├── .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 │ ├── TestConvert.java │ ├── TestStats.java │ ├── TestTools.java │ └── TestValidate.java └── resources ├── .gitignore └── workflows └── t2flow └── as.t2flow /.gitignore: -------------------------------------------------------------------------------- 1 | .project 2 | .settings 3 | .classpath 4 | target 5 | .gitignore 6 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | # Licensed to the Apache Software Foundation (ASF) under one or more 2 | # contributor license agreements. See the NOTICE file distributed with 3 | # this work for additional information regarding copyright ownership. 4 | # The ASF licenses this file to You under the Apache License, Version 2.0 5 | # (the "License"); you may not use this file except in compliance with 6 | # the License. You may obtain a copy of the License at 7 | # 8 | # http://www.apache.org/licenses/LICENSE-2.0 9 | # 10 | # Unless required by applicable law or agreed to in writing, software 11 | # distributed under the License is distributed on an "AS IS" BASIS, 12 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | # See the License for the specific language governing permissions and 14 | # limitations under the License. 15 | language: java 16 | -------------------------------------------------------------------------------- /DEPENDENCIES: -------------------------------------------------------------------------------- 1 | Dependencies are declared within each Maven submodule. 2 | 3 | See */target/classes/META-INF/DEPENDENCIES 4 | after running: mvn process-resources 5 | -------------------------------------------------------------------------------- /DISCLAIMER: -------------------------------------------------------------------------------- 1 | Taverna is no longer maintained and this code base 2 | is provided for archive purposes only. 3 | -------------------------------------------------------------------------------- /NOTICE: -------------------------------------------------------------------------------- 1 | This product is based on: 2 | Apache Taverna Language 3 | Copyright 2014-2020 The Apache Software Foundation 4 | 5 | This product includes software developed at 6 | The Apache Software Foundation (http://www.apache.org/). 7 | 8 | Portions of this software were originally based on the following: 9 | - Copyright 2010-2014 University of Manchester, UK 10 | These have been licensed to the Apache Software Foundation under a software grant. 11 | 12 | ----------------------------------------------------------------------------------- 13 | ./taverna-scufl2-schemas/src/main/resources/org/apache/taverna/scufl2/rdfxml/xsd/roevo.xsd 14 | 15 | roevo.xsd derived from 16 | Research Object Evolution Ontology (roevo) 17 | http://w3id.org/ro/roevo 18 | 19 | Copyright (c) 2011-2014 20 | Raul Palma, PSNC 21 | Jun Zhao, University of Oxford 22 | Khalid Belhajjame, University of Manchester 23 | Stian Soiland-Reyes, University of Manchester 24 | Oscar Corcho, UPM 25 | 26 | Creative Commons Attribution 3.0 License 27 | http://creativecommons.org/licenses/by/3.0 28 | 29 | -------------------------------------------------------------------------------- /taverna-baclava-language/src/main/java/org/apache/taverna/baclava/BaclavaReader.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.baclava; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import java.io.Reader; 24 | 25 | import javax.xml.bind.JAXBContext; 26 | import javax.xml.bind.JAXBElement; 27 | import javax.xml.bind.JAXBException; 28 | import javax.xml.bind.Unmarshaller; 29 | 30 | 31 | public class BaclavaReader { 32 | 33 | private static final JAXBContext jaxbContext = initContext(); 34 | 35 | private static JAXBContext initContext() { 36 | try { 37 | return JAXBContext.newInstance("org.apache.taverna.baclava"); 38 | } catch (JAXBException e) { 39 | return null; 40 | } 41 | } 42 | 43 | public static DataThingMapType readBaclava(Reader r) throws JAXBException { 44 | Unmarshaller unmarshaller = jaxbContext.createUnmarshaller(); 45 | JAXBElement jb = (JAXBElement) unmarshaller.unmarshal(r); 46 | return (DataThingMapType) jb.getValue(); 47 | } 48 | } 49 | -------------------------------------------------------------------------------- /taverna-baclava-language/src/main/java/org/apache/taverna/baclava/BaclavaWriter.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.baclava; 5 | 6 | /* 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | */ 24 | 25 | 26 | import java.io.Writer; 27 | 28 | import javax.xml.bind.JAXBContext; 29 | import javax.xml.bind.JAXBException; 30 | import javax.xml.bind.Marshaller; 31 | 32 | /** 33 | * @author alanrw 34 | * 35 | */ 36 | public class BaclavaWriter { 37 | 38 | private static final JAXBContext jaxbContext = initContext(); 39 | 40 | private static JAXBContext initContext() { 41 | try { 42 | return JAXBContext.newInstance("org.apache.taverna.baclava"); 43 | } catch (JAXBException e) { 44 | return null; 45 | } 46 | } 47 | 48 | public static void writeBaclava(DataThingMapType d, Writer w) throws JAXBException { 49 | Marshaller marshaller = jaxbContext.createMarshaller(); 50 | marshaller.setProperty("jaxb.formatted.output", true); 51 | 52 | ObjectFactory of = new ObjectFactory(); 53 | marshaller.marshal(of.createDataThingMap(d), w); 54 | } 55 | 56 | } 57 | -------------------------------------------------------------------------------- /taverna-baclava-language/src/main/resources/xsd/xscufl.xsd: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | -------------------------------------------------------------------------------- /taverna-databundle/src/main/java/org/apache/taverna/databundle/ErrorDocument.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.databundle; 2 | /* 3 | * 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | * 21 | */ 22 | 23 | 24 | import java.nio.file.Path; 25 | import java.util.ArrayList; 26 | import java.util.List; 27 | 28 | public class ErrorDocument { 29 | private List causedBy = new ArrayList<>(); 30 | private String message = ""; 31 | private String trace = ""; 32 | 33 | public List getCausedBy() { 34 | return causedBy; 35 | } 36 | 37 | public String getMessage() { 38 | return message; 39 | } 40 | 41 | public String getTrace() { 42 | return trace; 43 | } 44 | 45 | public void setCausedBy(List causedBy) { 46 | this.causedBy.clear(); 47 | if (causedBy != null) 48 | this.causedBy.addAll(causedBy); 49 | } 50 | 51 | public void setMessage(String message) { 52 | if (message == null) 53 | message = ""; 54 | this.message = message; 55 | } 56 | 57 | public void setTrace(String trace) { 58 | if (trace == null) 59 | trace = ""; 60 | this.trace = trace; 61 | } 62 | 63 | @Override 64 | public String toString() { 65 | return "Error: " + getMessage() + "\n" + trace; 66 | // TODO: also include the causedBy paths? 67 | } 68 | 69 | } 70 | -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/Graphical_output.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/Graphical_output.png -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/Workflow16_getStatus_output_status.txt: -------------------------------------------------------------------------------- 1 | FINISHED -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/email.txt: -------------------------------------------------------------------------------- 1 | soiland-reyes@cs.manchester.ac.uk -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/getResult_output_output.octet-stream: -------------------------------------------------------------------------------- 1 | Sequence "TMM43_HUMAN" crc64 checksum: 70FDDD4ED1AA11DF length: 400 aa. 2 | 3 | InterPro IPR012430 Transmembrane protein 43 family 4 | method AccNumber shortName location 5 | HMMPanther PTHR13416 UNCHARACTERIZED T[1-400] 2.8e-209 6 | HMMPfam PF07787 DUF1625 T[121-373] 5.2e-82 7 | 8 | InterPro NULL NULL 9 | method AccNumber shortName location 10 | HMMPanther PTHR13416:SF0 SUBFAMILY NOT NAMED T[1-400] 2.8e-209 11 | TMHMM tmhmm transmembrane_regions ?[33-51] NA ?[313-331] NA ?[350-370] NA ?[375-395] NA 12 | 13 | -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/intermediates/00/00548907-43e1-4484-9582-bfa8727d44ca.txt: -------------------------------------------------------------------------------- 1 | RUNNING -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/intermediates/07/079d289b-796e-45cf-a759-82f91a0aa3d5.txt: -------------------------------------------------------------------------------- 1 | RUNNING -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/intermediates/0a/0a2b3aa2-5b11-433d-b48f-1009424bb486.txt: -------------------------------------------------------------------------------- 1 | iprscan-S20130531-112044-0159-59919420-oy -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/intermediates/0b/0bd05e27-46d6-4de5-b76b-0988638f9231.txt: -------------------------------------------------------------------------------- 1 | soiland-reyes@cs.manchester.ac.uk>sp|Q9BTV4|TMM43_HUMAN Transmembrane protein 43 OS=Homo sapiens GN=TMEM43 PE=1 SV=1 2 | MAANYSSTSTRREHVKVKTSSQPGFLERLSETSGGMFVGLMAFLLSFYLIFTNEGRALKT 3 | ATSLAEGLSLVVSPDSIHSVAPENEGRLVHIIGALRTSKLLSDPNYGVHLPAVKLRRHVE 4 | MYQWVETEESREYTEDGQVKKETRYSYNTEWRSEIINSKNFDREIGHKNPSAMAVESFMA 5 | TAPFVQIGRFFLSSGLIDKVDNFKSLSLSKLEDPHVDIIRRGDFFYHSENPKYPEVGDLR 6 | VSFSYAGLSGDDPDLGPAHVVTVIARQRGDQLVPFSTKSGDTLLLLHHGDFSAEEVFHRE 7 | LRSNSMKTWGLRAAGWMAMFMGLNLMTRILYTLVDWFPVFRDLVNIGLKAFAFCVATSLT 8 | LLTVAAGWLFYRPLWALLIAGLALVPILVARTRVPAKKLE -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/intermediates/0c/0c29c209-b442-49c5-bee2-5b5efdacad0e.txt: -------------------------------------------------------------------------------- 1 | iprscan-S20130531-112044-0159-59919420-oy -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/intermediates/0f/0f93d00f-131b-42ec-bbba-22b50582903e.txt: -------------------------------------------------------------------------------- 1 | iprscan-S20130531-112044-0159-59919420-oy -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/intermediates/11/111e5771-37b7-4ef8-9888-e50eadbc2a5c.txt: -------------------------------------------------------------------------------- 1 | RUNNING -------------------------------------------------------------------------------- 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/taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/intermediates/1f/1f536bcf-ba43-44ec-a983-b30a45f2b739.txt: -------------------------------------------------------------------------------- 1 | RUNNING -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/intermediates/21/219626eb-a4fc-4c83-9132-67b2b40d5a68.txt: -------------------------------------------------------------------------------- 1 | FINISHED -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/intermediates/26/268a47b4-34aa-42d0-96ad-98b99601a4e5.txt: -------------------------------------------------------------------------------- 1 | RUNNING -------------------------------------------------------------------------------- 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 -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/intermediates/f2/f273b491-edd2-4e18-aba5-106279f491d8.txt: -------------------------------------------------------------------------------- 1 | iprscan-S20130531-112044-0159-59919420-oy -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/intermediates/f7/f7e2a950-6426-4e3f-b9f0-844bfae9ed96.txt: -------------------------------------------------------------------------------- 1 | RUNNING -------------------------------------------------------------------------------- /taverna-databundle/src/test/resources/full-example/ebi-wfrun-2013-05-31/sequence.txt: -------------------------------------------------------------------------------- 1 | >sp|Q9BTV4|TMM43_HUMAN Transmembrane protein 43 OS=Homo sapiens GN=TMEM43 PE=1 SV=1 2 | MAANYSSTSTRREHVKVKTSSQPGFLERLSETSGGMFVGLMAFLLSFYLIFTNEGRALKT 3 | ATSLAEGLSLVVSPDSIHSVAPENEGRLVHIIGALRTSKLLSDPNYGVHLPAVKLRRHVE 4 | MYQWVETEESREYTEDGQVKKETRYSYNTEWRSEIINSKNFDREIGHKNPSAMAVESFMA 5 | TAPFVQIGRFFLSSGLIDKVDNFKSLSLSKLEDPHVDIIRRGDFFYHSENPKYPEVGDLR 6 | VSFSYAGLSGDDPDLGPAHVVTVIARQRGDQLVPFSTKSGDTLLLLHHGDFSAEEVFHRE 7 | LRSNSMKTWGLRAAGWMAMFMGLNLMTRILYTLVDWFPVFRDLVNIGLKAFAFCVATSLT 8 | LLTVAAGWLFYRPLWALLIAGLALVPILVARTRVPAKKLE -------------------------------------------------------------------------------- /taverna-ro-vocabs/pom.xml: -------------------------------------------------------------------------------- 1 | 2 | 18 | 19 | 4.0.0 20 | 21 | org.apache.taverna.language 22 | apache-taverna-language 23 | 0.16.0-incubating-SNAPSHOT 24 | 25 | taverna-ro-vocabs 26 | bundle 27 | Apache Taverna Research Object vocabularies 28 | Constants for vocabularies used in Research Objects 29 | 30 | 31 | 32 | org.apache.jena 33 | jena-arq 34 | ${jena.version} 35 | 36 | 37 | 38 | org.apache.jena 39 | jena-osgi 40 | ${jena.version} 41 | 42 | 43 | 44 | 45 | -------------------------------------------------------------------------------- /taverna-ro-vocabs/src/main/java/org/apache/taverna/ro/vocabs/package-info.java: -------------------------------------------------------------------------------- 1 | /* 2 | * Licensed to the Apache Software Foundation (ASF) under one or more 3 | * contributor license agreements. See the NOTICE file distributed with 4 | * this work for additional information regarding copyright ownership. 5 | * The ASF licenses this file to You under the Apache License, Version 2.0 6 | * (the "License"); you may not use this file except in compliance with 7 | * the License. You may obtain a copy of the License at 8 | * 9 | * http://www.apache.org/licenses/LICENSE-2.0 10 | * 11 | * Unless required by applicable law or agreed to in writing, software 12 | * distributed under the License is distributed on an "AS IS" BASIS, 13 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | * See the License for the specific language governing permissions and 15 | * limitations under the License. 