Merge branch 'master' into cwl
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/f9e46e07 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/f9e46e07 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/f9e46e07 Branch: refs/heads/cwl Commit: f9e46e072f43eaa1c10ac8753ae60b1ee2c322cd Parents: c4aaad9 32a439e Author: Stian Soiland-Reyes <[email protected]> Authored: Fri May 20 11:04:35 2016 +0200 Committer: Stian Soiland-Reyes <[email protected]> Committed: Fri May 20 11:04:35 2016 +0200 ---------------------------------------------------------------------- LICENSE | 228 +++ NOTICE | 185 +- README.md | 94 +- pom.xml | 60 +- taverna-baclava-language/pom.xml | 4 +- taverna-databundle/README.md | 66 +- taverna-databundle/pom.xml | 9 +- .../apache/taverna/databundle/DataBundles.java | 9 +- taverna-language-commandline/.gitignore | 1 - taverna-language-commandline/README.md | 98 - taverna-language-commandline/pom.xml | 209 --- .../src/main/java/.gitignore | 0 .../apache/taverna/tavlang/CommandLineTool.java | 354 ---- .../taverna/tavlang/TavernaCommandline.java | 29 - .../org/apache/taverna/tavlang/tools/Tools.java | 97 - .../tavlang/tools/convert/Scufl2Convert.java | 211 --- .../taverna/tavlang/tools/convert/ToJson.java | 298 ---- .../tavlang/tools/convert/ToRobundle.java | 67 - .../tavlang/tools/inspect/ProcessorNames.java | 169 -- .../tavlang/tools/inspect/ServiceTypes.java | 112 -- .../taverna/tavlang/tools/stats/GetWfStat.java | 195 -- .../tavlang/tools/validate/Validate.java | 153 -- .../src/main/resources/.gitignore | 0 .../src/test/java/.gitignore | 0 .../taverna/tavlang/test/CommandLineTest.java | 43 - .../taverna/tavlang/test/Scufl2ConvertTest.java | 34 - .../src/test/resources/.gitignore | 0 taverna-robundle/README.md | 91 +- taverna-robundle/pom.xml | 32 +- .../robundle/manifest/PathAnnotation.java | 7 + .../robundle/manifest/RDFToManifest.java | 34 +- .../manifest/combine/CombineManifest.java | 49 +- .../taverna/robundle/manifest/odf/ODFJaxb.java | 119 ++ .../robundle/manifest/odf/ODFManifest.java | 91 +- .../apache/taverna/robundle/utils/RDFUtils.java | 10 +- .../taverna/robundle/validator/RoValidator.java | 162 ++ .../robundle/validator/ValidationReport.java | 138 ++ .../src/main/resources/META-INF/LICENSE | 391 ++++ .../src/main/resources/META-INF/NOTICE | 124 -- .../src/main/resources/contexts/bundle.jsonld | 1 - .../src/main/resources/ontologies/oa.rdf | 2 +- .../src/main/resources/ontologies/pav.rdf | 5 +- taverna-robundle/src/main/xsd/binding.xjb | 50 + taverna-robundle/src/main/xsd/container.xsd | 7 - .../taverna/robundle/manifest/TestManifest.java | 16 +- .../robundle/manifest/TestManifestJSON.java | 64 +- .../robundle/validator/ValidatorTest.java | 50 + .../src/test/resources/workflowrun.bundle.zip | Bin 7740 -> 8137 bytes taverna-scufl2-annotation/pom.xml | 9 +- .../scufl2/annotation/AnnotationTools.java | 14 +- .../scufl2/annotation/TestAnnotationTools.java | 8 +- taverna-scufl2-api/README.md | 149 +- taverna-scufl2-api/pom.xml | 4 +- .../taverna/scufl2/api/core/Processor.java | 4 +- taverna-scufl2-examples/README.md | 94 +- taverna-scufl2-examples/pom.xml | 33 +- .../org/apache/taverna/examples/Scufl2Tool.java | 101 -- taverna-scufl2-integration-tests/pom.xml | 4 +- taverna-scufl2-schemas/pom.xml | 4 +- .../src/main/resources/META-INF/LICENSE | 238 +++ .../src/main/resources/META-INF/NOTICE | 35 - 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.../src/main/xsd/container.xsd | 199 --- .../src/main/xsd/xenc-schema.xsd | 146 -- .../src/main/xsd/xmldsig-core-schema.xsd | 308 ---- .../scufl2/ucfpackage/TestUCFPackage.java | 34 +- taverna-scufl2-wfbundle/pom.xml | 4 +- .../taverna/scufl2/rdfxml/AbstractParser.java | 2 +- .../taverna/scufl2/rdfxml/ProfileParser.java | 44 +- .../taverna/scufl2/rdfxml/RDFXMLSerializer.java | 124 +- .../taverna/scufl2/rdfxml/RevisionParser.java | 20 +- .../scufl2/rdfxml/WorkflowBundleParser.java | 80 +- .../taverna/scufl2/rdfxml/WorkflowParser.java | 46 +- .../taverna/scufl2/rdfxml/DummyParserTest.java | 18 +- .../taverna/scufl2/rdfxml/example.wfbundle | Bin 40331 -> 51856 bytes .../taverna/scufl2/rdfxml/example/LICENSE | 430 +++++ .../rdfxml/example/META-INF/container.xml | 2 - .../scufl2/rdfxml/example/META-INF/manifest.xml | 7 - .../apache/taverna/scufl2/rdfxml/example/NOTICE | 11 + .../rdfxml/example/workflow/HelloWorld.rdf | 2 + .../taverna/scufl2/rdfxml/update-bundle.sh | 6 +- taverna-scufl2-wfdesc/README.md | 202 +-- taverna-scufl2-wfdesc/pom.xml | 525 ++---- .../taverna/scufl2/wfdesc/ConvertToWfdesc.java | 76 - .../apache/taverna/scufl2/wfdesc/Labelled.java | 36 - .../taverna/scufl2/wfdesc/ROEvoSerializer.java | 97 +- .../scufl2/wfdesc/TurtleWriterWithBase.java | 71 - .../taverna/scufl2/wfdesc/WfdescAgent.java | 9 +- .../taverna/scufl2/wfdesc/WfdescSerialiser.java | 552 +++--- .../src/main/resources/META-INF/LICENSE | 266 +++ .../src/main/resources/META-INF/NOTICE | 56 - .../org/purl/wf4ever/wfdesc/wfdesc.ttl | 1 - .../org/purl/wf4ever/wfdesc/wfprov.ttl | 1 - .../taverna/scufl2/wfdesc/TestAllTypes.java | 157 +- .../scufl2/wfdesc/TestAnnotationQuoting.java | 109 +- .../scufl2/wfdesc/TestConvertToWfdesc.java | 191 -- .../scufl2/wfdesc/TestLocalDependency.java | 64 +- .../taverna/scufl2/wfdesc/TestNested.java | 193 +- .../scufl2/wfdesc/TestRoEvoSerializer.java | 26 +- .../scufl2/wfdesc/TestSemanticAnnotations.java | 15 +- .../taverna/scufl2/wfdesc/TestWfdescWriter.java | 78 +- taverna-tavlang-tool/.gitignore | 1 + taverna-tavlang-tool/README.md | 370 ++++ taverna-tavlang-tool/pom.xml | 214 +++ taverna-tavlang-tool/src/main/java/.gitignore | 0 .../apache/taverna/tavlang/CommandLineTool.java | 349 ++++ .../taverna/tavlang/TavernaCommandline.java | 29 + .../org/apache/taverna/tavlang/tools/Tools.java | 88 + .../tavlang/tools/convert/Scufl2Convert.java | 206 +++ .../taverna/tavlang/tools/convert/ToJson.java | 298 ++++ .../tavlang/tools/convert/ToRobundle.java | 66 + .../tavlang/tools/inspect/ProcessorNames.java | 169 ++ .../tavlang/tools/inspect/ServiceTypes.java | 112 ++ .../taverna/tavlang/tools/stats/GetWfStat.java | 193 ++ .../tavlang/tools/validate/Validate.java | 151 ++ .../src/main/resources/.gitignore | 0 taverna-tavlang-tool/src/test/java/.gitignore | 0 .../taverna/tavlang/test/CommandLineTest.java | 43 + .../taverna/tavlang/test/TestConvert.java | 34 + .../apache/taverna/tavlang/test/TestStats.java | 34 + .../apache/taverna/tavlang/test/TestTools.java | 80 + .../taverna/tavlang/test/TestValidate.java | 49 + .../src/test/resources/.gitignore | 0 .../test/resources/workflows/t2flow/as.t2flow | 1674 ++++++++++++++++++ 145 files changed, 7977 insertions(+), 5640 deletions(-) ----------------------------------------------------------------------
