Download scufl2 Free Java Code

.gitignore//from  w w  w. ja  v a 2  s .c  om
LICENSE.txt
README.md
pom.xml
scufl2-api/.gitignore
scufl2-api/pom.xml
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/activity/Activity.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/activity/package-info.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/annotation/Annotation.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/annotation/Revision.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/annotation/Revisioned.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/annotation/package-info.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/AbstractCloneable.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/AbstractNamed.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/AbstractRevisioned.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/Child.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/Configurable.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/Named.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/NamedSet.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/Ported.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/Root.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/Scufl2Tools.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/Typed.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/URITools.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/Visitor.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/WorkflowBean.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/common/package-info.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/configurations/Configuration.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/container/WorkflowBundle.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/container/package-info.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/core/BlockingControlLink.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/core/ControlLink.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/core/DataLink.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/core/Processor.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/core/Workflow.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/core/package-info.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/impl/IterableComparator.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/impl/LazyMap.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/impl/NullSafeComparator.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/io/ReaderException.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/io/WorkflowBundleIO.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/io/WorkflowBundleReader.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/io/WorkflowBundleWriter.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/io/WriterException.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/io/structure/StructureReader.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/io/structure/StructureWriter.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/iterationstrategy/CrossProduct.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/iterationstrategy/DotProduct.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/iterationstrategy/IterationStrategyNode.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/iterationstrategy/IterationStrategyParent.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/iterationstrategy/IterationStrategyStack.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/iterationstrategy/IterationStrategyTopNode.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/iterationstrategy/PortNode.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/iterationstrategy/package-info.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/package-info.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/AbstractDepthPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/AbstractGranularDepthPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/ActivityPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/DepthPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/GranularDepthPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/InputActivityPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/InputPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/InputProcessorPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/InputWorkflowPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/OutputActivityPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/OutputPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/OutputProcessorPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/OutputWorkflowPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/Port.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/ProcessorPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/ReceiverPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/SenderPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/WorkflowPort.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/port/package-info.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/profiles/ProcessorBinding.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/profiles/ProcessorInputPortBinding.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/profiles/ProcessorOutputPortBinding.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/profiles/ProcessorPortBinding.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/profiles/Profile.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/profiles/package-info.java