16 | */ 17 | /** 18 | * Constants for vocabularies used by Research Object model 19 | * 20 | * @see https://w3id.org/ro/2016-01-28/ 21 | * 22 | */ 23 | package org.apache.taverna.ro.vocabs; -------------------------------------------------------------------------------- /taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/Agent.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.robundle.manifest; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import java.net.URI; 24 | 25 | import com.fasterxml.jackson.annotation.JsonPropertyOrder; 26 | 27 | @JsonPropertyOrder(value = { "uri", "orcid", "name" }) 28 | public class Agent { 29 | private String name; 30 | private URI orcid; 31 | private URI uri; 32 | 33 | public Agent() { 34 | } 35 | 36 | public Agent(String name) { 37 | setName(name); 38 | } 39 | 40 | public String getName() { 41 | return name; 42 | } 43 | 44 | public URI getOrcid() { 45 | return orcid; 46 | } 47 | 48 | public URI getUri() { 49 | return uri; 50 | } 51 | 52 | public void setName(String name) { 53 | this.name = name; 54 | } 55 | 56 | public void setOrcid(URI orcid) { 57 | this.orcid = orcid; 58 | } 59 | 60 | public void setUri(URI uri) { 61 | this.uri = uri; 62 | } 63 | } 64 | -------------------------------------------------------------------------------- /taverna-robundle/src/main/java/org/apache/taverna/robundle/utils/PathHelper.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.robundle.utils; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import java.net.URI; 24 | 25 | public class PathHelper { 26 | private static final URI ROOT = URI.create("/"); 27 | 28 | public static URI relativizeFromBase(String uri, URI base) { 29 | return relativizeFromBase(URI.create(uri), base); 30 | } 31 | 32 | public static URI relativizeFromBase(URI uri, URI base) { 33 | return ROOT.resolve(base.relativize(uri)); 34 | } 35 | } 36 | -------------------------------------------------------------------------------- /taverna-robundle/src/main/java/org/apache/taverna/robundle/utils/RecursiveDeleteVisitor.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.robundle.utils; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import static java.nio.file.FileVisitResult.CONTINUE; 24 | import static java.nio.file.Files.delete; 25 | import static java.nio.file.Files.isDirectory; 26 | import static java.nio.file.Files.walkFileTree; 27 | 28 | import java.io.IOException; 29 | import java.nio.file.FileVisitResult; 30 | import java.nio.file.Path; 31 | import java.nio.file.SimpleFileVisitor; 32 | import java.nio.file.attribute.BasicFileAttributes; 33 | 34 | public class RecursiveDeleteVisitor extends SimpleFileVisitor { 35 | public static void deleteRecursively(Path p) throws IOException { 36 | if (isDirectory(p)) 37 | walkFileTree(p, new RecursiveDeleteVisitor()); 38 | else 39 | delete(p); 40 | } 41 | 42 | @Override 43 | public FileVisitResult postVisitDirectory(Path dir, IOException exc) 44 | throws IOException { 45 | super.postVisitDirectory(dir, exc); 46 | delete(dir); 47 | return CONTINUE; 48 | } 49 | 50 | @Override 51 | public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) 52 | throws IOException { 53 | delete(file); 54 | return CONTINUE; 55 | } 56 | } 57 | -------------------------------------------------------------------------------- /taverna-robundle/src/main/java/org/apache/taverna/robundle/utils/TemporaryFiles.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.robundle.utils; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import static java.nio.file.Files.createTempDirectory; 24 | 25 | import java.io.IOException; 26 | import java.nio.file.Path; 27 | 28 | public class TemporaryFiles { 29 | public static Path temporaryBundle() throws IOException { 30 | Path tempDir = createTempDirectory("robundle"); 31 | tempDir.toFile().deleteOnExit(); 32 | /* 33 | * Why inside a tempDir? Because ZipFileSystemProvider creates 34 | * neighbouring temporary files per file that is written to zip, which 35 | * could mean a lot of temporary files directly in /tmp - making it 36 | * difficult to clean up 37 | */ 38 | Path bundle = tempDir.resolve("robundle.zip"); 39 | bundle.toFile().deleteOnExit(); 40 | return bundle; 41 | } 42 | } 43 | -------------------------------------------------------------------------------- /taverna-robundle/src/main/resources/META-INF/services/java.nio.file.spi.FileSystemProvider: -------------------------------------------------------------------------------- 1 | org.apache.taverna.robundle.fs.BundleFileSystemProvider 2 | -------------------------------------------------------------------------------- /taverna-robundle/src/main/resources/META-INF/services/java.nio.file.spi.FileTypeDetector: -------------------------------------------------------------------------------- 1 | org.apache.taverna.robundle.fs.BundleFileTypeDetector 2 | -------------------------------------------------------------------------------- /taverna-robundle/src/main/resources/jarcache.json: -------------------------------------------------------------------------------- 1 | [ 2 | { 3 | "Content-Location": "https://w3id.org/bundle/context", 4 | "X-Classpath": "contexts/bundle.jsonld", 5 | "Content-Type": "application/ld+json" 6 | } 7 | ] 8 | 9 | -------------------------------------------------------------------------------- /taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/Helper.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.robundle.fs; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import java.io.IOException; 24 | import java.nio.file.Files; 25 | import java.nio.file.Path; 26 | 27 | import org.apache.taverna.robundle.Bundles; 28 | import org.apache.taverna.robundle.fs.BundleFileSystem; 29 | import org.apache.taverna.robundle.fs.BundleFileSystemProvider; 30 | import org.junit.After; 31 | import org.junit.Before; 32 | 33 | public class Helper { 34 | protected BundleFileSystem fs; 35 | 36 | @Before 37 | public void makeFS() throws IOException { 38 | fs = BundleFileSystemProvider.newFileSystemFromTemporary(); 39 | } 40 | 41 | @After 42 | public void closeAndDeleteFS() throws IOException { 43 | fs.close(); 44 | Path source = fs.getSource(); 45 | Files.deleteIfExists(source); 46 | if (source.getParent().getFileName().toString().startsWith("robundle")) { 47 | Bundles.deleteRecursively(source.getParent()); 48 | } 49 | } 50 | } 51 | -------------------------------------------------------------------------------- /taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/utils/TestRecursiveCopyFileVisitorInBundle.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.robundle.manifest.utils; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import java.io.IOException; 24 | import java.nio.file.Files; 25 | import java.nio.file.Path; 26 | 27 | import org.apache.taverna.robundle.Bundle; 28 | import org.apache.taverna.robundle.Bundles; 29 | import org.junit.After; 30 | import org.junit.Before; 31 | 32 | public class TestRecursiveCopyFileVisitorInBundle extends 33 | TestRecursiveCopyFileVisitor { 34 | 35 | private Bundle bundle; 36 | 37 | @Before 38 | public void createBundle() throws IOException { 39 | bundle = Bundles.createBundle(); 40 | } 41 | 42 | @After 43 | public void closeBundle() throws IOException { 44 | if (bundle != null) { 45 | bundle.close(); 46 | } 47 | bundle = null; 48 | } 49 | 50 | @Override 51 | protected Path tempDir(String name) throws IOException { 52 | return Files.createTempDirectory(bundle.getRoot(), name); 53 | } 54 | } 55 | -------------------------------------------------------------------------------- /taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/utils/TestRecursiveCopyFileVisitorMultipleBundles.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.robundle.manifest.utils; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import java.io.IOException; 24 | import java.nio.file.Files; 25 | import java.nio.file.Path; 26 | import java.util.ArrayList; 27 | import java.util.List; 28 | 29 | import org.apache.taverna.robundle.Bundle; 30 | import org.apache.taverna.robundle.Bundles; 31 | import org.junit.After; 32 | 33 | public class TestRecursiveCopyFileVisitorMultipleBundles extends 34 | TestRecursiveCopyFileVisitor { 35 | 36 | private List bundles = new ArrayList<>(); 37 | 38 | @After 39 | public void closeBundle() throws IOException { 40 | for (Bundle b : bundles) { 41 | b.close(); 42 | } 43 | } 44 | 45 | @Override 46 | protected Path tempDir(String name) throws IOException { 47 | Bundle bundle = Bundles.createBundle(); 48 | bundles.add(bundle); 49 | return Files.createTempDirectory(bundle.getRoot(), name); 50 | } 51 | } 52 | -------------------------------------------------------------------------------- /taverna-robundle/src/test/java/org/apache/taverna/robundle/validator/ValidatorTest.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.robundle.validator; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | import static org.junit.Assert.assertNotNull; 22 | 23 | import java.nio.file.Files; 24 | import java.nio.file.Path; 25 | import java.nio.file.StandardCopyOption; 26 | 27 | import org.junit.Test; 28 | 29 | public class ValidatorTest { 30 | 31 | Path path; 32 | 33 | @Test 34 | public void test() throws Exception{ 35 | 36 | path = Files.createTempFile("test", ".bundle.zip"); 37 | path.toFile().deleteOnExit(); 38 | Files.copy(getClass().getResourceAsStream("/workflowrun.bundle.zip"), path, StandardCopyOption.REPLACE_EXISTING); 39 | 40 | RoValidator validator = new RoValidator(path); 41 | ValidationReport r = validator.check(); 42 | 43 | assertNotNull("Errors List", r.getErrorList_l()); 44 | assertNotNull("Warnings List", r.getInfoWarnings()); 45 | assertNotNull("Info Warnings List", r.getInfoWarnings_l()); 46 | 47 | Files.delete(path); 48 | } 49 | 50 | } 51 | -------------------------------------------------------------------------------- /taverna-robundle/src/test/resources/bag-of-bags-manifest.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": [ 3 | "https://w3id.org/bundle/context" 4 | ], 5 | "@id": "../", 6 | "aggregates": [ 7 | { 8 | "bundledAs": { 9 | "filename": "bag1.zip", 10 | "folder": "../data/" 11 | }, 12 | "conformsTo": [ 13 | "https://tools.ietf.org/html/draft-kunze-bagit-14", 14 | "https://w3id.org/ro/bagit/profile" 15 | ], 16 | "uri": "http://n2t.net/ark:/57799/b90h3c" 17 | } 18 | ], 19 | "annotations": [ 20 | { 21 | "about": "../", 22 | "oa:motivatedBy": { 23 | "@id": "oa:describing" 24 | }, 25 | "uri": "../data/README" 26 | } 27 | ], 28 | "authoredBy": { 29 | "name": "Stian Soiland-Reyes", 30 | "uri": "mbox:stain@apache.org", 31 | "orcid": "https://orcid.org/0000-0001-9842-9718" 32 | }, 33 | "authoredOn": "2018-05-10T16:07:00+00:00", 34 | "createdBy": { 35 | "name": "BDBag version: 1.1.5 (Bagit version: 1.6.3)", 36 | "uri": "https://github.com/ini-bdds/bdbag" 37 | }, 38 | "createdOn": "2018-05-10T16:07:00+00:00" 39 | } 40 | -------------------------------------------------------------------------------- /taverna-robundle/src/test/resources/combine/Boris-skeleton.omex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-robundle/src/test/resources/combine/Boris-skeleton.omex -------------------------------------------------------------------------------- /taverna-robundle/src/test/resources/combine/DirectoryMadness-skeleton.omex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-robundle/src/test/resources/combine/DirectoryMadness-skeleton.omex 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See the NOTICE file 7 | * distributed with this work for additional information 8 | * regarding copyright ownership. The ASF licenses this file 9 | * to you under the Apache License, Version 2.0 (the 10 | * "License"); you may not use this file except in compliance 11 | * with the License. You may obtain a copy of the License at 12 | * 13 | * http://www.apache.org/licenses/LICENSE-2.0 14 | * 15 | * Unless required by applicable law or agreed to in writing, 16 | * software distributed under the License is distributed on an 17 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 18 | * KIND, either express or implied. See the License for the 19 | * specific language governing permissions and limitations 20 | * under the License. 21 | */ 22 | 23 | 24 | 25 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/annotation/package-info.java: -------------------------------------------------------------------------------- 1 | /** 2 | * Common annotations 3 | * 4 | */ 5 | package org.apache.taverna.scufl2.api.annotation; 6 | 7 | /* 8 | * Licensed to the Apache Software Foundation (ASF) under one 9 | * or more contributor license agreements. See the NOTICE file 10 | * distributed with this work for additional information 11 | * regarding copyright ownership. The ASF licenses this file 12 | * to you under the Apache License, Version 2.0 (the 13 | * "License"); you may not use this file except in compliance 14 | * with the License. You may obtain a copy of the License at 15 | * 16 | * http://www.apache.org/licenses/LICENSE-2.0 17 | * 18 | * Unless required by applicable law or agreed to in writing, 19 | * software distributed under the License is distributed on an 20 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 21 | * KIND, either express or implied. See the License for the 22 | * specific language governing permissions and limitations 23 | * under the License. 24 | */ 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/common/Configurable.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.common; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import org.apache.taverna.scufl2.api.configurations.Configuration; 24 | 25 | /** 26 | * {@link WorkflowBean WorkflowBeans} that can have a 27 | * {@link org.apache.taverna.scufl2.api.configurations.Configuration Configuration}. 28 | *

