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Posted to commits@taverna.apache.org by st...@apache.org on 2016/05/26 13:43:41 UTC
[45/50] incubator-taverna-language git commit: Merge branch 'master'
into cwl
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 <st...@apache.org>
Authored: Fri May 20 11:04:35 2016 +0200
Committer: Stian Soiland-Reyes <st...@apache.org>
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 -
.../taverna/scufl2/rdfxml/xsd/binding.xjb | 27 +
.../apache/taverna/scufl2/rdfxml/xsd/owl.xsd | 14 +-
.../apache/taverna/scufl2/rdfxml/xsd/prov.xsd | 3 +-
.../apache/taverna/scufl2/rdfxml/xsd/rdf.xsd | 13 +-
.../apache/taverna/scufl2/rdfxml/xsd/rdfs.xsd | 14 +-
.../apache/taverna/scufl2/rdfxml/xsd/roevo.xsd | 3 +-
.../apache/taverna/scufl2/rdfxml/xsd/scufl2.xsd | 2 +-
taverna-scufl2-scufl/pom.xml | 4 +-
taverna-scufl2-t2flow/pom.xml | 4 +-
taverna-scufl2-ucfpackage/pom.xml | 29 +-
.../taverna/scufl2/ucfpackage/UCFPackage.java | 32 +-
.../ucfpackage/impl/odfdom/pkg/OdfPackage.java | 11 +-
.../impl/odfdom/pkg/OdfPackageStream.java | 16 +-
.../impl/odfdom/pkg/OdfXMLHelper.java | 5 +
.../impl/odfdom/pkg/StreamHelper.java | 67 +-
.../ucfpackage/impl/odfdom/pkg/TempDir.java | 19 +-
.../impl/odfdom/pkg/TempDirDeleter.java | 15 +-
.../impl/odfdom/pkg/manifest/Algorithm.java | 15 +-
.../odfdom/pkg/manifest/EncryptionData.java | 15 +-
.../impl/odfdom/pkg/manifest/KeyDerivation.java | 15 +-
.../impl/odfdom/pkg/manifest/OdfFileEntry.java | 19 +-
.../src/main/resources/META-INF/NOTICE | 42 -
.../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(-)
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