scufl2-api/src/main/java/uk/org/taverna/scufl2/api/reference/package-info.java
scufl2-api/src/main/resources/META-INF/services/uk.org.taverna.scufl2.api.io.WorkflowBundleReader
scufl2-api/src/main/resources/META-INF/services/uk.org.taverna.scufl2.api.io.WorkflowBundleWriter
scufl2-api/src/main/resources/META-INF/spring/scufl2-api-context-osgi.xml
scufl2-api/src/main/resources/META-INF/spring/scufl2-api-context.xml
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/EqualsOnArrayListsTest.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/ExampleWorkflow.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/TestAPICreation.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/TestAbstractRevisioned.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/TestExampleWorkflow.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/VisitorTest.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/annotation/TestAnnotations.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/common/AllBeansVisitor.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/common/TestAbstractCloneable.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/common/TestAbstractNamed.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/common/TestScufl2Tools.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/common/TestSetParent.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/common/TestURITools.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/common/TestURIToolsBeans.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/common/TestURIToolsResolve.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/configurations/ConfigurationTest.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/container/TestWorkflowBundleEquals.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/core/ControlLinkCompareTest.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/core/DataLinkCompareTest.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/core/PortOrderTest.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/impl/TestIterableComparator.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/impl/TestNullCompare.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/io/TestResources.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/io/TestStructureReader.java
scufl2-api/src/test/java/uk/org/taverna/scufl2/api/io/TestWorkflowBundleIO.java
scufl2-api/src/test/resources/roevo-test.ttl
scufl2-api/src/test/resources/uk/org/taverna/scufl2/api/io/HelloWorld.txt
scufl2-integration-tests/pom.xml
scufl2-integration-tests/src/test/java/uk/org/taverna/scufl2/integration/CloningIT.java
scufl2-integration-tests/src/test/java/uk/org/taverna/scufl2/integration/TestSimpleWf.java
scufl2-integration-tests/src/test/java/uk/org/taverna/scufl2/translator/t2flow/EmptyStackIT.java
scufl2-integration-tests/src/test/java/uk/org/taverna/scufl2/translator/t2flow/LiteralNamespacesIT.java
scufl2-integration-tests/src/test/java/uk/org/taverna/scufl2/translator/t2flow/PropertyListRoundtripIT.java
scufl2-integration-tests/src/test/resources/apiconsumer.t2flow
scufl2-integration-tests/src/test/resources/clone-error.wfbundle
scufl2-integration-tests/src/test/resources/rest.t2flow
scufl2-rdf/.gitignore
scufl2-rdf/pom.xml
scufl2-rdf/src/main/java/uk/org/taverna/scufl2/rdf/RdfWriter.java
scufl2-rdf/src/main/resources/scufl2.rdf
scufl2-rdf/src/main/resources/scufl2.ttl
scufl2-rdf/src/main/resources/taverna-2.2.rdf
scufl2-rdf/src/main/resources/taverna-2.2.ttl
scufl2-rdf/src/test/java/uk/org/taverna/scufl2/rdf/TestRDF.java
scufl2-rdf/src/test/resources/example.rdf
scufl2-rdf/src/test/resources/example.scufl2
scufl2-rdf/src/test/resources/example.t2flow
scufl2-rdf/src/test/resources/example.ttl
scufl2-rdf/src/test/resources/example/META-INF/container.xml
scufl2-rdf/src/test/resources/example/META-INF/manifest.xml
scufl2-rdf/src/test/resources/example/Thumbnails/thumbnail.png
scufl2-rdf/src/test/resources/example/Thumbnails/thumbnail.svg
scufl2-rdf/src/test/resources/example/annotation/workflow/HelloWorld.rdf
scufl2-rdf/src/test/resources/example/annotation/workflow/HelloWorld.ttl
scufl2-rdf/src/test/resources/example/annotation/workflowBundle.rdf
scufl2-rdf/src/test/resources/example/annotation/workflowBundle.ttl
scufl2-rdf/src/test/resources/example/diagram/workflow/HelloWorld.png