29 | * Configurables are {@link Typed}, but note that this type is different from 30 | * the type of the {@link Configuration}. 31 | * 32 | * @author Alan R Williams 33 | * @author Stian Soiland-Reyes 34 | */ 35 | public interface Configurable extends Typed { 36 | } 37 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/common/Named.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.common; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import java.util.regex.Pattern; 24 | 25 | /** 26 | * A named {@link WorkflowBean}. 27 | * 28 | * @author Alan R Williams 29 | */ 30 | @SuppressWarnings("rawtypes") 31 | public interface Named extends WorkflowBean, Comparable { 32 | /** 33 | * Name must not match this regular expression, e.g. must not include: slash 34 | * (/), colon (:), ASCII control characters 35 | */ 36 | Pattern INVALID_NAME = Pattern.compile("^$|[/:\\x7f\\x00-\\x1f]"); 37 | 38 | /** 39 | * Returns the name of the {@link WorkflowBean}. 40 | * 41 | * @return the name of the WorkflowBean 42 | */ 43 | String getName(); 44 | 45 | /** 46 | * Sets the name of the {@link WorkflowBean}. 47 | * 48 | * The name must not be null, not be an empty 49 | * String, and must not match the {@link #INVALID_NAME} regular expression. 50 | * 51 | * @param name 52 | * the name of the WorkflowBean 53 | */ 54 | void setName(String name); 55 | } 56 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/common/Ported.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.common; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import org.apache.taverna.scufl2.api.port.InputPort; 24 | import org.apache.taverna.scufl2.api.port.OutputPort; 25 | 26 | /** 27 | * A {@link WorkflowBean} that has 28 | * {@link org.apache.taverna.scufl2.api.portInputPort InputPorts} and 29 | * {@link org.apache.taverna.scufl2.api.portOutputPort OutputPorts}. 30 | */ 31 | public interface Ported extends WorkflowBean { 32 | /** 33 | * Returns the {@link org.apache.taverna.scufl2.api.port.InputPort InputPorts}. 34 | * 35 | * @return the input ports 36 | */ 37 | NamedSet getInputPorts(); 38 | 39 | /** 40 | * Returns the {@link org.apache.taverna.scufl2.api.port.OutputPort OutputPorts} 41 | * . 42 | * 43 | * @return the output ports 44 | */ 45 | NamedSet getOutputPorts(); 46 | } 47 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/common/Root.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.common; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import java.net.URI; 24 | 25 | public interface Root extends WorkflowBean { 26 | URI getGlobalBaseURI(); 27 | 28 | void setGlobalBaseURI(URI globalBaseURI); 29 | } 30 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/common/Typed.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.common; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import java.net.URI; 24 | 25 | /** 26 | * A typed {@link WorkflowBean}. 27 | * 28 | * @author Stian Soiland-Reyes 29 | */ 30 | public interface Typed extends WorkflowBean { 31 | /** 32 | * Returns the type of the {@link WorkflowBean}. 33 | * 34 | * @return the type of the WorkflowBean 35 | */ 36 | URI getType(); 37 | 38 | /** 39 | * Sets the type of the {@link WorkflowBean}. 40 | * 41 | * @param type 42 | * the type of the WorkflowBean. 43 | */ 44 | void setType(URI type); 45 | } 46 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/common/package-info.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.common; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | 24 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/container/package-info.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.container; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/core/ControlLink.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.core; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import org.apache.taverna.scufl2.api.common.Child; 24 | 25 | /** 26 | * A link between two workflow components where one component controls the other in some way. 27 | * 28 | * @author Alan R Williams 29 | * @author Stian Soiland-Reyes 30 | */ 31 | @SuppressWarnings("rawtypes") 32 | public interface ControlLink extends Child, Comparable { 33 | 34 | } 35 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/core/package-info.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.core; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/iterationstrategy/IterationStrategyNode.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.iterationstrategy; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import org.apache.taverna.scufl2.api.common.Child; 24 | 25 | /** 26 | * @author Alan R Williams 27 | */ 28 | public interface IterationStrategyNode extends 29 | Child { 30 | } 31 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/iterationstrategy/IterationStrategyParent.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.iterationstrategy; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 24 | 25 | public interface IterationStrategyParent extends WorkflowBean { 26 | } 27 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/iterationstrategy/IterationStrategyTopNode.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.iterationstrategy; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import java.util.List; 24 | 25 | /** 26 | * @author Stian Soiland-Reyes 27 | */ 28 | public interface IterationStrategyTopNode extends IterationStrategyNode, 29 | List, IterationStrategyParent { 30 | } 31 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/iterationstrategy/package-info.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.iterationstrategy; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/port/ActivityPort.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.port; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import org.apache.taverna.scufl2.api.activity.Activity; 24 | import org.apache.taverna.scufl2.api.common.Child; 25 | 26 | /** 27 | * A Port that specifies the data consumed or produced by an 28 | * {@link Activity}. 29 | */ 30 | public interface ActivityPort extends DepthPort, Child { 31 | 32 | } 33 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/port/DepthPort.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.port; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | public interface DepthPort extends Port { 24 | /** 25 | * Returns the depth of the Port. 26 | * 27 | * @return the depth of the Port 28 | */ 29 | Integer getDepth(); 30 | 31 | /** 32 | * Sets the depth of the Port. 33 | * 34 | * @param depth 35 | * the depth of the Port 36 | */ 37 | void setDepth(Integer depth); 38 | } 39 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/port/GranularDepthPort.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.port; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | public interface GranularDepthPort extends DepthPort { 24 | /** 25 | * Returns the granular depth of the Port. 26 | * 27 | * @return the granular depth of the Port 28 | */ 29 | Integer getGranularDepth(); 30 | 31 | /** 32 | * Sets the granular depth of the Port. 33 | * 34 | * @param granularDepth 35 | * the granular depth of the Port 36 | */ 37 | void setGranularDepth(Integer granularDepth); 38 | } 39 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/port/InputPort.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.port; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | /** 24 | * A Port that specifies inputs to a {@link org.apache.taverna.scufl2.api.core.Workflow 25 | * Workflow} component. 26 | */ 27 | public interface InputPort extends DepthPort { 28 | 29 | } 30 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/port/OutputPort.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.port; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | /** 24 | * A Port that specifies outputs from a {@link org.apache.taverna.scufl2.api.core.Workflow 25 | * Workflow} component. 26 | */ 27 | public interface OutputPort extends Port { 28 | 29 | } 30 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/port/Port.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.port; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import org.apache.taverna.scufl2.api.common.Named; 24 | 25 | /** 26 | * A Port specifies the data consumed or produced by a 27 | * {@link org.apache.taverna.scufl2.api.core.Workflow Workflow} component. 28 | * 29 | * @author Alan R Williams 30 | */ 31 | public interface Port extends Named { 32 | } 33 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/port/ProcessorPort.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.port; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import org.apache.taverna.scufl2.api.common.Child; 24 | import org.apache.taverna.scufl2.api.core.Processor; 25 | 26 | /** 27 | * A Port that specifies the data consumed or produced by an 28 | * {@link Processor}. 29 | * 30 | * @author Alan R Williams 31 | */ 32 | public interface ProcessorPort extends Port, Child { 33 | } 34 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/port/ReceiverPort.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.port; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import org.apache.taverna.scufl2.api.core.DataLink; 24 | import org.apache.taverna.scufl2.api.core.Workflow; 25 | 26 | /** 27 | * A Port that receives data from a {@link DataLink} in a {@link Workflow}. 28 | * 29 | * @see SenderPort 30 | * @see DataLink 31 | * @author Alan R Williams 32 | * @author Stian Soiland-Reyes 33 | */ 34 | public interface ReceiverPort extends Port { 35 | 36 | } 37 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/port/SenderPort.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.port; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import org.apache.taverna.scufl2.api.core.DataLink; 24 | import org.apache.taverna.scufl2.api.core.Workflow; 25 | 26 | /** 27 | * A Port that sends data out to a {@link DataLink} in a {@link Workflow}. 28 | * 29 | * @see DataLink 30 | * @see Workflow 31 | * @author Alan R Williams 32 | * @author Stian Soiland-Reyes 33 | */ 34 | public interface SenderPort extends Port { 35 | 36 | } 37 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/port/WorkflowPort.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.port; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import org.apache.taverna.scufl2.api.common.Child; 24 | import org.apache.taverna.scufl2.api.core.Workflow; 25 | 26 | /** 27 | * A Port that specifies the data consumed or produced by an 28 | * {@link Workflow}. 29 | * 30 | * @author Alan R Williams 31 | */ 32 | public interface WorkflowPort extends Port, Child { 33 | 34 | } 35 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/port/package-info.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.port; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | 24 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/profiles/package-info.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.profiles; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/api/reference/package-info.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.reference; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | 24 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/Status.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | /** 28 | * @author alanrw 29 | */ 30 | public enum Status { 31 | OK, WARNING, SEVERE 32 | } 33 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/ValidationException.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | /** 28 | * @author alanrw 29 | */ 30 | @SuppressWarnings("serial") 31 | public class ValidationException extends Exception { 32 | public ValidationException(String string) { 33 | super(string); 34 | } 35 | 36 | public ValidationException(String string, Throwable throwable) { 37 | super(string, throwable); 38 | } 39 | } 40 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/ValidationProblem.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 28 | 29 | /** 30 | * @author alanrw 31 | */ 32 | public abstract class ValidationProblem { 33 | private final WorkflowBean bean; 34 | 35 | public ValidationProblem(WorkflowBean bean) { 36 | this.bean = bean; 37 | } 38 | 39 | /** 40 | * @return the bean 41 | */ 42 | public WorkflowBean getBean() { 43 | return bean; 44 | } 45 | } 46 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/ValidationReport.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.validation; 2 | /* 3 | * 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | * 21 | */ 22 | 23 | 24 | public interface ValidationReport { 25 | /** 26 | * @return Whether any problems were detected during the validation. 27 | */ 28 | boolean detectedProblems(); 29 | 30 | /** 31 | * @return An exception to throw to report the problems, or null if 32 | * there are no problems to report. 33 | */ 34 | ValidationException getException(); 35 | } 36 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/Validator.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.validation; 2 | /* 3 | * 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | * 21 | */ 22 | 23 | 24 | import org.apache.taverna.scufl2.api.container.WorkflowBundle; 25 | 26 | /** 27 | * How to check a workflow bundle for validity in some sense. 28 | * 29 | * @param 30 | * The type of the validation reports produced by this validator. 31 | * @author Donal Fellows 32 | */ 33 | public interface Validator { 34 | /** 35 | * Validate the given workflow bundle. 36 | * 37 | * @param workflowBundle 38 | * The bundle to validate. 39 | * @return A description of whether the bundle is valid, and if not, how it 40 | * is invalid. (Determining the nature of the invalidity may require 41 | * knowing more about the nature of the validator than this 42 | * interface describes.) 43 | */ 44 | T validate(WorkflowBundle workflowBundle); 45 | } 46 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/WorkflowBeanReport.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.validation; 2 | /* 3 | * 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | * 21 | */ 22 | 23 | 24 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 25 | 26 | public interface WorkflowBeanReport { 27 | /** 28 | * @return the bean 29 | */ 30 | WorkflowBean getBean(); 31 | } 32 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/correctness/CorrectnessValidator.