └── scufl2 │ │ └── annotation │ │ └── AnnotationTools.java │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── scufl2 │ │ └── annotation │ │ └── TestAnnotationTools.java │ └── resources │ ├── helloanyone.t2flow │ └── valid_component_imagemagickconvert.t2flow ├── taverna-scufl2-api ├── .gitignore ├── README.md ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── scufl2 │ │ │ ├── api │ │ │ ├── activity │ │ │ │ ├── Activity.java │ │ │ │ └── package-info.java │ │ │ ├── annotation │ │ │ │ ├── Annotation.java │ │ │ │ ├── Revision.java │ │ │ │ ├── Revisioned.java │ │ │ │ └── package-info.java │ │ │ ├── common │ │ │ │ ├── AbstractCloneable.java │ │ │ │ ├── AbstractNamed.java │ │ │ │ ├── AbstractRevisioned.java │ │ │ │ ├── Child.java │ │ │ │ ├── Configurable.java │ │ │ │ ├── Named.java │ │ │ │ ├── NamedSet.java │ │ │ │ ├── Ported.java │ │ │ │ ├── Root.java │ │ │ │ ├── Scufl2Tools.java │ │ │ │ ├── Typed.java │ │ │ │ ├── URITools.java │ │ │ │ ├── Visitor.java │ │ │ │ ├── WorkflowBean.java │ │ │ │ └── package-info.java │ │ │ ├── configurations │ │ │ │ └── Configuration.java │ │ │ ├── container │ │ │ │ ├── WorkflowBundle.java │ │ │ │ └── package-info.java │ │ │ ├── core │ │ │ │ ├── BlockingControlLink.java │ │ │ │ ├── ControlLink.java │ │ │ │ ├── DataLink.java │ │ │ │ ├── Processor.java │ │ │ │ ├── Workflow.java │ │ │ │ └── package-info.java │ │ │ ├── impl │ │ │ │ ├── IterableComparator.java │ │ │ │ ├── LazyMap.java │ │ │ │ └── NullSafeComparator.java │ │ │ ├── io │ │ │ │ ├── ReaderException.java │ │ │ │ ├── WorkflowBundleIO.java │ │ │ │ ├── WorkflowBundleReader.java │ │ │ │ ├── WorkflowBundleWriter.java │ │ │ │ ├── WriterException.java │ │ │ │ └── structure │ │ │ │ │ ├── StructureReader.java │ │ │ │ │ └── StructureWriter.java │ │ │ ├── iterationstrategy │ │ │ │ ├── CrossProduct.java │ │ │ │ ├── DotProduct.java │ │ │ │ ├── IterationStrategyNode.java │ │ │ │ ├── IterationStrategyParent.java │ │ │ │ ├── IterationStrategyStack.java │ │ │ │ ├── IterationStrategyTopNode.java │ │ │ │ ├── PortNode.java │ │ │ │ └── package-info.java │ │ │ ├── package-info.java │ │ │ ├── port │ │ │ │ ├── AbstractDepthPort.java │ │ │ │ ├── AbstractGranularDepthPort.java │ │ │ │ ├── ActivityPort.java │ │ │ │ ├── DepthPort.java │ │ │ │ ├── GranularDepthPort.java │ │ │ │ ├── InputActivityPort.java │ │ │ │ ├── InputPort.java │ │ │ │ ├── InputProcessorPort.java │ │ │ │ ├── InputWorkflowPort.java │ │ │ │ ├── OutputActivityPort.java │ │ │ │ ├── OutputPort.java │ │ │ │ ├── OutputProcessorPort.java │ │ │ │ ├── OutputWorkflowPort.java │ │ │ │ ├── Port.java │ │ │ │ ├── ProcessorPort.java │ │ │ │ ├── ReceiverPort.java │ │ │ │ ├── SenderPort.java │ │ │ │ ├── WorkflowPort.java │ │ │ │ └── package-info.java │ │ │ ├── profiles │ │ │ │ ├── ProcessorBinding.java │ │ │ │ ├── ProcessorInputPortBinding.java │ │ │ │ ├── ProcessorOutputPortBinding.java │ │ │ │ ├── ProcessorPortBinding.java │ │ │ │ ├── Profile.java │ │ │ │ └── package-info.java │ │ │ └── reference │ │ │ │ └── package-info.java │ │ │ └── validation │ │ │ ├── Status.java │ │ │ ├── ValidationException.java │ │ │ ├── ValidationProblem.java │ │ │ ├── ValidationReport.java │ │ │ ├── Validator.java │ │ │ ├── WorkflowBeanReport.java │ │ │ ├── correctness │ │ │ ├── CorrectnessValidationListener.java │ │ │ ├── CorrectnessValidator.java │ │ │ ├── CorrectnessVisitor.java │ │ │ ├── DefaultCorrectnessValidationListener.java │ │ │ ├── DefaultDispatchingVisitor.java │ │ │ ├── DispatchingVisitor.java │ │ │ ├── ReportCorrectnessValidationListener.java │ │ │ └── report │ │ │ │ ├── EmptyIterationStrategyTopNodeProblem.java │ │ │ │ ├── IncompatibleGranularDepthProblem.java │ │ │ │ ├── MismatchConfigurableTypeProblem.java │ │ │ │ ├── NegativeValueProblem.java │ │ │ │ ├── NonAbsoluteURIProblem.java │ │ │ │ ├── NullFieldProblem.java │ │ │ │ ├── OutOfScopeValueProblem.java │ │ │ │ ├── PortMentionedTwiceProblem.java │ │ │ │ ├── PortMissingFromIterationStrategyStackProblem.java │ │ │ │ └── WrongParentProblem.java │ │ │ └── structural │ │ │ ├── DefaultStructuralValidationListener.java │ │ │ ├── ReportStructuralValidationListener.java │ │ │ ├── StructuralValidationListener.java │ │ │ ├── StructuralValidator.java │ │ │ ├── ValidatorState.java │ │ │ └── report │ │ │ ├── DotProductIterationMismatchProblem.java │ │ │ ├── EmptyCrossProductProblem.java │ │ │ ├── EmptyDotProductProblem.java │ │ │ ├── FailedProcessorProblem.java │ │ │ ├── IncompleteWorkflowProblem.java │ │ │ ├── MissingIterationStrategyStackProblem.java │ │ │ ├── MissingMainIncomingDataLinkProblem.java │ │ │ ├── UnrecognizedIterationStrategyNodeProblem.java │ │ │ ├── UnresolvedOutputProblem.java │ │ │ └── UnresolvedProcessorProblem.java │ └── resources │ │ └── META-INF │ │ ├── services │ │ ├── org.apache.taverna.scufl2.api.io.WorkflowBundleReader │ │ └── org.apache.taverna.scufl2.api.io.WorkflowBundleWriter │ │ └── spring │ │ ├── scufl2-api-context-osgi.xml │ │ └── scufl2-api-context.xml │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── scufl2 │ │ ├── api │ │ ├── EqualsOnArrayListsTest.java │ │ ├── ExampleWorkflow.java │ │ ├── TestAPICreation.java │ │ ├── TestAbstractRevisioned.java │ │ ├── TestExampleWorkflow.java │ │ ├── VisitorTest.java │ │ ├── annotation │ │ │ └── TestAnnotations.java │ │ ├── common │ │ │ ├── AllBeansVisitor.java │ │ │ ├── TestAbstractCloneable.java │ │ │ ├── TestAbstractNamed.java │ │ │ ├── TestScufl2Tools.java │ │ │ ├── TestSetParent.java │ │ │ ├── TestURITools.java │ │ │ ├── TestURIToolsBeans.java │ │ │ └── TestURIToolsResolve.java │ │ ├── configurations │ │ │ └── ConfigurationTest.java │ │ ├── container │ │ │ └── TestWorkflowBundleEquals.java │ │ ├── core │ │ │ ├── ControlLinkCompareTest.java │ │ │ ├── DataLinkCompareTest.java │ │ │ └── PortOrderTest.java │ │ ├── impl │ │ │ ├── TestIterableComparator.java │ │ │ └── TestNullCompare.java │ │ └── io │ │ │ ├── TestResources.java │ │ │ ├── TestStructureReader.java │ │ │ └── TestWorkflowBundleIO.java │ │ └── validation │ │ ├── correctness │ │ ├── DummyProfile.java │ │ ├── DummyWorkflow.java │ │ ├── DummyWorkflowBundle.java │ │ ├── TestAbstractDepthPort.java │ │ ├── TestAbstractGranularDepthPort.java │ │ ├── TestBlockingControlLink.java │ │ ├── TestChild.java │ │ ├── TestConfiguration.java │ │ ├── TestDataLink.java │ │ ├── TestIterationStrategyStack.java │ │ ├── TestIterationStrategyTopNode.java │ │ ├── TestNamed.java │ │ ├── TestPortNode.java │ │ ├── TestPorted.java │ │ ├── TestProcessor.java │ │ ├── TestProcessorBinding.java │ │ ├── TestProcessorInputPortBinding.java │ │ ├── TestProcessorOutputPortBinding.java │ │ ├── TestProfile.java │ │ ├── TestRoot.java │ │ ├── TestTyped.java │ │ ├── TestWorkflow.java │ │ └── TestWorkflowBundle.java │ │ └── structural │ │ ├── CrossProductTest.java │ │ ├── DepthInheritanceTest.java │ │ ├── DotProductTest.java │ │ ├── StagedCombinationTest.java │ │ └── WorkflowTest.java │ └── resources │ ├── org │ └── apache │ │ └── taverna │ │ └── scufl2 │ │ └── api │ │ └── io │ │ └── HelloWorld.txt │ └── roevo-test.ttl ├── taverna-scufl2-cwl ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── scufl2 │ │ │ └── cwl │ │ │ ├── CWLParser.java │ │ │ ├── CWLReader.java │ │ │ ├── Converter.java │ │ │ ├── TavernaConverter.java │ │ │ ├── WorkflowParser.java │ │ │ ├── YAMLHelper.java │ │ │ └── components │ │ │ ├── CommandLineTool.java │ │ │ ├── InputPort.java │ │ │ ├── OutputPort.java │ │ │ ├── PortDetail.java │ │ │ ├── Process.java │ │ │ ├── ProcessFactory.java │ │ │ ├── Reference.java │ │ │ ├── Step.java │ │ │ └── WorkflowProcess.java │ └── resources │ │ ├── META-INF │ │ └── services │ │ │ └── org.apache.taverna.scufl2.api.io.WorkflowBundleReader │ │ └── hello_world.cwl │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── scufl2 │ │ └── cwl │ │ ├── TestConverting.java │ │ ├── TestParser.java │ │ ├── TestTavernaConverter.java │ │ ├── TestWorkflowNesting.java │ │ └── TestWorkflowProcess.java │ └── resources │ ├── 1st-tool.cwl │ ├── hello_world.cwl │ ├── int_input.cwl │ ├── simple_string_input.cwl │ ├── workflow_with_command.cwl │ └── workflow_with_workflow.cwl ├── taverna-scufl2-examples ├── README.md ├── examples │ ├── helloanyone.json │ ├── helloanyone.t2flow │ ├── helloanyone.wfbundle │ ├── helloworld.json │ ├── helloworld.t2flow │ └── helloworld.wfbundle ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── examples │ │ │ ├── ConvertT2flowToWorkflowBundle.java │ │ │ ├── JsonExport.java │ │ │ ├── ProcessorNames.java │ │ │ ├── ServiceTypes.java │ │ │ └── WorkflowMaker.java │ ├── python │ │ └── processorNames.py │ ├── resources │ │ └── context.json │ └── ruby │ │ └── processors.rb │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── examples │ │ ├── TestConvertT2flowScufl2.java │ │ ├── TestJsonExport.java │ │ ├── TestProcessorNames.java │ │ └── TestServiceTypes.java │ └── resources │ └── workflows │ ├── t2flow │ ├── as.t2flow │ ├── defaultActivitiesTaverna2.2.t2flow │ ├── helloanyone.t2flow │ └── helloworld.t2flow │ └── wfbundle │ ├── as.wfbundle │ └── defaultActivitiesTaverna2.wfbundle ├── taverna-scufl2-integration-tests ├── pom.xml └── src │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── scufl2 │ │ ├── integration │ │ ├── CloningIT.java │ │ └── TestSimpleWf.java │ │ └── translator │ │ └── t2flow │ │ ├── EmptyStackIT.java │ │ ├── LiteralNamespacesIT.java │ │ └── PropertyListRoundtripIT.java │ └── resources │ ├── apiconsumer.t2flow │ ├── clone-error.wfbundle │ ├── rest.t2flow │ ├── t172starterpacklist │ └── t230starterpacklist ├── taverna-scufl2-schemas ├── pom.xml └── src │ └── main │ └── resources │ ├── META-INF │ ├── LICENSE │ └── LICENSE.w3c.document │ └── org │ └── apache │ └── taverna │ └── scufl2 │ ├── rdf │ ├── scufl2.rdf │ ├── scufl2.ttl │ ├── taverna-2.2.rdf │ └── taverna-2.2.ttl │ └── rdfxml │ └── xsd │ ├── owl.xsd │ ├── prov.xsd │ ├── rdf.xsd │ ├── rdfs.xsd │ ├── roevo.xsd │ ├── scufl2.xsd │ └── xml.xsd ├── taverna-scufl2-scufl ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── scufl2 │ │ │ └── translator │ │ │ └── scufl │ │ │ ├── ParserState.java │ │ │ ├── ScuflExtensionParser.java │ │ │ ├── ScuflParser.java │ │ │ ├── ScuflReader.java │ │ │ └── processorelement │ │ │ ├── AbstractExtensionParser.java │ │ │ ├── AbstractProcessorExtensionParser.java │ │ │ ├── ApiConsumerExtensionParser.java │ │ │ ├── BeanshellExtensionParser.java │ │ │ ├── BiomartExtensionParser.java │ │ │ ├── BiomobyExtensionParser.java │ │ │ ├── LocalExtensionParser.java │ │ │ ├── RshellExtensionParser.java │ │ │ ├── SoaplabExtensionParser.java │ │ │ ├── StringConstantExtensionParser.java │ │ │ └── WsdlExtensionParser.java │ └── resources │ │ ├── META-INF │ │ └── services │ │ │ ├── org.apache.taverna.scufl2.api.io.WorkflowBundleReader │ │ │ └── org.apache.taverna.scufl2.translator.scufl.ScuflExtensionParser │ │ └── org │ │ └── apache │ │ └── taverna │ │ └── scufl2 │ │ └── translator │ │ └── scufl │ │ └── xsd │ │ ├── scufl-abstract.xsd │ │ ├── scufl-apiconsumer.xsd │ │ ├── scufl-beanshell.xsd │ │ ├── scufl-biomart.xsd │ │ ├── scufl-biomoby.xsd │ │ ├── scufl-dependency.xsd │ │ ├── scufl-inferno.xsd │ │ ├── scufl-local.xsd │ │ ├── scufl-notification.xsd │ │ ├── scufl-rshell.xsd │ │ ├── scufl-soaplab.xsd │ │ ├── scufl-stringconstant.xsd │ │ ├── scufl-wsdl.xsd │ │ └── scufl.xsd │ └── test │ └── java │ └── org │ └── apache │ └── taverna │ └── scufl2 │ └── translator │ └── scufl2 │ └── TestStarterPack.java ├── taverna-scufl2-t2flow ├── .gitignore ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── scufl2 │ │ │ └── translator │ │ │ └── t2flow │ │ │ ├── ParserState.java │ │ │ ├── T2FlowParser.java │ │ │ ├── T2FlowReader.java │ │ │ ├── T2Parser.java │ │ │ ├── defaultactivities │ │ │ ├── AbstractActivityParser.java │ │ │ ├── ApiConsomerActivityParser.java │ │ │ ├── BeanshellActivityParser.java │ │ │ ├── BiomartActivityParser.java │ │ │ ├── BiomobyActivityParser.java │ │ │ ├── ComponentActivityParser.java │ │ │ ├── DataflowActivityParser.java │ │ │ ├── InteractionActivityParser.java │ │ │ ├── RshellActivityParser.java │ │ │ ├── SoaplabActivityParser.java │ │ │ ├── SpreadsheetActivityParser.java │ │ │ ├── StringConstantActivityParser.java │ │ │ ├── WSDLActivityParser.java │ │ │ └── WSDLXMLSplitterParser.java │ │ │ ├── defaultdispatchstack │ │ │ ├── ErrorBounceParser.java │ │ │ ├── FailoverParser.java │ │ │ ├── InvokeParser.java │ │ │ ├── LoopParser.java │ │ │ ├── ParallelizeParser.java │ │ │ └── RetryParser.java │ │ │ └── t23activities │ │ │ ├── ExternalToolActivityParser.java │ │ │ ├── RESTActivityParser.java │ │ │ └── XPathActivityParser.java │ └── resources │ │ ├── META-INF │ │ ├── services │ │ │ ├── org.apache.taverna.scufl2.api.io.WorkflowBundleReader │ │ │ └── org.apache.taverna.scufl2.translator.t2flow.T2Parser │ │ └── spring │ │ │ ├── scufl2-t2flow-context-osgi.xml │ │ │ └── scufl2-t2flow-context.xml │ │ └── org │ │ └── apache │ │ └── taverna │ │ └── scufl2 │ │ └── translator │ │ └── t2flow │ │ └── xsd │ │ ├── componentactivity.xsd │ │ ├── externaltoolactivity.xsd │ │ ├── interactionactivity.xsd │ │ ├── restactivity.xsd │ │ ├── t2activities.xsd │ │ ├── t2annotations.xsd │ │ ├── t2flow-extended.xsd │ │ ├── t2flow.xsd │ │ ├── t2layers.xsd │ │ └── xpathactivity.xsd │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── scufl2 │ │ └── translator │ │ └── t2flow │ │ ├── MergeParsingTest.java │ │ ├── TestActivityParsing.java │ │ ├── TestActivityParsingRshell.java │ │ ├── TestAnnotationParsing.java │ │ ├── TestBeanshellActivityParser.java │ │ ├── TestComponentActivityParser.java │ │ ├── TestDispatchLayerParsing.java │ │ ├── TestFastaWorkflow.java │ │ ├── TestInteractionActivityParser.java │ │ ├── TestIterationStrategies.java │ │ ├── TestSpreadsheetActivityParser.java │ │ ├── TestT2FlowParser.java │ │ ├── TestT2FlowReader.java │ │ ├── TestT2FlowTranslator.java │ │ └── t23activities │ │ ├── TestRESTActivityParser.java │ │ └── TestXPathActivityParser.java │ └── resources │ ├── T3-1226-annotations-with-quotes.t2flow │ ├── annotated2.2.t2flow │ ├── annotation_with_backslash.t2flow │ ├── as.t2flow │ ├── as.txt │ ├── beanshell-deps.t2flow │ ├── component_simple.t2flow │ ├── dataflow_link_then_merge.t2flow │ ├── defaultActivitiesTaverna2.2.t2flow │ ├── dispatchlayers.t2flow │ ├── fasta_and_pscan.t2flow │ ├── fasta_pscan_and_dbfetch.t2flow │ ├── interaction-with-strange-loop.t2flow │ ├── interaction_multiple_choice.t2flow │ ├── interaction_simple_tell.t2flow │ ├── iterationstrategies.t2flow │ ├── merge_fun.t2flow │ ├── merge_then_dataflow_link.t2flow │ ├── missing_merge.t2flow │ ├── random.t2flow │ ├── rest-2-2.t2flow │ ├── rshell-2-2.t2flow │ ├── semantic_annotations__eclipse.t2flow │ ├── simple_fasta.t2flow │ ├── sleepers.t2flow │ ├── spreadsheet_activity_defaults_892.t2flow │ └── xpath_workflow.t2flow ├── taverna-scufl2-ucfpackage ├── .gitignore ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── apache │ │ └── taverna │ │ └── scufl2 │ │ └── ucfpackage │ │ ├── UCFPackage.java │ │ └── impl │ │ └── odfdom │ │ └── pkg │ │ ├── OdfPackage.java │ │ ├── OdfPackageStream.java │ │ ├── OdfXMLHelper.java │ │ ├── StreamHelper.java │ │ ├── TempDir.java │ │ ├── TempDirDeleter.java │ │ └── manifest │ │ ├── Algorithm.java │ │ ├── EncryptionData.java │ │ ├── KeyDerivation.java │ │ └── OdfFileEntry.java │ └── test │ └── java │ └── org │ └── apache │ └── taverna │ └── scufl2 │ └── ucfpackage │ └── TestUCFPackage.java ├── taverna-scufl2-wfbundle ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── scufl2 │ │ │ └── rdfxml │ │ │ ├── AbstractParser.java │ │ │ ├── ParserState.java │ │ │ ├── ProfileParser.java │ │ │ ├── RDFXMLReader.java │ │ │ ├── RDFXMLSerializer.java │ │ │ ├── RDFXMLWriter.java │ │ │ ├── RevisionParser.java │ │ │ ├── WorkflowBundleParser.java │ │ │ ├── WorkflowParser.java │ │ │ └── impl │ │ │ └── NamespacePrefixMapperJAXB_RI.java │ └── resources │ │ └── META-INF │ │ ├── services │ │ ├── org.apache.taverna.scufl2.api.io.WorkflowBundleReader │ │ └── org.apache.taverna.scufl2.api.io.WorkflowBundleWriter │ │ └── spring │ │ ├── scufl2-rdfxml-context-osgi.xml │ │ └── scufl2-rdfxml-context.xml │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── scufl2 │ │ └── rdfxml │ │ ├── DummyParserTest.java │ │ ├── TestProfileParser.java │ │ ├── TestRDFXMLReader.java │ │ ├── TestRDFXMLSerializer.java │ │ ├── TestRDFXMLWriter.java │ │ ├── TestResourcesInZip.java │ │ └── TestRevisionParsing.java │ └── resources │ └── org │ └── apache │ └── taverna │ └── scufl2 │ └── rdfxml │ ├── example.wfbundle │ ├── example │ ├── LICENSE │ ├── META-INF │ │ ├── container.xml │ │ └── manifest.xml │ ├── NOTICE │ ├── Thumbnails │ │ ├── thumbnail.png │ │ └── thumbnail.svg │ ├── annotation │ │ ├── workflow │ │ │ └── HelloWorld.rdf │ │ └── workflowBundle.rdf │ ├── diagram │ │ └── workflow │ │ │ ├── HelloWorld.png │ │ │ └── HelloWorld.svg │ ├── mimetype │ ├── ontologies │ │ └── taverna2.2.rdf │ ├── profile │ │ ├── tavernaServer.rdf │ │ └── tavernaWorkbench.rdf │ ├── workflow │ │ └── HelloWorld.rdf │ └── workflowBundle.rdf │ ├── megaProfile.rdf │ ├── roevo-test.xml │ └── update-bundle.sh ├── taverna-scufl2-wfdesc ├── README.md ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── scufl2 │ │ │ └── wfdesc │ │ │ ├── ROEvoSerializer.java │ │ │ ├── WfdescAgent.java │ │ │ ├── WfdescReader.java │ │ │ ├── WfdescSerialiser.java │ │ │ └── WfdescWriter.java │ └── resources │ │ └── META-INF │ │ ├── LICENSE │ │ ├── services │ │ ├── org.apache.taverna.scufl2.api.io.WorkflowBundleReader │ │ └── org.apache.taverna.scufl2.api.io.WorkflowBundleWriter │ │ └── spring │ │ ├── scufl2-wfdesc-context-osgi.xml │ │ └── scufl2-wfdesc-context.xml │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── scufl2 │ │ └── wfdesc │ │ ├── TestAllTypes.java │ │ ├── TestAnnotationQuoting.java │ │ ├── TestLocalDependency.java │ │ ├── TestNested.java │ │ ├── TestRoEvoSerializer.java │ │ ├── TestSemanticAnnotations.java │ │ ├── TestWfdescReader.java │ │ └── TestWfdescWriter.java │ └── resources │ ├── T3-1226-annotations-with-quotes.t2flow │ ├── allTypes.links.sparql.json │ ├── allTypes.t2flow │ ├── helloanyone.t2flow │ ├── helloworld.t2flow │ ├── helloworld.wfdesc.ttl │ ├── localdependency.t2flow │ ├── nested.t2flow │ ├── rdf-in-example-annotation.t2flow │ └── valid_component_imagemagickconvert.t2flow └── taverna-tavlang-tool ├── .gitignore ├── README.md ├── pom.xml └── src ├── main ├── java │ ├── .gitignore │ └── org │ │ └── apache │ │ └── taverna │ │ └── tavlang │ │ ├── CommandLineTool.java │ │ ├── TavernaCommandline.java │ │ └── tools │ │ ├── Tools.java │ │ ├── convert │ │ ├── Scufl2Convert.java │ │ ├── ToJson.java │ │ └── ToRobundle.java │ │ ├── inspect │ │ ├── ProcessorNames.java │ │ └── ServiceTypes.java │ │ ├── stats │ │ └── GetWfStat.java │ │ └── validate │ │ └── Validate.java └── resources │ └── .gitignore └── test ├── java ├── .gitignore └── org │ └── apache │ └── taverna │ └── tavlang │ └── test │ ├── CommandLineTest.java │ ├── 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