scufl2-rdf/src/test/resources/example/diagram/workflow/HelloWorld.svg
scufl2-rdf/src/test/resources/example/mimetype
scufl2-rdf/src/test/resources/example/profile/tavernaServer.rdf
scufl2-rdf/src/test/resources/example/profile/tavernaServer.ttl
scufl2-rdf/src/test/resources/example/profile/tavernaWorkbench.rdf
scufl2-rdf/src/test/resources/example/profile/tavernaWorkbench.ttl
scufl2-rdf/src/test/resources/example/workflow/HelloWorld.rdf
scufl2-rdf/src/test/resources/example/workflow/HelloWorld.ttl
scufl2-rdf/src/test/resources/example/workflowBundle.rdf
scufl2-rdf/src/test/resources/example/workflowBundle.ttl
scufl2-rdfxml/.gitignore
scufl2-rdfxml/pom.xml
scufl2-rdfxml/src/main/java/uk/org/taverna/scufl2/rdfxml/AbstractParser.java
scufl2-rdfxml/src/main/java/uk/org/taverna/scufl2/rdfxml/ParserState.java
scufl2-rdfxml/src/main/java/uk/org/taverna/scufl2/rdfxml/ProfileParser.java
scufl2-rdfxml/src/main/java/uk/org/taverna/scufl2/rdfxml/RDFXMLReader.java
scufl2-rdfxml/src/main/java/uk/org/taverna/scufl2/rdfxml/RDFXMLSerializer.java
scufl2-rdfxml/src/main/java/uk/org/taverna/scufl2/rdfxml/RDFXMLWriter.java
scufl2-rdfxml/src/main/java/uk/org/taverna/scufl2/rdfxml/RevisionParser.java
scufl2-rdfxml/src/main/java/uk/org/taverna/scufl2/rdfxml/WorkflowBundleParser.java
scufl2-rdfxml/src/main/java/uk/org/taverna/scufl2/rdfxml/WorkflowParser.java
scufl2-rdfxml/src/main/java/uk/org/taverna/scufl2/rdfxml/impl/NamespacePrefixMapperJAXB_RI.java
scufl2-rdfxml/src/main/resources/META-INF/services/uk.org.taverna.scufl2.api.io.WorkflowBundleReader
scufl2-rdfxml/src/main/resources/META-INF/services/uk.org.taverna.scufl2.api.io.WorkflowBundleWriter
scufl2-rdfxml/src/main/resources/META-INF/spring/scufl2-rdfxml-context-osgi.xml
scufl2-rdfxml/src/main/resources/META-INF/spring/scufl2-rdfxml-context.xml
scufl2-rdfxml/src/main/resources/uk/org/taverna/scufl2/rdfxml/xsd/owl.xsd
scufl2-rdfxml/src/main/resources/uk/org/taverna/scufl2/rdfxml/xsd/prov.xsd
scufl2-rdfxml/src/main/resources/uk/org/taverna/scufl2/rdfxml/xsd/rdf.xsd
scufl2-rdfxml/src/main/resources/uk/org/taverna/scufl2/rdfxml/xsd/rdfs.xsd
scufl2-rdfxml/src/main/resources/uk/org/taverna/scufl2/rdfxml/xsd/roevo.xsd
scufl2-rdfxml/src/main/resources/uk/org/taverna/scufl2/rdfxml/xsd/scufl2.xsd
scufl2-rdfxml/src/main/resources/uk/org/taverna/scufl2/rdfxml/xsd/xml.xsd
scufl2-rdfxml/src/test/java/uk/org/taverna/scufl2/rdfxml/DummyParserTest.java
scufl2-rdfxml/src/test/java/uk/org/taverna/scufl2/rdfxml/TestProfileParser.java
scufl2-rdfxml/src/test/java/uk/org/taverna/scufl2/rdfxml/TestRDFXMLReader.java
scufl2-rdfxml/src/test/java/uk/org/taverna/scufl2/rdfxml/TestRDFXMLSerializer.java
scufl2-rdfxml/src/test/java/uk/org/taverna/scufl2/rdfxml/TestRDFXMLWriter.java
scufl2-rdfxml/src/test/java/uk/org/taverna/scufl2/rdfxml/TestResourcesInZip.java
scufl2-rdfxml/src/test/java/uk/org/taverna/scufl2/rdfxml/TestRevisionParsing.java
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example.wfbundle
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example/META-INF/container.xml
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example/META-INF/manifest.xml
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example/Thumbnails/thumbnail.png
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example/Thumbnails/thumbnail.svg
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example/annotation/workflow/HelloWorld.rdf
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example/annotation/workflowBundle.rdf
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example/diagram/workflow/HelloWorld.png
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example/diagram/workflow/HelloWorld.svg
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example/mimetype
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example/ontologies/taverna2.2.rdf
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example/profile/tavernaServer.rdf
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example/profile/tavernaWorkbench.rdf
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example/workflow/HelloWorld.rdf
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/example/workflowBundle.rdf
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/megaProfile.rdf
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/roevo-test.xml
scufl2-rdfxml/src/test/resources/uk/org/taverna/scufl2/rdfxml/update-bundle.sh
scufl2-scufl/pom.xml
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/ParserState.java
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/ScuflExtensionParser.java
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/ScuflParser.java
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/ScuflReader.java
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/processorelement/AbstractExtensionParser.java
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/processorelement/AbstractProcessorExtensionParser.java