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation.correctness; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 28 | import org.apache.taverna.scufl2.api.container.WorkflowBundle; 29 | import org.apache.taverna.scufl2.validation.Validator; 30 | 31 | 32 | /** 33 | * @author alanrw 34 | */ 35 | public class CorrectnessValidator implements Validator { 36 | public void checkCorrectness(WorkflowBean bean, boolean checkComplete, 37 | CorrectnessValidationListener listener) { 38 | CorrectnessVisitor visitor = new CorrectnessVisitor(checkComplete, 39 | listener); 40 | bean.accept(visitor); 41 | } 42 | 43 | @Override 44 | public CorrectnessValidationListener validate(WorkflowBundle workflowBundle) { 45 | CorrectnessValidationListener l = new ReportCorrectnessValidationListener(); 46 | checkCorrectness(workflowBundle, false, l); 47 | return l; 48 | } 49 | } 50 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/correctness/report/EmptyIterationStrategyTopNodeProblem.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.validation.correctness.report; 2 | /* 3 | * 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | * 21 | */ 22 | 23 | 24 | import org.apache.taverna.scufl2.api.iterationstrategy.IterationStrategyTopNode; 25 | import org.apache.taverna.scufl2.validation.ValidationProblem; 26 | 27 | 28 | /** 29 | * @author alanrw 30 | * 31 | */ 32 | public class EmptyIterationStrategyTopNodeProblem extends ValidationProblem { 33 | public EmptyIterationStrategyTopNodeProblem(IterationStrategyTopNode bean) { 34 | super(bean); 35 | } 36 | 37 | @Override 38 | public String toString() { 39 | return getBean() + " is empty"; 40 | } 41 | } 42 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/correctness/report/IncompatibleGranularDepthProblem.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.validation.correctness.report; 2 | /* 3 | * 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | * 21 | */ 22 | 23 | 24 | import org.apache.taverna.scufl2.api.port.AbstractGranularDepthPort; 25 | import org.apache.taverna.scufl2.validation.ValidationProblem; 26 | 27 | 28 | /** 29 | * @author alanrw 30 | */ 31 | public class IncompatibleGranularDepthProblem extends ValidationProblem { 32 | private final Integer depth; 33 | private final Integer granularDepth; 34 | 35 | public IncompatibleGranularDepthProblem(AbstractGranularDepthPort bean, 36 | Integer depth, Integer granularDepth) { 37 | super(bean); 38 | this.depth = depth; 39 | this.granularDepth = granularDepth; 40 | } 41 | 42 | /** 43 | * @return the depth 44 | */ 45 | public Integer getDepth() { 46 | return depth; 47 | } 48 | 49 | /** 50 | * @return the granularDepth 51 | */ 52 | public Integer getGranularDepth() { 53 | return granularDepth; 54 | } 55 | 56 | @Override 57 | public String toString() { 58 | return getBean() + " has depth " + depth + " and granular depth " 59 | + granularDepth; 60 | } 61 | } 62 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/correctness/report/MismatchConfigurableTypeProblem.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation.correctness.report; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import org.apache.taverna.scufl2.api.common.Configurable; 28 | import org.apache.taverna.scufl2.api.configurations.Configuration; 29 | import org.apache.taverna.scufl2.validation.ValidationProblem; 30 | 31 | 32 | public class MismatchConfigurableTypeProblem extends ValidationProblem { 33 | private final Configurable configurable; 34 | 35 | public MismatchConfigurableTypeProblem(Configuration configuration, 36 | Configurable configurable) { 37 | super(configuration); 38 | this.configurable = configurable; 39 | } 40 | 41 | /** 42 | * @return the configurable 43 | */ 44 | public Configurable getConfigurable() { 45 | return configurable; 46 | } 47 | 48 | @Override 49 | public String toString() { 50 | return "The types of " + getBean() + " and " + configurable 51 | + " are mismatched"; 52 | } 53 | } 54 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/correctness/report/NegativeValueProblem.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation.correctness.report; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 28 | import org.apache.taverna.scufl2.validation.ValidationProblem; 29 | 30 | 31 | public class NegativeValueProblem extends ValidationProblem { 32 | private final String fieldName; 33 | private final Integer fieldValue; 34 | 35 | public NegativeValueProblem(WorkflowBean bean, String fieldName, 36 | Integer fieldValue) { 37 | super(bean); 38 | this.fieldName = fieldName; 39 | this.fieldValue = fieldValue; 40 | } 41 | 42 | /** 43 | * @return the fieldName 44 | */ 45 | public String getFieldName() { 46 | return fieldName; 47 | } 48 | 49 | /** 50 | * @return the fieldValue 51 | */ 52 | public Integer getFieldValue() { 53 | return fieldValue; 54 | } 55 | 56 | @Override 57 | public String toString() { 58 | return getBean() + " has " + fieldName + " of value " + fieldValue; 59 | } 60 | } 61 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/correctness/report/NonAbsoluteURIProblem.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation.correctness.report; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import java.net.URI; 28 | 29 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 30 | import org.apache.taverna.scufl2.validation.ValidationProblem; 31 | 32 | 33 | public class NonAbsoluteURIProblem extends ValidationProblem { 34 | private String fieldName; 35 | private URI fieldValue; 36 | 37 | public NonAbsoluteURIProblem(WorkflowBean bean, String fieldName, 38 | URI fieldValue) { 39 | super(bean); 40 | this.fieldName = fieldName; 41 | this.fieldValue = fieldValue; 42 | } 43 | 44 | /** 45 | * @return the fieldName 46 | */ 47 | public String getFieldName() { 48 | return fieldName; 49 | } 50 | 51 | /** 52 | * @return the fieldValue 53 | */ 54 | public URI getFieldValue() { 55 | return fieldValue; 56 | } 57 | 58 | @Override 59 | public String toString() { 60 | return getBean() + "has a non-absolute URI in field " + fieldName 61 | + " of value " + fieldValue; 62 | } 63 | } 64 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/correctness/report/NullFieldProblem.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation.correctness.report; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 28 | import org.apache.taverna.scufl2.validation.ValidationProblem; 29 | 30 | 31 | public class NullFieldProblem extends ValidationProblem { 32 | private final String fieldName; 33 | 34 | public NullFieldProblem(WorkflowBean bean, String fieldName) { 35 | super(bean); 36 | this.fieldName = fieldName; 37 | } 38 | 39 | /** 40 | * @return the fieldName 41 | */ 42 | public String getFieldName() { 43 | return fieldName; 44 | } 45 | 46 | @Override 47 | public String toString() { 48 | return getBean() + " has a null " + fieldName; 49 | } 50 | } 51 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/correctness/report/OutOfScopeValueProblem.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.validation.correctness.report; 2 | /* 3 | * 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | * 21 | */ 22 | 23 | 24 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 25 | import org.apache.taverna.scufl2.validation.ValidationProblem; 26 | 27 | 28 | /** 29 | * @author alanrw 30 | */ 31 | public class OutOfScopeValueProblem extends ValidationProblem { 32 | private final String fieldName; 33 | private final Object value; 34 | 35 | public OutOfScopeValueProblem(WorkflowBean bean, String fieldName, 36 | Object value) { 37 | super(bean); 38 | this.fieldName = fieldName; 39 | this.value = value; 40 | } 41 | 42 | /** 43 | * @return the fieldName 44 | */ 45 | public String getFieldName() { 46 | return fieldName; 47 | } 48 | 49 | /** 50 | * @return the value 51 | */ 52 | public Object getValue() { 53 | return value; 54 | } 55 | 56 | @Override 57 | public String toString() { 58 | return getBean() + " has " + fieldName + " with out of scope value " + value; 59 | } 60 | } 61 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/correctness/report/PortMentionedTwiceProblem.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.validation.correctness.report; 2 | /* 3 | * 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | * 21 | */ 22 | 23 | 24 | import org.apache.taverna.scufl2.api.iterationstrategy.IterationStrategyNode; 25 | import org.apache.taverna.scufl2.validation.ValidationProblem; 26 | 27 | 28 | /** 29 | * @author alanrw 30 | */ 31 | public class PortMentionedTwiceProblem extends ValidationProblem { 32 | private final IterationStrategyNode duplicateNode; 33 | 34 | public PortMentionedTwiceProblem(IterationStrategyNode originalNode, 35 | IterationStrategyNode duplicateNode) { 36 | super(originalNode); 37 | this.duplicateNode = duplicateNode; 38 | } 39 | 40 | /** 41 | * @return the iterationStrategyNode 42 | */ 43 | public IterationStrategyNode getDuplicateNode() { 44 | return duplicateNode; 45 | } 46 | 47 | @Override 48 | public String toString() { 49 | return (getBean() + " and " + duplicateNode + " reference the same port"); 50 | } 51 | } 52 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/correctness/report/PortMissingFromIterationStrategyStackProblem.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.validation.correctness.report; 2 | /* 3 | * 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | * 21 | */ 22 | 23 | 24 | import org.apache.taverna.scufl2.api.iterationstrategy.IterationStrategyStack; 25 | import org.apache.taverna.scufl2.api.port.Port; 26 | import org.apache.taverna.scufl2.validation.ValidationProblem; 27 | 28 | 29 | /** 30 | * @author alanrw 31 | * 32 | */ 33 | public class PortMissingFromIterationStrategyStackProblem extends 34 | ValidationProblem { 35 | private final Port port; 36 | 37 | public PortMissingFromIterationStrategyStackProblem(Port port, 38 | IterationStrategyStack iterationStrategyStack) { 39 | super(iterationStrategyStack); 40 | this.port = port; 41 | } 42 | 43 | /** 44 | * @return the port 45 | */ 46 | public Port getPort() { 47 | return port; 48 | } 49 | 50 | @Override 51 | public String toString() { 52 | return getBean() + " does not include " + port; 53 | } 54 | } 55 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/correctness/report/WrongParentProblem.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation.correctness.report; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 28 | import org.apache.taverna.scufl2.validation.ValidationProblem; 29 | 30 | 31 | public class WrongParentProblem extends ValidationProblem { 32 | public WrongParentProblem(WorkflowBean bean) { 33 | super(bean); 34 | } 35 | 36 | @Override 37 | public String toString() { 38 | return getBean() + " does not have the correct parent"; 39 | } 40 | } 41 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/structural/report/DotProductIterationMismatchProblem.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation.structural.report; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 28 | import org.apache.taverna.scufl2.validation.ValidationProblem; 29 | 30 | 31 | /** 32 | * @author alanrw 33 | */ 34 | public class DotProductIterationMismatchProblem extends ValidationProblem { 35 | public DotProductIterationMismatchProblem(WorkflowBean bean) { 36 | super(bean); 37 | } 38 | } 39 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/structural/report/EmptyCrossProductProblem.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.validation.structural.report; 2 | /* 3 | * 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | * 21 | */ 22 | 23 | 24 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 25 | import org.apache.taverna.scufl2.validation.ValidationProblem; 26 | 27 | 28 | public class EmptyCrossProductProblem extends ValidationProblem { 29 | public EmptyCrossProductProblem(WorkflowBean bean) { 30 | super(bean); 31 | } 32 | } 33 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/structural/report/EmptyDotProductProblem.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.validation.structural.report; 2 | /* 3 | * 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | * 21 | */ 22 | 23 | 24 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 25 | import org.apache.taverna.scufl2.validation.ValidationProblem; 26 | 27 | 28 | public class EmptyDotProductProblem extends ValidationProblem { 29 | public EmptyDotProductProblem(WorkflowBean bean) { 30 | super(bean); 31 | } 32 | } 33 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/structural/report/FailedProcessorProblem.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation.structural.report; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 28 | import org.apache.taverna.scufl2.validation.ValidationProblem; 29 | 30 | 31 | /** 32 | * @author alanrw 33 | */ 34 | public class FailedProcessorProblem extends ValidationProblem { 35 | public FailedProcessorProblem(WorkflowBean bean) { 36 | super(bean); 37 | } 38 | } 39 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/structural/report/IncompleteWorkflowProblem.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation.structural.report; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 28 | import org.apache.taverna.scufl2.validation.ValidationProblem; 29 | 30 | 31 | /** 32 | * @author alanrw 33 | */ 34 | public class IncompleteWorkflowProblem extends ValidationProblem { 35 | public IncompleteWorkflowProblem(WorkflowBean bean) { 36 | super(bean); 37 | } 38 | } 39 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/structural/report/MissingIterationStrategyStackProblem.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.validation.structural.report; 2 | /* 3 | * 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | * 21 | */ 22 | 23 | 24 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 25 | import org.apache.taverna.scufl2.validation.ValidationProblem; 26 | 27 | 28 | public class MissingIterationStrategyStackProblem extends ValidationProblem { 29 | public MissingIterationStrategyStackProblem(WorkflowBean bean) { 30 | super(bean); 31 | } 32 | } 33 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/structural/report/MissingMainIncomingDataLinkProblem.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation.structural.report; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 28 | import org.apache.taverna.scufl2.validation.ValidationProblem; 29 | 30 | 31 | /** 32 | * @author alanrw 33 | */ 34 | public class MissingMainIncomingDataLinkProblem extends ValidationProblem { 35 | public MissingMainIncomingDataLinkProblem(WorkflowBean bean) { 36 | super(bean); 37 | } 38 | } 39 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/structural/report/UnrecognizedIterationStrategyNodeProblem.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation.structural.report; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 28 | import org.apache.taverna.scufl2.validation.ValidationProblem; 29 | 30 | 31 | /** 32 | * @author alanrw 33 | */ 34 | public class UnrecognizedIterationStrategyNodeProblem extends ValidationProblem { 35 | public UnrecognizedIterationStrategyNodeProblem(WorkflowBean bean) { 36 | super(bean); 37 | } 38 | } 39 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/structural/report/UnresolvedOutputProblem.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation.structural.report; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 28 | import org.apache.taverna.scufl2.validation.ValidationProblem; 29 | 30 | 31 | /** 32 | * @author alanrw 33 | */ 34 | public class UnresolvedOutputProblem extends ValidationProblem { 35 | public UnresolvedOutputProblem(WorkflowBean bean) { 36 | super(bean); 37 | } 38 | } 39 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/java/org/apache/taverna/scufl2/validation/structural/report/UnresolvedProcessorProblem.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.validation.structural.report; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 28 | import org.apache.taverna.scufl2.validation.ValidationProblem; 29 | 30 | 31 | /** 32 | * @author alanrw 33 | */ 34 | public class UnresolvedProcessorProblem extends ValidationProblem { 35 | public UnresolvedProcessorProblem(WorkflowBean bean) { 36 | super(bean); 37 | } 38 | } 39 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/resources/META-INF/services/org.apache.taverna.scufl2.api.io.WorkflowBundleReader: -------------------------------------------------------------------------------- 1 | # Licensed to the Apache Software Foundation (ASF) under one or more # contributor license agreements. See the NOTICE file distributed with # this work for additional information regarding copyright ownership. # The ASF licenses this file to You under the Apache License, Version 2.0 # (the "License"); you may not use this file except in compliance with # the License. You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. org.apache.taverna.scufl2.api.io.structure.StructureReader -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/resources/META-INF/services/org.apache.taverna.scufl2.api.io.WorkflowBundleWriter: -------------------------------------------------------------------------------- 1 | # Licensed to the Apache Software Foundation (ASF) under one or more # contributor license agreements. See the NOTICE file distributed with # this work for additional information regarding copyright ownership. # The ASF licenses this file to You under the Apache License, Version 2.0 # (the "License"); you may not use this file except in compliance with # the License. You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. org.apache.taverna.scufl2.api.io.structure.StructureWriter -------------------------------------------------------------------------------- /taverna-scufl2-api/src/main/resources/META-INF/spring/scufl2-api-context.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 21 | 22 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/test/java/org/apache/taverna/scufl2/api/TestAbstractRevisioned.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import static org.junit.Assert.*; 24 | 25 | import java.util.UUID; 26 | 27 | import org.apache.taverna.scufl2.api.container.WorkflowBundle; 28 | import org.apache.taverna.scufl2.api.core.Workflow; 29 | import org.apache.taverna.scufl2.api.profiles.Profile; 30 | import org.junit.Test; 31 | 32 | 33 | public class TestAbstractRevisioned { 34 | @Test 35 | public void profileName() throws Exception { 36 | Profile p = new Profile(); 37 | UUID uuid = UUID.fromString(p.getName()); 38 | assertEquals(4, uuid.version()); 39 | 40 | } 41 | 42 | @Test 43 | public void workflow() throws Exception { 44 | Workflow wf = new Workflow(); 45 | UUID uuid = UUID.fromString(wf.getName()); 46 | assertEquals(4, uuid.version()); 47 | } 48 | 49 | @Test 50 | public void workflowBundle() throws Exception { 51 | WorkflowBundle wfBundle = new WorkflowBundle(); 52 | UUID uuid = UUID.fromString(wfBundle.getName()); 53 | assertEquals(4, uuid.version()); 54 | } 55 | } 56 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/test/java/org/apache/taverna/scufl2/api/TestExampleWorkflow.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import org.junit.Test; 24 | 25 | public class TestExampleWorkflow extends ExampleWorkflow { 26 | 27 | @Test 28 | public void makeflowBundle() throws Exception { 29 | makeWorkflowBundle(); 30 | // TODO: Check fields 31 | } 32 | 33 | } 34 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/test/java/org/apache/taverna/scufl2/api/annotation/TestAnnotations.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.annotation; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import org.apache.taverna.scufl2.api.annotation.Annotation; 24 | import org.apache.taverna.scufl2.api.container.WorkflowBundle; 25 | 26 | public class TestAnnotations { 27 | 28 | 29 | public void addAnnotation() { 30 | WorkflowBundle wfBundle = new WorkflowBundle(); 31 | Annotation ann = new Annotation(); 32 | wfBundle.getAnnotations().add(ann); 33 | 34 | } 35 | 36 | } 37 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/test/java/org/apache/taverna/scufl2/api/common/AllBeansVisitor.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.common; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import java.util.ArrayList; 24 | import java.util.List; 25 | 26 | import org.apache.taverna.scufl2.api.common.Visitor; 27 | import org.apache.taverna.scufl2.api.common.WorkflowBean; 28 | import org.apache.taverna.scufl2.api.common.Visitor.VisitorWithPath; 29 | 30 | 31 | public class AllBeansVisitor extends VisitorWithPath implements Visitor { 32 | 33 | private final List allBeans = new ArrayList(); 34 | 35 | @Override 36 | public boolean visit() { 37 | getAllBeans().add(getCurrentNode()); 38 | return true; 39 | } 40 | 41 | public List getAllBeans() { 42 | return allBeans; 43 | } 44 | 45 | public static List allBeansFrom(WorkflowBean bean) { 46 | AllBeansVisitor visitor = new AllBeansVisitor(); 47 | bean.accept(visitor); 48 | return visitor.getAllBeans(); 49 | } 50 | 51 | 52 | 53 | } 54 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/test/java/org/apache/taverna/scufl2/api/impl/TestNullCompare.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.impl; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import static org.junit.Assert.assertEquals; 24 | 25 | import java.util.Arrays; 26 | import java.util.Collections; 27 | import java.util.List; 28 | 29 | import org.apache.taverna.scufl2.api.impl.NullSafeComparator; 30 | import org.junit.Test; 31 | 32 | public class TestNullCompare { 33 | @Test 34 | public void testNullCompare() throws Exception { 35 | List values = Arrays.asList("c", null, "b", null, "a", "c"); 36 | Collections.sort(values, new NullSafeComparator()); 37 | assertEquals(Arrays.asList(null, null, "a", "b", "c", "c"), values); 38 | } 39 | } 40 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/test/java/org/apache/taverna/scufl2/api/io/TestResources.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.api.io; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import static org.junit.Assert.assertTrue; 24 | 25 | import org.apache.taverna.scufl2.api.ExampleWorkflow; 26 | import org.apache.taverna.scufl2.api.container.WorkflowBundle; 27 | import org.apache.taverna.scufl2.ucfpackage.UCFPackage; 28 | import org.junit.Before; 29 | import org.junit.Test; 30 | 31 | 32 | public class TestResources { 33 | 34 | private WorkflowBundle wb; 35 | ExampleWorkflow exampleWorkflow = new ExampleWorkflow(); 36 | 37 | @Test 38 | public void emptyResources() throws Exception { 39 | UCFPackage resources = wb.getResources(); 40 | assertTrue(resources.listResources().isEmpty()); 41 | } 42 | 43 | @Before 44 | public void makeBundle() { 45 | wb = exampleWorkflow.makeWorkflowBundle(); 46 | } 47 | 48 | @Test 49 | public void singleFile() throws Exception { 50 | UCFPackage resources = wb.getResources(); 51 | resources.addResource("Hello there", "hello.txt", "text/plain"); 52 | assertTrue(resources.listResources().containsKey("hello.txt")); 53 | } 54 | } 55 | -------------------------------------------------------------------------------- /taverna-scufl2-api/src/test/resources/org/apache/taverna/scufl2/api/io/HelloWorld.txt: -------------------------------------------------------------------------------- 1 | WorkflowBundle 'HelloWorld' 2 | MainWorkflow 'HelloWorld' 3 | Workflow 'HelloWorld' 4 | In 'yourName' 5 | Out 'results' 6 | Processor 'Hello' 7 | In 'name' 8 | Out 'greeting' 9 | Processor 'wait4me' 10 | Links 11 | 'Hello:greeting' -> 'results' 12 | 'yourName' -> 'Hello:name' 13 | 'yourName' -> 'results' 14 | Controls 15 | block 'Hello' until 'wait4me' finish 16 | MainProfile 'tavernaWorkbench' 17 | Profile 'tavernaServer' 18 | Activity 'HelloScript' 19 | Type 20 | In 'personName' 21 | Out 'hello' 22 | ProcessorBinding 'Hello' 23 | Activity 'HelloScript' 24 | Processor 'HelloWorld:Hello' 25 | InputPortBindings 26 | 'name' -> 'personName' 27 | OutputPortBindings 28 | 'hello' -> 'greeting' 29 | Configuration 'Hello' 30 | Type 31 | Configures 'activity/HelloScript' 32 | {"script":"hello = \"Hello, \" + personName;\nSystem.out.println(\"Server says: \" + hello);"} 33 | Profile 'tavernaWorkbench' 34 | Activity 'HelloScript' 35 | Type 36 | In 'personName' 37 | Out 'hello' 38 | ProcessorBinding 'Hello' 39 | Activity 'HelloScript' 40 | Processor 'HelloWorld:Hello' 41 | InputPortBindings 42 | 'name' -> 'personName' 43 | OutputPortBindings 44 | 'hello' -> 'greeting' 45 | Configuration 'Hello' 46 | Type 47 | Configures 'activity/HelloScript' 48 | {"script":"hello = \"Hello, \" + personName;\nJOptionPane.showMessageDialog(null, hello);"} -------------------------------------------------------------------------------- /taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/InputPort.java: -------------------------------------------------------------------------------- 1 | /* 2 | * Licensed to the Apache Software Foundation (ASF) under one 3 | * or more contributor license agreements. See the NOTICE file 4 | * distributed with this work for additional information 5 | * regarding copyright ownership. The ASF licenses this file 6 | * to you under the Apache License, Version 2.0 (the 7 | * "License"); you may not use this file except in compliance 8 | * with the License. You may obtain a copy of the License at 9 | * 10 | * http://www.apache.org/licenses/LICENSE-2.0 11 | * 12 | * Unless required by applicable law or agreed to in writing, 13 | * software distributed under the License is distributed on an 14 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 15 | * KIND, either express or implied. See the License for the 16 | * specific language governing permissions and limitations 17 | * under the License. 18 | */ 19 | 20 | package org.apache.taverna.scufl2.cwl.components; 21 | 22 | public class InputPort { 23 | 24 | private String name; 25 | 26 | private String source; 27 | 28 | public InputPort() { 29 | this.name = ""; 30 | this.source = ""; 31 | } 32 | 33 | public InputPort(String name, String source) { 34 | this.name = name; 35 | this.source = source; 36 | } 37 | 38 | public String getName() { 39 | return this.name; 40 | } 41 | 42 | public void setName(String name) { 43 | this.name = name; 44 | } 45 | 46 | public String getSource() { 47 | return source; 48 | } 49 | 50 | public void setSource(String source) { 51 | this.source = source; 52 | } 53 | } -------------------------------------------------------------------------------- /taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/OutputPort.java: -------------------------------------------------------------------------------- 1 | /* 2 | * Licensed to the Apache Software Foundation (ASF) under one 3 | * or more contributor license agreements. See the NOTICE file 4 | * distributed with this work for additional information 5 | * regarding copyright ownership. The ASF licenses this file 6 | * to you under the Apache License, Version 2.0 (the 7 | * "License"); you may not use this file except in compliance 8 | * with the License. You may obtain a copy of the License at 9 | * 10 | * http://www.apache.org/licenses/LICENSE-2.0 11 | * 12 | * Unless required by applicable law or agreed to in writing, 13 | * software distributed under the License is distributed on an 14 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 15 | * KIND, either express or implied. See the License for the 16 | * specific language governing permissions and limitations 17 | * under the License. 