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/processorelement/ApiConsumerExtensionParser.java
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/processorelement/BeanshellExtensionParser.java
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/processorelement/BiomartExtensionParser.java
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/processorelement/BiomobyExtensionParser.java
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/processorelement/LocalExtensionParser.java
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/processorelement/RshellExtensionParser.java
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/processorelement/SoaplabExtensionParser.java
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/processorelement/StringConstantExtensionParser.java
scufl2-scufl/src/main/java/uk/org/taverna/scufl2/translator/scufl/processorelement/WsdlExtensionParser.java
scufl2-scufl/src/main/resources/META-INF/services/uk.org.taverna.scufl2.api.io.WorkflowBundleReader
scufl2-scufl/src/main/resources/META-INF/services/uk.org.taverna.scufl2.translator.scufl.ScuflExtensionParser
scufl2-scufl/src/main/resources/uk/org/taverna/scufl2/translator/scufl/xsd/scufl-abstract.xsd
scufl2-scufl/src/main/resources/uk/org/taverna/scufl2/translator/scufl/xsd/scufl-apiconsumer.xsd
scufl2-scufl/src/main/resources/uk/org/taverna/scufl2/translator/scufl/xsd/scufl-beanshell.xsd
scufl2-scufl/src/main/resources/uk/org/taverna/scufl2/translator/scufl/xsd/scufl-biomart.xsd
scufl2-scufl/src/main/resources/uk/org/taverna/scufl2/translator/scufl/xsd/scufl-biomoby.xsd
scufl2-scufl/src/main/resources/uk/org/taverna/scufl2/translator/scufl/xsd/scufl-dependency.xsd
scufl2-scufl/src/main/resources/uk/org/taverna/scufl2/translator/scufl/xsd/scufl-inferno.xsd
scufl2-scufl/src/main/resources/uk/org/taverna/scufl2/translator/scufl/xsd/scufl-local.xsd
scufl2-scufl/src/main/resources/uk/org/taverna/scufl2/translator/scufl/xsd/scufl-notification.xsd
scufl2-scufl/src/main/resources/uk/org/taverna/scufl2/translator/scufl/xsd/scufl-rshell.xsd
scufl2-scufl/src/main/resources/uk/org/taverna/scufl2/translator/scufl/xsd/scufl-soaplab.xsd
scufl2-scufl/src/main/resources/uk/org/taverna/scufl2/translator/scufl/xsd/scufl-stringconstant.xsd
scufl2-scufl/src/main/resources/uk/org/taverna/scufl2/translator/scufl/xsd/scufl-wsdl.xsd
scufl2-scufl/src/main/resources/uk/org/taverna/scufl2/translator/scufl/xsd/scufl.xsd
scufl2-scufl/src/test/java/uk/org/taverna/scufl2/translator/scufl2/TestScuflReader.java
scufl2-scufl/src/test/java/uk/org/taverna/scufl2/translator/scufl2/TestStarterPack.java
scufl2-scufl/src/test/resources/workflow10.xml
scufl2-t2flow/.gitignore
scufl2-t2flow/pom.xml
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/ParserState.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/T2FlowParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/T2FlowReader.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/T2Parser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultactivities/AbstractActivityParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultactivities/ApiConsomerActivityParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultactivities/BeanshellActivityParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultactivities/BiomartActivityParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultactivities/BiomobyActivityParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultactivities/DataflowActivityParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultactivities/RshellActivityParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultactivities/SoaplabActivityParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultactivities/SpreadsheetActivityParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultactivities/StringConstantActivityParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultactivities/WSDLActivityParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultactivities/WSDLXMLSplitterParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultdispatchstack/ErrorBounceParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultdispatchstack/FailoverParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultdispatchstack/InvokeParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultdispatchstack/LoopParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultdispatchstack/ParallelizeParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/defaultdispatchstack/RetryParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/t23activities/ExternalToolActivityParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/t23activities/RESTActivityParser.java
scufl2-t2flow/src/main/java/uk/org/taverna/scufl2/translator/t2flow/t23activities/XPathActivityParser.java
scufl2-t2flow/src/main/resources/META-INF/services/uk.org.taverna.scufl2.api.io.WorkflowBundleReader
scufl2-t2flow/src/main/resources/META-INF/services/uk.org.taverna.scufl2.translator.t2flow.T2Parser