18 | */ 19 | 20 | package org.apache.taverna.scufl2.cwl.components; 21 | 22 | public class OutputPort { 23 | 24 | private String name; 25 | 26 | public OutputPort() { 27 | this.name = ""; 28 | } 29 | 30 | public OutputPort(String name) { 31 | this.name = name; 32 | } 33 | 34 | public String getName() { 35 | return this.name; 36 | } 37 | 38 | public void setName(String name) { 39 | this.name = name; 40 | } 41 | } -------------------------------------------------------------------------------- /taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/Reference.java: -------------------------------------------------------------------------------- 1 | /* 2 | * Licensed to the Apache Software Foundation (ASF) under one 3 | * or more contributor license agreements. See the NOTICE file 4 | * distributed with this work for additional information 5 | * regarding copyright ownership. The ASF licenses this file 6 | * to you under the Apache License, Version 2.0 (the 7 | * "License"); you may not use this file except in compliance 8 | * with the License. You may obtain a copy of the License at 9 | * 10 | * http://www.apache.org/licenses/LICENSE-2.0 11 | * 12 | * Unless required by applicable law or agreed to in writing, 13 | * software distributed under the License is distributed on an 14 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 15 | * KIND, either express or implied. See the License for the 16 | * specific language governing permissions and limitations 17 | * under the License. 18 | */ 19 | 20 | package org.apache.taverna.scufl2.cwl.components; 21 | 22 | 23 | public class Reference extends Process { 24 | 25 | private String source; 26 | 27 | public Reference() { 28 | source = ""; 29 | name = ""; 30 | } 31 | 32 | public Reference(String src) { 33 | this.source = src; 34 | this.name = ""; 35 | } 36 | 37 | public void parse() { 38 | // TODO: read source file and parse nested workflow 39 | } 40 | 41 | public String toString() { 42 | return source; 43 | } 44 | 45 | public String getSource() { 46 | return source; 47 | } 48 | } -------------------------------------------------------------------------------- /taverna-scufl2-cwl/src/main/resources/META-INF/services/org.apache.taverna.scufl2.api.io.WorkflowBundleReader: -------------------------------------------------------------------------------- 1 | org.apache.taverna.scufl2.cwl.CWLReader -------------------------------------------------------------------------------- /taverna-scufl2-cwl/src/main/resources/hello_world.cwl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env cwl-runner 2 | 3 | # Licensed to the Apache Software Foundation (ASF) under one 4 | # or more contributor license agreements. See the NOTICE file 5 | # distributed with this work for additional information 6 | # regarding copyright ownership. The ASF licenses this file 7 | # to you under the Apache License, Version 2.0 (the 8 | # "License"); you may not use this file except in compliance 9 | # with the License. You may obtain a copy of the License at 10 | # 11 | # http://www.apache.org/licenses/LICENSE-2.0 12 | # 13 | # Unless required by applicable law or agreed to in writing, 14 | # software distributed under the License is distributed on an 15 | # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 16 | # KIND, either express or implied. See the License for the 17 | # specific language governing permissions and limitations 18 | # under the License. 19 | 20 | cwlVersion: v1.0 21 | class: Workflow 22 | 23 | inputs: 24 | name: string 25 | 26 | outputs: 27 | output1: string 28 | 29 | steps: 30 | step1: 31 | run: example.cwl 32 | 33 | inputs: 34 | - id: text 35 | source: "#x/name" 36 | 37 | outputs: [] 38 | -------------------------------------------------------------------------------- /taverna-scufl2-cwl/src/test/resources/1st-tool.cwl: -------------------------------------------------------------------------------- 1 | # Licensed to the Apache Software Foundation (ASF) under one 2 | # or more contributor license agreements. See the NOTICE file 3 | # distributed with this work for additional information 4 | # regarding copyright ownership. The ASF licenses this file 5 | # to you under the Apache License, Version 2.0 (the 6 | # "License"); you may not use this file except in compliance 7 | # with the License. You may obtain a copy of the License at 8 | # 9 | # http://www.apache.org/licenses/LICENSE-2.0 10 | # 11 | # Unless required by applicable law or agreed to in writing, 12 | # software distributed under the License is distributed on an 13 | # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 14 | # KIND, either express or implied. See the License for the 15 | # specific language governing permissions and limitations 16 | # under the License. 17 | cwlVersion: v1.0 18 | class: CommandLineTool 19 | baseCommand: echo 20 | inputs: 21 | message: 22 | type: string 23 | 24 | inputBinding: 25 | position: 1 26 | outputs: [] -------------------------------------------------------------------------------- /taverna-scufl2-cwl/src/test/resources/hello_world.cwl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env cwl-runner 2 | 3 | # Licensed to the Apache Software Foundation (ASF) under one 4 | # or more contributor license agreements. See the NOTICE file 5 | # distributed with this work for additional information 6 | # regarding copyright ownership. The ASF licenses this file 7 | # to you under the Apache License, Version 2.0 (the 8 | # "License"); you may not use this file except in compliance 9 | # with the License. You may obtain a copy of the License at 10 | # 11 | # http://www.apache.org/licenses/LICENSE-2.0 12 | # 13 | # Unless required by applicable law or agreed to in writing, 14 | # software distributed under the License is distributed on an 15 | # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 16 | # KIND, either express or implied. See the License for the 17 | # specific language governing permissions and limitations 18 | # under the License. 19 | 20 | cwlVersion: v1.0 21 | class: Workflow 22 | 23 | inputs: 24 | name: string 25 | 26 | outputs: 27 | output1: string 28 | 29 | steps: 30 | step1: 31 | run: example.cwl 32 | 33 | inputs: 34 | - id: text 35 | source: "name" 36 | 37 | outputs: [] 38 | -------------------------------------------------------------------------------- /taverna-scufl2-cwl/src/test/resources/int_input.cwl: -------------------------------------------------------------------------------- 1 | # Licensed to the Apache Software Foundation (ASF) under one 2 | # or more contributor license agreements. See the NOTICE file 3 | # distributed with this work for additional information 4 | # regarding copyright ownership. The ASF licenses this file 5 | # to you under the Apache License, Version 2.0 (the 6 | # "License"); you may not use this file except in compliance 7 | # with the License. You may obtain a copy of the License at 8 | # 9 | # http://www.apache.org/licenses/LICENSE-2.0 10 | # 11 | # Unless required by applicable law or agreed to in writing, 12 | # software distributed under the License is distributed on an 13 | # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 14 | # KIND, either express or implied. See the License for the 15 | # specific language governing permissions and limitations 16 | # under the License. 17 | inputs: 18 | example_int: 19 | type: int 20 | inputBinding: 21 | position: 2 22 | prefix: -i 23 | -------------------------------------------------------------------------------- /taverna-scufl2-cwl/src/test/resources/simple_string_input.cwl: -------------------------------------------------------------------------------- 1 | # Licensed to the Apache Software Foundation (ASF) under one 2 | # or more contributor license agreements. See the NOTICE file 3 | # distributed with this work for additional information 4 | # regarding copyright ownership. The ASF licenses this file 5 | # to you under the Apache License, Version 2.0 (the 6 | # "License"); you may not use this file except in compliance 7 | # with the License. You may obtain a copy of the License at 8 | # 9 | # http://www.apache.org/licenses/LICENSE-2.0 10 | # 11 | # Unless required by applicable law or agreed to in writing, 12 | # software distributed under the License is distributed on an 13 | # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 14 | # KIND, either express or implied. See the License for the 15 | # specific language governing permissions and limitations 16 | # under the License. 17 | inputs: 18 | example_string: string 19 | steps: 20 | step1: 21 | run: run1 -------------------------------------------------------------------------------- /taverna-scufl2-cwl/src/test/resources/workflow_with_command.cwl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env cwl-runner 2 | 3 | # Licensed to the Apache Software Foundation (ASF) under one 4 | # or more contributor license agreements. See the NOTICE file 5 | # distributed with this work for additional information 6 | # regarding copyright ownership. The ASF licenses this file 7 | # to you under the Apache License, Version 2.0 (the 8 | # "License"); you may not use this file except in compliance 9 | # with the License. You may obtain a copy of the License at 10 | # 11 | # http://www.apache.org/licenses/LICENSE-2.0 12 | # 13 | # Unless required by applicable law or agreed to in writing, 14 | # software distributed under the License is distributed on an 15 | # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 16 | # KIND, either express or implied. See the License for the 17 | # specific language governing permissions and limitations 18 | # under the License. 19 | 20 | cwlVersion: v1.0 21 | class: Workflow 22 | 23 | inputs: 24 | name: string 25 | 26 | outputs: [] 27 | 28 | steps: 29 | step1: 30 | run: 31 | class: CommandLineTool 32 | baseCommand: echo 33 | inputs: 34 | message: 35 | type: string 36 | 37 | inputBinding: 38 | position: 1 39 | outputs: [] 40 | 41 | inputs: 42 | - id: text 43 | source: "#x/name" 44 | 45 | outputs: [] 46 | -------------------------------------------------------------------------------- /taverna-scufl2-cwl/src/test/resources/workflow_with_workflow.cwl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env cwl-runner 2 | 3 | # Licensed to the Apache Software Foundation (ASF) under one 4 | # or more contributor license agreements. See the NOTICE file 5 | # distributed with this work for additional information 6 | # regarding copyright ownership. The ASF licenses this file 7 | # to you under the Apache License, Version 2.0 (the 8 | # "License"); you may not use this file except in compliance 9 | # with the License. You may obtain a copy of the License at 10 | # 11 | # http://www.apache.org/licenses/LICENSE-2.0 12 | # 13 | # Unless required by applicable law or agreed to in writing, 14 | # software distributed under the License is distributed on an 15 | # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 16 | # KIND, either express or implied. See the License for the 17 | # specific language governing permissions and limitations 18 | # under the License. 19 | cwlVersion: v1.0 20 | class: Workflow 21 | 22 | inputs: 23 | message: string 24 | 25 | outputs: 26 | download: 27 | type: File 28 | outputSource: "curl" 29 | 30 | steps: 31 | step1: 32 | run: 33 | class: Workflow 34 | inputs: 35 | name: string 36 | outputs: 37 | output1: string 38 | steps: 39 | step2: 40 | run: example.cwl 41 | inputs: 42 | - id: text 43 | source: "name" 44 | outputs: [] 45 | in: 46 | text: message 47 | 48 | out: [curl] 49 | -------------------------------------------------------------------------------- /taverna-scufl2-examples/examples/helloanyone.wfbundle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-scufl2-examples/examples/helloanyone.wfbundle -------------------------------------------------------------------------------- /taverna-scufl2-examples/examples/helloworld.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context" : [ "https://w3id.org/scufl2/context", { 3 | "@base" : "http://ns.taverna.org.uk/2010/workflowBundle/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/" 4 | } ], 5 | "id" : "http://ns.taverna.org.uk/2010/workflowBundle/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/", 6 | "workflow" : { 7 | "id" : "workflow/Hello_World/", 8 | "name" : "Hello_World", 9 | "revisions" : [ { 10 | "id" : "http://ns.taverna.org.uk/2010/workflow/8781d5f4-d0ba-48a8-a1d1-14281bd8a917/", 11 | "generatedAtTime" : "2012-01-03T15:12:21Z" 12 | } ], 13 | "inputs" : [ ], 14 | "outputs" : [ { 15 | "name" : "greeting", 16 | "id" : "workflow/Hello_World/out/greeting" 17 | } ], 18 | "processors" : [ { 19 | "id" : "workflow/Hello_World/processor/hello/", 20 | "name" : "hello", 21 | "inputs" : [ ], 22 | "outputs" : [ { 23 | "name" : "value", 24 | "id" : "workflow/Hello_World/processor/hello/out/value", 25 | "depth" : 0 26 | } ] 27 | } ], 28 | "datalinks" : [ { 29 | "receivesFrom" : "workflow/Hello_World/processor/hello/out/value", 30 | "sendsTo" : "workflow/Hello_World/out/greeting" 31 | } ], 32 | "controllinks" : [ ] 33 | }, 34 | "profile" : { 35 | "id" : "profile/taverna-2.2.0/" 36 | } 37 | } -------------------------------------------------------------------------------- /taverna-scufl2-examples/examples/helloworld.wfbundle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-scufl2-examples/examples/helloworld.wfbundle -------------------------------------------------------------------------------- /taverna-scufl2-examples/src/main/resources/context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context" : { 3 | "foaf": "http://xmlns.com/foaf/0.1/", 4 | "rdfs": "http://www.w3.org/2000/01/rdf-schema#", 5 | "prov": "http://www.w3.org.ns/prov#", 6 | "wfdesc": "http://purl.org/wf4ever/wfdesc#", 7 | "scufl2": "http://ns.taverna.org.uk/2010/scufl2#", 8 | 9 | "id": "@id", 10 | "name": "rdfs:label", 11 | "revisions": "prov:alternateOf", 12 | "processors": "wfdesc:hasSubProcess", 13 | "inputs": "wfdesc:hasInput", 14 | "outputs": "wfdesc:hasOutput", 15 | "depth": "scufl2:depth", 16 | "granularDepth": "scufl2:granularDepth", 17 | "workflow": "foaf:primaryTopic", 18 | "generatedAtTime": "prov:generatedAtTime" 19 | } 20 | } 21 | -------------------------------------------------------------------------------- /taverna-scufl2-examples/src/test/resources/workflows/wfbundle/as.wfbundle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-scufl2-examples/src/test/resources/workflows/wfbundle/as.wfbundle -------------------------------------------------------------------------------- /taverna-scufl2-examples/src/test/resources/workflows/wfbundle/defaultActivitiesTaverna2.wfbundle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-scufl2-examples/src/test/resources/workflows/wfbundle/defaultActivitiesTaverna2.wfbundle -------------------------------------------------------------------------------- /taverna-scufl2-integration-tests/src/test/resources/clone-error.wfbundle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-scufl2-integration-tests/src/test/resources/clone-error.wfbundle -------------------------------------------------------------------------------- /taverna-scufl2-integration-tests/src/test/resources/t172starterpacklist: -------------------------------------------------------------------------------- 1 | # 2 | # Licensed to the Apache Software Foundation (ASF) under one or more 3 | # contributor license agreements. See the NOTICE file distributed with 4 | # this work for additional information regarding copyright ownership. 5 | # The ASF licenses this file to You under the Apache License, Version 2.0 6 | # (the "License"); you may not use this file except in compliance with 7 | # the License. You may obtain a copy of the License at 8 | # 9 | # http://www.apache.org/licenses/LICENSE-2.0 10 | # 11 | # Unless required by applicable law or agreed to in writing, software 12 | # distributed under the License is distributed on an "AS IS" BASIS, 13 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | # See the License for the specific language governing permissions and 15 | # limitations under the License. 16 | http://www.myexperiment.org/workflows/157/download/example_of_a_conditional_execution_workflow_7882.xml?version=1 17 | -------------------------------------------------------------------------------- /taverna-scufl2-scufl/src/main/java/org/apache/taverna/scufl2/translator/scufl/ScuflExtensionParser.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.translator.scufl; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import java.net.URI; 28 | import java.util.List; 29 | 30 | /** 31 | * @author alanrw 32 | */ 33 | public interface ScuflExtensionParser { 34 | void setParserState(ParserState state); 35 | 36 | ParserState getParserState(); 37 | 38 | List getAdditionalSchemas(); 39 | 40 | void parseScuflObject(Object o); 41 | 42 | boolean canHandle(Class c); 43 | } 44 | -------------------------------------------------------------------------------- /taverna-scufl2-scufl/src/main/java/org/apache/taverna/scufl2/translator/scufl/processorelement/AbstractExtensionParser.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.translator.scufl.processorelement; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import org.apache.taverna.scufl2.translator.scufl.ParserState; 28 | import org.apache.taverna.scufl2.translator.scufl.ScuflExtensionParser; 29 | 30 | /** 31 | * @author alanrw 32 | */ 33 | public abstract class AbstractExtensionParser implements ScuflExtensionParser { 34 | private ParserState parserState; 35 | 36 | /** 37 | * @return the parserState 38 | */ 39 | @Override 40 | public ParserState getParserState() { 41 | return parserState; 42 | } 43 | 44 | /** 45 | * @param parserState the parserState to set 46 | */ 47 | @Override 48 | public void setParserState(ParserState parserState) { 49 | this.parserState = parserState; 50 | } 51 | } 52 | -------------------------------------------------------------------------------- /taverna-scufl2-scufl/src/main/java/org/apache/taverna/scufl2/translator/scufl/processorelement/AbstractProcessorExtensionParser.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.translator.scufl.processorelement; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import java.net.URI; 28 | import java.util.Collections; 29 | import java.util.List; 30 | 31 | /** 32 | * @author alanrw 33 | */ 34 | public class AbstractProcessorExtensionParser extends AbstractExtensionParser { 35 | @Override 36 | public boolean canHandle(Class c) { 37 | return c.equals(org.apache.taverna.scufl2.xml.scufl.jaxb.AbstractprocessorType.class); 38 | } 39 | 40 | @Override 41 | public List getAdditionalSchemas() { 42 | return Collections.emptyList(); 43 | } 44 | 45 | @Override 46 | public void parseScuflObject(Object o) { 47 | System.err.println(this.getClass() + " is not yet implemented"); 48 | } 49 | } 50 | -------------------------------------------------------------------------------- /taverna-scufl2-scufl/src/main/java/org/apache/taverna/scufl2/translator/scufl/processorelement/WsdlExtensionParser.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.translator.scufl.processorelement; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | import java.net.URI; 28 | import java.net.URISyntaxException; 29 | import java.net.URL; 30 | import java.util.Arrays; 31 | import java.util.List; 32 | 33 | /** 34 | * @author alanrw 35 | */ 36 | public class WsdlExtensionParser extends AbstractExtensionParser { 37 | private static final String WSDL_XSD = "/uk/org/taverna/scufl2/translator/scufl/xsd/scufl-wsdl.xsd"; 38 | 39 | @Override 40 | public boolean canHandle(Class c) { 41 | return c.equals(org.apache.taverna.scufl2.xml.scufl.jaxb.WsdlType.class); 42 | } 43 | 44 | @Override 45 | public List getAdditionalSchemas() { 46 | URL wsdlXsd = getClass().getResource(WSDL_XSD); 47 | try { 48 | return Arrays.asList(wsdlXsd.toURI()); 49 | } catch (URISyntaxException e) { 50 | throw new IllegalStateException("Can't find WSDL schema " + wsdlXsd); 51 | } 52 | } 53 | 54 | @Override 55 | public void parseScuflObject(Object o) { 56 | // TODO write to log? 57 | System.err.println(this.getClass() + " is not yet implemented"); 58 | } 59 | } 60 | -------------------------------------------------------------------------------- /taverna-scufl2-scufl/src/main/resources/META-INF/services/org.apache.taverna.scufl2.api.io.WorkflowBundleReader: -------------------------------------------------------------------------------- 1 | org.apache.taverna.scufl2.translator.scufl.ScuflReader -------------------------------------------------------------------------------- /taverna-scufl2-scufl/src/main/resources/META-INF/services/org.apache.taverna.scufl2.translator.scufl.ScuflExtensionParser: -------------------------------------------------------------------------------- 1 | org.apache.taverna.scufl2.translator.scufl.processorelement.AbstractProcessorExtensionParser 2 | org.apache.taverna.scufl2.translator.scufl.processorelement.ApiConsumerExtensionParser 3 | org.apache.taverna.scufl2.translator.scufl.processorelement.BeanshellExtensionParser 4 | org.apache.taverna.scufl2.translator.scufl.processorelement.BiomartExtensionParser 5 | org.apache.taverna.scufl2.translator.scufl.processorelement.BiomobyExtensionParser 6 | org.apache.taverna.scufl2.translator.scufl.processorelement.LocalExtensionParser 7 | org.apache.taverna.scufl2.translator.scufl.processorelement.RshellExtensionParser 8 | org.apache.taverna.scufl2.translator.scufl.processorelement.SoaplabExtensionParser 9 | org.apache.taverna.scufl2.translator.scufl.processorelement.StringConstantExtensionParser 10 | org.apache.taverna.scufl2.translator.scufl.processorelement.WsdlExtensionParser 11 | -------------------------------------------------------------------------------- /taverna-scufl2-scufl/src/main/resources/org/apache/taverna/scufl2/translator/scufl/xsd/scufl-biomart.xsd: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /taverna-scufl2-scufl/src/main/resources/org/apache/taverna/scufl2/translator/scufl/xsd/scufl-notification.xsd: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /taverna-scufl2-scufl/src/main/resources/org/apache/taverna/scufl2/translator/scufl/xsd/scufl-soaplab.xsd: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | -------------------------------------------------------------------------------- /taverna-scufl2-scufl/src/main/resources/org/apache/taverna/scufl2/translator/scufl/xsd/scufl-stringconstant.xsd: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | -------------------------------------------------------------------------------- /taverna-scufl2-scufl/src/test/java/org/apache/taverna/scufl2/translator/scufl2/TestStarterPack.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package org.apache.taverna.scufl2.translator.scufl2; 5 | /* 6 | * 7 | * Licensed to the Apache Software Foundation (ASF) under one 8 | * or more contributor license agreements. See the NOTICE file 9 | * distributed with this work for additional information 10 | * regarding copyright ownership. The ASF licenses this file 11 | * to you under the Apache License, Version 2.0 (the 12 | * "License"); you may not use this file except in compliance 13 | * with the License. You may obtain a copy of the License at 14 | * 15 | * http://www.apache.org/licenses/LICENSE-2.0 16 | * 17 | * Unless required by applicable law or agreed to in writing, 18 | * software distributed under the License is distributed on an 19 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 20 | * KIND, either express or implied. See the License for the 21 | * specific language governing permissions and limitations 22 | * under the License. 23 | * 24 | */ 25 | 26 | 27 | /** 28 | * @author alanrw 29 | * 30 | */ 31 | public class TestStarterPack { 32 | 33 | } 34 | -------------------------------------------------------------------------------- /taverna-scufl2-t2flow/.gitignore: -------------------------------------------------------------------------------- 1 | target 2 | .settings 3 | .classpath 4 | .project 5 | -------------------------------------------------------------------------------- /taverna-scufl2-t2flow/src/main/java/org/apache/taverna/scufl2/translator/t2flow/T2Parser.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.translator.t2flow; 2 | /* 3 | * 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | * 21 | */ 22 | 23 | 24 | import java.net.URI; 25 | import java.util.List; 26 | 27 | import org.apache.taverna.scufl2.api.configurations.Configuration; 28 | import org.apache.taverna.scufl2.api.io.ReaderException; 29 | 30 | import org.apache.taverna.scufl2.xml.t2flow.jaxb.ConfigBean; 31 | 32 | public interface T2Parser { 33 | boolean canHandlePlugin(URI pluginURI); 34 | 35 | URI mapT2flowRavenIdToScufl2URI(URI t2flowActivity); 36 | 37 | Configuration parseConfiguration(T2FlowParser t2FlowParser, 38 | ConfigBean configBean, ParserState parserState) 39 | throws ReaderException; 40 | 41 | List getAdditionalSchemas(); 42 | } 43 | -------------------------------------------------------------------------------- /taverna-scufl2-t2flow/src/main/resources/META-INF/services/org.apache.taverna.scufl2.api.io.WorkflowBundleReader: -------------------------------------------------------------------------------- 1 | org.apache.taverna.scufl2.translator.t2flow.T2FlowReader -------------------------------------------------------------------------------- /taverna-scufl2-t2flow/src/main/resources/META-INF/services/org.apache.taverna.scufl2.translator.t2flow.T2Parser: -------------------------------------------------------------------------------- 1 | org.apache.taverna.scufl2.translator.t2flow.defaultactivities.DataflowActivityParser 2 | org.apache.taverna.scufl2.translator.t2flow.defaultactivities.BeanshellActivityParser 3 | org.apache.taverna.scufl2.translator.t2flow.defaultactivities.RshellActivityParser 4 | org.apache.taverna.scufl2.translator.t2flow.defaultactivities.SpreadsheetActivityParser 5 | org.apache.taverna.scufl2.translator.t2flow.defaultactivities.StringConstantActivityParser 6 | org.apache.taverna.scufl2.translator.t2flow.defaultactivities.BiomobyActivityParser 7 | org.apache.taverna.scufl2.translator.t2flow.defaultactivities.SoaplabActivityParser 8 | org.apache.taverna.scufl2.translator.t2flow.defaultactivities.WSDLActivityParser 9 | org.apache.taverna.scufl2.translator.t2flow.defaultactivities.WSDLXMLSplitterParser 10 | org.apache.taverna.scufl2.translator.t2flow.defaultactivities.BiomartActivityParser 11 | org.apache.taverna.scufl2.translator.t2flow.defaultactivities.ApiConsomerActivityParser 12 | org.apache.taverna.scufl2.translator.t2flow.defaultactivities.InteractionActivityParser 13 | org.apache.taverna.scufl2.translator.t2flow.defaultactivities.ComponentActivityParser 14 | 15 | org.apache.taverna.scufl2.translator.t2flow.t23activities.ExternalToolActivityParser 16 | org.apache.taverna.scufl2.translator.t2flow.t23activities.RESTActivityParser 17 | org.apache.taverna.scufl2.translator.t2flow.t23activities.XPathActivityParser 18 | 19 | org.apache.taverna.scufl2.translator.t2flow.defaultdispatchstack.ParallelizeParser 20 | org.apache.taverna.scufl2.translator.t2flow.defaultdispatchstack.ErrorBounceParser 21 | org.apache.taverna.scufl2.translator.t2flow.defaultdispatchstack.FailoverParser 22 | org.apache.taverna.scufl2.translator.t2flow.defaultdispatchstack.RetryParser 23 | org.apache.taverna.scufl2.translator.t2flow.defaultdispatchstack.LoopParser 24 | org.apache.taverna.scufl2.translator.t2flow.defaultdispatchstack.InvokeParser -------------------------------------------------------------------------------- /taverna-scufl2-ucfpackage/.gitignore: -------------------------------------------------------------------------------- 1 | /target 2 | -------------------------------------------------------------------------------- /taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/impl/odfdom/pkg/manifest/Algorithm.java: -------------------------------------------------------------------------------- 1 | /************************************************************************ 2 | * 3 | * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER 4 | * 5 | * Copyright 2008, 2010 Oracle and/or its affiliates. All rights reserved. 6 | * 7 | * Use is subject to license terms. 