scufl2-t2flow/src/main/resources/META-INF/spring/scufl2-t2flow-context-osgi.xml
scufl2-t2flow/src/main/resources/META-INF/spring/scufl2-t2flow-context.xml
scufl2-t2flow/src/main/resources/uk/org/taverna/scufl2/translator/t2flow/xsd/externaltoolactivity.xsd
scufl2-t2flow/src/main/resources/uk/org/taverna/scufl2/translator/t2flow/xsd/restactivity.xsd
scufl2-t2flow/src/main/resources/uk/org/taverna/scufl2/translator/t2flow/xsd/t2activities.xsd
scufl2-t2flow/src/main/resources/uk/org/taverna/scufl2/translator/t2flow/xsd/t2annotations.xsd
scufl2-t2flow/src/main/resources/uk/org/taverna/scufl2/translator/t2flow/xsd/t2flow-extended.xsd
scufl2-t2flow/src/main/resources/uk/org/taverna/scufl2/translator/t2flow/xsd/t2flow.xsd
scufl2-t2flow/src/main/resources/uk/org/taverna/scufl2/translator/t2flow/xsd/t2layers.xsd
scufl2-t2flow/src/main/resources/uk/org/taverna/scufl2/translator/t2flow/xsd/xpathactivity.xsd
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/MergeParsingTest.java
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/TestActivityParsing.java
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/TestActivityParsingRshell.java
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/TestAnnotationParsing.java
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/TestBeanshellActivityParser.java
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/TestDispatchLayerParsing.java
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/TestFastaWorkflow.java
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/TestIterationStrategies.java
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/TestSpreadsheetActivityParser.java
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/TestT2FlowParser.java
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/TestT2FlowReader.java
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/TestT2FlowTranslator.java
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/t23activities/TestExternalToolActivityParser.java.disabled
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/t23activities/TestRESTActivityParser.java
scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/t23activities/TestXPathActivityParser.java
scufl2-t2flow/src/test/resources/annotated2.2-xsd.t2flow
scufl2-t2flow/src/test/resources/annotated2.2.t2flow
scufl2-t2flow/src/test/resources/annotations_2_4-xsd.t2flow
scufl2-t2flow/src/test/resources/annotations_2_4.t2flow
scufl2-t2flow/src/test/resources/as.t2flow
scufl2-t2flow/src/test/resources/as.txt
scufl2-t2flow/src/test/resources/beanshell-deps.t2flow
scufl2-t2flow/src/test/resources/dataflow_link_then_merge.t2flow
scufl2-t2flow/src/test/resources/defaultActivitiesTaverna2.2-xsd.t2flow
scufl2-t2flow/src/test/resources/defaultActivitiesTaverna2.2.t2flow
scufl2-t2flow/src/test/resources/dispatchlayers-xsd.t2flow
scufl2-t2flow/src/test/resources/dispatchlayers.t2flow
scufl2-t2flow/src/test/resources/fasta_and_pscan.t2flow
scufl2-t2flow/src/test/resources/fasta_pscan_and_dbfetch.t2flow
scufl2-t2flow/src/test/resources/interaction-with-strange-loop.t2flow
scufl2-t2flow/src/test/resources/iterationstrategies.t2flow
scufl2-t2flow/src/test/resources/merge_fun.t2flow
scufl2-t2flow/src/test/resources/merge_then_dataflow_link.t2flow
scufl2-t2flow/src/test/resources/missing_merge.t2flow
scufl2-t2flow/src/test/resources/missing_produced_by_941.t2flow
scufl2-t2flow/src/test/resources/random.t2flow
scufl2-t2flow/src/test/resources/rest-2-2-saved-2-3-xsd.t2flow
scufl2-t2flow/src/test/resources/rest-2-2-saved-2-3.t2flow
scufl2-t2flow/src/test/resources/rest-2-2-xsd.t2flow
scufl2-t2flow/src/test/resources/rest-2-2.t2flow
scufl2-t2flow/src/test/resources/rest-2-3-xsd.t2flow
scufl2-t2flow/src/test/resources/rest-2-3.t2flow
scufl2-t2flow/src/test/resources/rshell-2-2.t2flow
scufl2-t2flow/src/test/resources/rshell-2-3.t2flow
scufl2-t2flow/src/test/resources/rshell-simple-2-3-xsd.t2flow
scufl2-t2flow/src/test/resources/rshell-simple-2-3.t2flow
scufl2-t2flow/src/test/resources/semantic_annotations__eclipse-xsd.t2flow
scufl2-t2flow/src/test/resources/semantic_annotations__eclipse.t2flow
scufl2-t2flow/src/test/resources/simple_fasta.t2flow
scufl2-t2flow/src/test/resources/sleepers.t2flow
scufl2-t2flow/src/test/resources/spreadsheet_activity_defaults_892.t2flow
scufl2-t2flow/src/test/resources/tool-2-2-resaved-2-3-xsd.t2flow
scufl2-t2flow/src/test/resources/tool-2-2-resaved-2-3.t2flow
scufl2-t2flow/src/test/resources/tool-2-2-tweaked-xsd.t2flow
scufl2-t2flow/src/test/resources/tool-2-2.t2flow
scufl2-t2flow/src/test/resources/tool-2-3-xsd.t2flow
scufl2-t2flow/src/test/resources/tool-2-3.t2flow
scufl2-t2flow/src/test/resources/xpath_workflow.t2flow
scufl2-ucfpackage/.gitignore
scufl2-ucfpackage/LICENSE-odfdom.txt
scufl2-ucfpackage/pom.xml
scufl2-ucfpackage/src/main/java/uk/org/taverna/scufl2/ucfpackage/UCFPackage.java