8 | * 9 | * Licensed under the Apache License, Version 2.0 (the "License"); you may not 10 | * use this file except in compliance with the License. You may obtain a copy 11 | * of the License at http://www.apache.org/licenses/LICENSE-2.0. You can also 12 | * obtain a copy of the License at http://odftoolkit.org/docs/license.txt 13 | * 14 | * Unless required by applicable law or agreed to in writing, software 15 | * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT 16 | * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 17 | * 18 | * See the License for the specific language governing permissions and 19 | * limitations under the License. 20 | * 21 | ************************************************************************/ 22 | /* This file is derived from ODFDOM 0.8.6, and 23 | * has been modified for Apache Taverna. 24 | * (c) 2010-2014 University of Manchester 25 | * (c) 2015 The Apache Software Foundation 26 | */ 27 | package org.apache.taverna.scufl2.ucfpackage.impl.odfdom.pkg.manifest; 28 | 29 | public class Algorithm { 30 | private String name; 31 | private String initializationVector; 32 | 33 | public Algorithm() { 34 | } 35 | 36 | public Algorithm(String name, String initializationVector) { 37 | this.name = name; 38 | this.initializationVector = initializationVector; 39 | } 40 | 41 | public void setName(String name) { 42 | this.name = name; 43 | } 44 | 45 | public String getName() { 46 | return name; 47 | } 48 | 49 | public void setInitializationVector(String initializationVector) { 50 | this.initializationVector = initializationVector; 51 | } 52 | 53 | public String getInitializationVector() { 54 | return initializationVector; 55 | } 56 | } 57 | -------------------------------------------------------------------------------- /taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/impl/NamespacePrefixMapperJAXB_RI.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.scufl2.rdfxml.impl; 2 | /* 3 | * 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | * 21 | */ 22 | 23 | 24 | import com.sun.xml.bind.marshaller.NamespacePrefixMapper; 25 | 26 | public class NamespacePrefixMapperJAXB_RI extends NamespacePrefixMapper { 27 | @Override 28 | public String getPreferredPrefix(String namespaceUri, String suggestion, 29 | boolean requirePrefix) { 30 | switch (namespaceUri) { 31 | case "http://www.w3.org/2001/XMLSchema-instance": 32 | return "xsi"; 33 | case "http://ns.taverna.org.uk/2010/scufl2#": 34 | return ""; // default 35 | case "http://www.w3.org/1999/02/22-rdf-syntax-ns#": 36 | return "rdf"; 37 | case "http://www.w3.org/2000/01/rdf-schema#": 38 | return "rdfs"; 39 | case "http://purl.org/dc/elements/1.1/": 40 | return "dc"; 41 | case "http://purl.org/dc/terms/": 42 | return "dcterms"; 43 | case "http://www.w3.org/2002/07/owl#": 44 | return "owl"; 45 | default: 46 | return suggestion; 47 | } 48 | } 49 | 50 | @Override 51 | public String[] getPreDeclaredNamespaceUris() { 52 | return new String[] {}; 53 | } 54 | } 55 | -------------------------------------------------------------------------------- /taverna-scufl2-wfbundle/src/main/resources/META-INF/services/org.apache.taverna.scufl2.api.io.WorkflowBundleReader: -------------------------------------------------------------------------------- 1 | org.apache.taverna.scufl2.rdfxml.RDFXMLReader 2 | -------------------------------------------------------------------------------- /taverna-scufl2-wfbundle/src/main/resources/META-INF/services/org.apache.taverna.scufl2.api.io.WorkflowBundleWriter: -------------------------------------------------------------------------------- 1 | org.apache.taverna.scufl2.rdfxml.RDFXMLWriter 2 | -------------------------------------------------------------------------------- /taverna-scufl2-wfbundle/src/main/resources/META-INF/spring/scufl2-rdfxml-context-osgi.xml: -------------------------------------------------------------------------------- 1 | 2 | 22 | 23 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /taverna-scufl2-wfbundle/src/main/resources/META-INF/spring/scufl2-rdfxml-context.xml: -------------------------------------------------------------------------------- 1 | 2 | 22 | 23 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example.wfbundle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example.wfbundle -------------------------------------------------------------------------------- /taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/META-INF/container.xml: -------------------------------------------------------------------------------- 1 | 2 | 22 | 23 | 25 | 26 | 28 | 29 | 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/NOTICE: -------------------------------------------------------------------------------- 1 | Apache Taverna Language 2 | Copyright 2014-2018 The Apache Software Foundation 3 | 4 | This product includes software developed at 5 | The Apache Software Foundation (http://www.apache.org/). 6 | 7 | Portions of this software were originally based on the following: 8 | - Copyright 2010-2014 University of Manchester, UK 9 | These have been licensed to the Apache Software Foundation under a software grant. 10 | 11 | ----------------------------------------------------------------------------------- 12 | -------------------------------------------------------------------------------- /taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/Thumbnails/thumbnail.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/Thumbnails/thumbnail.png -------------------------------------------------------------------------------- /taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/annotation/workflowBundle.rdf: -------------------------------------------------------------------------------- 1 | 2 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 32 | 33 | 34 | 2010-07-29T14:12:14+01:00 35 | 2010-07-29T14:12:14+01:00 36 | Stian Soiland-Reyes 37 | An example workflow to illustrate SCUFL2 38 | 39 | 40 | -------------------------------------------------------------------------------- /taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/diagram/workflow/HelloWorld.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/diagram/workflow/HelloWorld.png -------------------------------------------------------------------------------- /taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/example/mimetype: -------------------------------------------------------------------------------- 1 | application/vnd.taverna.scufl2.workflow-bundle -------------------------------------------------------------------------------- /taverna-scufl2-wfbundle/src/test/resources/org/apache/taverna/scufl2/rdfxml/update-bundle.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | # 3 | # 4 | # Licensed to the Apache Software Foundation (ASF) under one 5 | # or more contributor license agreements. See the NOTICE file 6 | # distributed with this work for additional information 7 | # regarding copyright ownership. The ASF licenses this file 8 | # to you under the Apache License, Version 2.0 (the 9 | # "License"); you may not use this file except in compliance 10 | # with the License. You may obtain a copy of the License at 11 | # 12 | # http://www.apache.org/licenses/LICENSE-2.0 13 | # 14 | # Unless required by applicable law or agreed to in writing, 15 | # software distributed under the License is distributed on an 16 | # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | # KIND, either express or implied. See the License for the 18 | # specific language governing permissions and limitations 19 | # under the License. 20 | # 21 | # 22 | set -e 23 | rm example.wfbundle 24 | cd example 25 | zip -0 -X ../example.wfbundle mimetype 26 | zip -r ../example.wfbundle . -x mimetype 27 | -------------------------------------------------------------------------------- /taverna-scufl2-wfdesc/src/main/resources/META-INF/services/org.apache.taverna.scufl2.api.io.WorkflowBundleReader: -------------------------------------------------------------------------------- 1 | org.apache.taverna.scufl2.wfdesc.WfdescReader 2 | -------------------------------------------------------------------------------- /taverna-scufl2-wfdesc/src/main/resources/META-INF/services/org.apache.taverna.scufl2.api.io.WorkflowBundleWriter: -------------------------------------------------------------------------------- 1 | org.apache.taverna.scufl2.wfdesc.WfdescWriter 2 | -------------------------------------------------------------------------------- /taverna-scufl2-wfdesc/src/main/resources/META-INF/spring/scufl2-wfdesc-context-osgi.xml: -------------------------------------------------------------------------------- 1 | 2 | 22 | 23 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /taverna-scufl2-wfdesc/src/main/resources/META-INF/spring/scufl2-wfdesc-context.xml: -------------------------------------------------------------------------------- 1 | 2 | 22 | 23 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /taverna-tavlang-tool/.gitignore: -------------------------------------------------------------------------------- 1 | dependency-reduced-pom.xml 2 | -------------------------------------------------------------------------------- /taverna-tavlang-tool/src/main/java/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-tavlang-tool/src/main/java/.gitignore -------------------------------------------------------------------------------- /taverna-tavlang-tool/src/main/java/org/apache/taverna/tavlang/TavernaCommandline.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.tavlang; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | public class TavernaCommandline { 23 | 24 | public static void main(String args[]){ 25 | CommandLineTool tool = new CommandLineTool(); 26 | tool.parse(args); 27 | 28 | } 29 | } 30 | -------------------------------------------------------------------------------- /taverna-tavlang-tool/src/main/resources/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-tavlang-tool/src/main/resources/.gitignore -------------------------------------------------------------------------------- /taverna-tavlang-tool/src/test/java/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-tavlang-tool/src/test/java/.gitignore -------------------------------------------------------------------------------- /taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/CommandLineTest.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.tavlang.test; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import org.apache.taverna.tavlang.CommandLineTool; 24 | import org.junit.Assert; 25 | import org.junit.Test; 26 | 27 | public class CommandLineTest { 28 | CommandLineTool commandLineTool = new CommandLineTool(); 29 | 30 | @Test 31 | public void testHelp(){ 32 | commandLineTool.parse(); 33 | commandLineTool.parse("version"); 34 | commandLineTool.parse("help"); 35 | commandLineTool.parse("help", "convert"); 36 | commandLineTool.parse("help", "inspect"); 37 | commandLineTool.parse("help", "validate"); 38 | commandLineTool.parse("help", "help"); 39 | } 40 | 41 | 42 | 43 | } 44 | -------------------------------------------------------------------------------- /taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/TestConvert.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.tavlang.test; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | import static org.junit.Assert.*; 23 | 24 | import org.junit.Test; 25 | 26 | public class TestConvert{ 27 | 28 | @Test 29 | public void testConvertS() { 30 | // fail("Not yet implemented"); 31 | 32 | } 33 | 34 | } 35 | -------------------------------------------------------------------------------- /taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/TestStats.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.tavlang.test; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import static org.junit.Assert.*; 24 | 25 | import org.junit.Test; 26 | 27 | public class TestStats { 28 | 29 | @Test 30 | public void test() { 31 | // fail("Not yet implemented"); 32 | } 33 | 34 | } 35 | -------------------------------------------------------------------------------- /taverna-tavlang-tool/src/test/java/org/apache/taverna/tavlang/test/TestValidate.java: -------------------------------------------------------------------------------- 1 | package org.apache.taverna.tavlang.test; 2 | 3 | /* 4 | * Licensed to the Apache Software Foundation (ASF) under one 5 | * or more contributor license agreements. See the NOTICE file 6 | * distributed with this work for additional information 7 | * regarding copyright ownership. The ASF licenses this file 8 | * to you under the Apache License, Version 2.0 (the 9 | * "License"); you may not use this file except in compliance 10 | * with the License. You may obtain a copy of the License at 11 | * 12 | * http://www.apache.org/licenses/LICENSE-2.0 13 | * 14 | * Unless required by applicable law or agreed to in writing, 15 | * software distributed under the License is distributed on an 16 | * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY 17 | * KIND, either express or implied. See the License for the 18 | * specific language governing permissions and limitations 19 | * under the License. 20 | */ 21 | 22 | 23 | import static org.junit.Assert.*; 24 | 25 | import java.awt.List; 26 | import java.util.ArrayList; 27 | 28 | import org.apache.taverna.robundle.Bundle; 29 | import org.apache.taverna.tavlang.tools.validate.Validate; 30 | import org.junit.Assert; 31 | import org.junit.Test; 32 | 33 | import com.google.common.collect.Lists; 34 | 35 | public class TestValidate { 36 | 37 | 38 | 39 | @Test 40 | public void test() { 41 | ArrayList list = Lists.newArrayList(); 42 | list.add("src/test/resources/workflows/t2flow/as.t2flow"); 43 | Validate val = new Validate(list, null, false); 44 | 45 | assertEquals(false, val.getCheck()); 46 | 47 | } 48 | 49 | } 50 | -------------------------------------------------------------------------------- /taverna-tavlang-tool/src/test/resources/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-language/1a823c548486dec1c44a8ffc9cba795f823d382b/taverna-tavlang-tool/src/test/resources/.gitignore --------------------------------------------------------------------------------