scufl2-ucfpackage/src/main/java/uk/org/taverna/scufl2/ucfpackage/impl/odfdom/pkg/OdfPackage.java
scufl2-ucfpackage/src/main/java/uk/org/taverna/scufl2/ucfpackage/impl/odfdom/pkg/OdfPackageStream.java
scufl2-ucfpackage/src/main/java/uk/org/taverna/scufl2/ucfpackage/impl/odfdom/pkg/OdfXMLHelper.java
scufl2-ucfpackage/src/main/java/uk/org/taverna/scufl2/ucfpackage/impl/odfdom/pkg/StreamHelper.java
scufl2-ucfpackage/src/main/java/uk/org/taverna/scufl2/ucfpackage/impl/odfdom/pkg/TempDir.java
scufl2-ucfpackage/src/main/java/uk/org/taverna/scufl2/ucfpackage/impl/odfdom/pkg/TempDirDeleter.java
scufl2-ucfpackage/src/main/java/uk/org/taverna/scufl2/ucfpackage/impl/odfdom/pkg/manifest/Algorithm.java
scufl2-ucfpackage/src/main/java/uk/org/taverna/scufl2/ucfpackage/impl/odfdom/pkg/manifest/EncryptionData.java
scufl2-ucfpackage/src/main/java/uk/org/taverna/scufl2/ucfpackage/impl/odfdom/pkg/manifest/KeyDerivation.java
scufl2-ucfpackage/src/main/java/uk/org/taverna/scufl2/ucfpackage/impl/odfdom/pkg/manifest/OdfFileEntry.java
scufl2-ucfpackage/src/main/xsd/container.xsd
scufl2-ucfpackage/src/main/xsd/xenc-schema.xsd
scufl2-ucfpackage/src/main/xsd/xmldsig-core-schema.xsd
scufl2-ucfpackage/src/test/java/uk/org/taverna/scufl2/ucfpackage/TestUCFPackage.java
scufl2-usecases/.gitignore
scufl2-usecases/LICENSE.txt
scufl2-usecases/pom.xml
scufl2-usecases/src/main/python/processorNames.py
scufl2-usecases/src/main/resources/sample-output.data-bundle
scufl2-usecases/src/main/resources/sample-output/META-INF/container.xml
scufl2-usecases/src/main/resources/sample-output/META-INF/manifest.xml
scufl2-usecases/src/main/resources/sample-output/inputs.rdf
scufl2-usecases/src/main/resources/sample-output/inputs.ttl
scufl2-usecases/src/main/resources/sample-output/mimetype
scufl2-usecases/src/main/resources/sample-output/outputs-nested-tiny.rdf
scufl2-usecases/src/main/resources/sample-output/outputs-nested-tiny.ttl
scufl2-usecases/src/main/resources/sample-output/outputs-nested.rdf
scufl2-usecases/src/main/resources/sample-output/outputs-nested.ttl
scufl2-usecases/src/main/resources/sample-output/outputs.rdf
scufl2-usecases/src/main/resources/sample-output/outputs.ttl
scufl2-usecases/src/main/resources/sample-output/outputs/fish/0
scufl2-usecases/src/main/resources/sample-output/outputs/fish/1
scufl2-usecases/src/main/resources/sample-output/outputs/results
scufl2-usecases/src/main/resources/sample-output/outputs/soup/0/0
scufl2-usecases/src/main/resources/sample-output/outputs/soup/0/1
scufl2-usecases/src/main/resources/workflows/t2flow/a_workflow_version_of_the_emboss_tutorial_676679.t2flow
scufl2-usecases/src/main/resources/workflows/t2flow/annotated2.2.t2flow
scufl2-usecases/src/main/resources/workflows/t2flow/as.t2flow
scufl2-usecases/src/main/resources/workflows/t2flow/biomartandembossanalysis_904962.t2flow
scufl2-usecases/src/main/resources/workflows/t2flow/biomoby_tutorial_workflow_877727.t2flow
scufl2-usecases/src/main/resources/workflows/t2flow/defaultActivitiesTaverna2.2.t2flow
scufl2-usecases/src/main/resources/workflows/t2flow/demonstration_of_configurable_iteration_114130.t2flow
scufl2-usecases/src/main/resources/workflows/t2flow/ebi_interproscan_for_taverna_2_317472.t2flow
scufl2-usecases/src/main/resources/workflows/t2flow/fetch_pdb_flatfile_from_rcsb_server_969361.t2flow
scufl2-usecases/src/main/resources/workflows/t2flow/fetch_today_s_xkcd_comic_568671.t2flow
scufl2-usecases/src/main/resources/workflows/t2flow/gbseq_test_457824.t2flow
scufl2-usecases/src/main/resources/workflows/t2flow/merge_fun.t2flow
scufl2-usecases/src/main/resources/workflows/t2flow/pipelined_list_iteration_902021.t2flow
scufl2-usecases/src/main/resources/workflows/t2flow/retrieve_sequence_in_embl_format_32794.t2flow
scufl2-usecases/src/main/ruby/processors.rb
scufl2-validation-correctness/pom.xml
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/CorrectnessValidationListener.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/CorrectnessValidator.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/CorrectnessVisitor.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/DefaultCorrectnessValidationListener.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/DefaultDispatchingVisitor.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/DispatchingVisitor.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/ReportCorrectnessValidationListener.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/report/EmptyIterationStrategyTopNodeProblem.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/report/IncompatibleGranularDepthProblem.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/report/MismatchConfigurableTypeProblem.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/report/NegativeValueProblem.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/report/NonAbsoluteURIProblem.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/report/NullFieldProblem.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/report/OutOfScopeValueProblem.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/report/PortMentionedTwiceProblem.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/report/PortMissingFromIterationStrategyStackProblem.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/report/ReportCorrectnessValidationListener.java
scufl2-validation-correctness/src/main/java/uk/org/taverna/scufl2/validation/correctness/report/WrongParentProblem.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/DummyProfile.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/DummyWorkflow.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/DummyWorkflowBundle.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestAbstractDepthPort.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestAbstractGranularDepthPort.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestBlockingControlLink.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestChild.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestConfiguration.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestDataLink.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestIterationStrategyStack.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestIterationStrategyTopNode.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestNamed.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestPortNode.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestPorted.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestProcessor.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestProcessorBinding.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestProcessorInputPortBinding.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestProcessorOutputPortBinding.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestProfile.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestRoot.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestTyped.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestWorkflow.java
scufl2-validation-correctness/src/test/java/uk/org/taverna/scufl2/validation/correctness/TestWorkflowBundle.java
scufl2-validation-integration/pom.xml
scufl2-validation-integration/src/test/java/uk/org/taverna/scufl2/validation/integration/scufl/Test172StarterPack.java
scufl2-validation-integration/src/test/java/uk/org/taverna/scufl2/validation/integration/t2flow/Test230StarterPack.java
scufl2-validation-integration/src/test/resources/t172starterpacklist
scufl2-validation-integration/src/test/resources/t230starterpacklist
scufl2-validation-structural/pom.xml
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/DefaultStructuralValidationListener.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/ReportStructuralValidationListener.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/StructuralValidationListener.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/StructuralValidator.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/ValidatorState.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/report/DotProductIterationMismatchProblem.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/report/EmptyCrossProductProblem.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/report/EmptyDotProductProblem.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/report/FailedProcessorProblem.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/report/IncompleteWorkflowProblem.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/report/MissingIterationStrategyStackProblem.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/report/MissingMainIncomingDataLinkProblem.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/report/ReportStructuralValidationListener.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/report/UnrecognizedIterationStrategyNodeProblem.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/report/UnresolvedOutputProblem.java
scufl2-validation-structural/src/main/java/uk/org/taverna/scufl2/validation/structural/report/UnresolvedProcessorProblem.java
scufl2-validation-structural/src/test/java/uk/org/taverna/scufl2/validation/structural/CrossProductTest.java
scufl2-validation-structural/src/test/java/uk/org/taverna/scufl2/validation/structural/DepthInheritanceTest.java
scufl2-validation-structural/src/test/java/uk/org/taverna/scufl2/validation/structural/DotProductTest.java
scufl2-validation-structural/src/test/java/uk/org/taverna/scufl2/validation/structural/StagedCombinationTest.java
scufl2-validation-structural/src/test/java/uk/org/taverna/scufl2/validation/structural/WorkflowTest.java
scufl2-validation/pom.xml
scufl2-validation/src/main/java/uk/org/taverna/scufl2/validation/Status.java
scufl2-validation/src/main/java/uk/org/taverna/scufl2/validation/ValidationException.java
scufl2-validation/src/main/java/uk/org/taverna/scufl2/validation/ValidationProblem.java
scufl2-validation/src/main/java/uk/org/taverna/scufl2/validation/WorkflowBeanReport.java