├── .gitignore ├── .travis.yml ├── DISCLAIMER ├── LICENSE ├── NOTICE ├── README.md ├── pom.xml ├── src └── license │ └── THIRD-PARTY.properties ├── taverna-activity-archetype ├── pom.xml └── src │ ├── main │ └── resources │ │ ├── META-INF │ │ └── maven │ │ │ └── archetype-metadata.xml │ │ └── archetype-resources │ │ ├── __rootArtifactId__-activity-ui │ │ ├── pom.xml │ │ └── src │ │ │ └── main │ │ │ ├── java │ │ │ └── ui │ │ │ │ ├── config │ │ │ │ ├── __classPrefix__ConfigurationPanel.java │ │ │ │ └── __classPrefix__ConfigureAction.java │ │ │ │ ├── menu │ │ │ │ └── __classPrefix__ConfigureMenuAction.java │ │ │ │ ├── serviceprovider │ │ │ │ ├── __classPrefix__ServiceDesc.java │ │ │ │ ├── __classPrefix__ServiceIcon.java │ │ │ │ └── __classPrefix__ServiceProvider.java │ │ │ │ └── view │ │ │ │ ├── __classPrefix__ActivityContextViewFactory.java │ │ │ │ └── __classPrefix__ContextualView.java │ │ │ └── resources │ │ │ ├── META-INF │ │ │ └── spring │ │ │ │ ├── context-osgi.xml │ │ │ │ └── context.xml │ │ │ ├── exampleIcon.png │ │ │ └── exampleIcon.xcf │ │ ├── __rootArtifactId__-activity │ │ ├── pom.xml │ │ └── src │ │ │ ├── main │ │ │ ├── java │ │ │ │ ├── __classPrefix__Activity.java │ │ │ │ ├── __classPrefix__ActivityFactory.java │ │ │ │ └── __classPrefix__ActivityHealthChecker.java │ │ │ └── resources │ │ │ │ ├── schema.json │ │ │ │ └── spring │ │ │ │ ├── context-osgi.xml │ │ │ │ └── context.xml │ │ │ └── test │ │ │ └── java │ │ │ ├── __classPrefix__ActivityFactoryTest.java │ │ │ └── __classPrefix__ActivityTest.java │ │ ├── __rootArtifactId__-plugin │ │ └── pom.xml │ │ └── pom.xml │ └── test │ └── resources │ └── projects │ └── dummyActivity │ ├── archetype.properties │ └── goal.txt ├── taverna-activity-test-utils ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── activities │ │ └── testutils │ │ ├── ActivityInvoker.java │ │ ├── DummyCallback.java │ │ └── LocationConstants.java │ └── resources │ ├── context-parts │ ├── componentservices.xml │ ├── dao_hibernate.xml │ ├── dao_hibernate_transactional.xml │ ├── dao_inmemory.xml │ ├── hibernateprops_derby.xml │ ├── raven_local.xml │ └── referenceservice.xml │ └── inMemoryActivityTestsContext.xml ├── taverna-capability-api ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── apache │ └── taverna │ └── platform │ └── capability │ └── api │ ├── ActivityConfigurationException.java │ ├── ActivityNotFoundException.java │ ├── ActivityService.java │ ├── ConfigurationException.java │ ├── DispatchLayerConfigurationException.java │ ├── DispatchLayerNotFoundException.java │ └── DispatchLayerService.java ├── taverna-capability-impl ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── platform │ │ └── capability │ │ ├── activity │ │ └── impl │ │ │ └── ActivityServiceImpl.java │ │ └── dispatch │ │ └── impl │ │ └── DispatchLayerServiceImpl.java │ └── resources │ └── META-INF │ └── spring │ ├── taverna-capability-context-osgi.xml │ └── taverna-capability-context.xml ├── taverna-credential-manager-api ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── security │ │ │ └── credentialmanager │ │ │ ├── CMException.java │ │ │ ├── CMNotInitialisedException.java │ │ │ ├── CredentialManager.java │ │ │ ├── DistinguishedNameParser.java │ │ │ ├── JavaTruststorePasswordProvider.java │ │ │ ├── KeystoreChangedEvent.java │ │ │ ├── MasterPasswordProvider.java │ │ │ ├── ParsedDistinguishedName.java │ │ │ ├── ServiceUsernameAndPasswordProvider.java │ │ │ ├── TrustConfirmationProvider.java │ │ │ └── UsernamePassword.java │ └── resources │ │ └── META-INF │ │ └── services │ │ └── org.apache.taverna.security.credentialmanager.CredentialProviderSPI │ └── test │ └── resources │ ├── html │ └── test.html │ └── realm.properties ├── taverna-credential-manager-impl ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── security │ │ │ └── credentialmanager │ │ │ └── impl │ │ │ ├── CredentialManagerAuthenticator.java │ │ │ ├── CredentialManagerImpl.java │ │ │ ├── DefaultMasterPasswordProvider.java │ │ │ ├── DistinguishedNameParserImpl.java │ │ │ └── ParsedDistinguishedNameImpl.java │ └── resources │ │ └── META-INF │ │ └── spring │ │ ├── credential-manager-impl-context-osgi.xml │ │ └── credential-manager-impl-context.xml │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── security │ │ └── credentialmanager │ │ └── impl │ │ ├── CredentialManagerImplIT.java │ │ ├── CredentialManagerImplTest.java │ │ ├── DummyJavaTruststorePasswordProvider.java │ │ ├── DummyMasterPasswordProvider.java │ │ ├── DummyServiceUsernameAndPasswordProvider.java │ │ ├── HTTPAuthenticatorIT.java │ │ ├── HTTPAuthenticatorServiceUsernameAndPasswordProvider.java │ │ ├── HTTPSConnectionAndTrustConfirmationIT.java │ │ ├── PossibleURILookupsTest.java │ │ ├── TrustAlwaysTrustConfirmationProvider.java │ │ └── TrustNeverTrustConfimationProvider.java │ └── resources │ ├── html │ └── test.html │ └── security │ ├── google-trusted-certificate.pem │ ├── t2keystore.ubr │ ├── t2truststore.ubr │ ├── test-private-key-cert.p12 │ └── tomcat_heater_certificate.pem ├── taverna-database-configuration-api ├── .project ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── apache │ └── taverna │ └── configuration │ └── database │ ├── DatabaseConfiguration.java │ └── DatabaseManager.java ├── taverna-database-configuration-impl ├── .project ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── configuration │ │ └── database │ │ └── impl │ │ ├── DatabaseConfigurationImpl.java │ │ └── DatabaseManagerImpl.java │ └── resources │ └── META-INF │ └── spring │ ├── database-context-osgi.xml │ └── database-context.xml ├── taverna-dataflow-activity ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── activities │ │ │ └── dataflow │ │ │ ├── DataflowActivity.java │ │ │ ├── DataflowActivityFactory.java │ │ │ └── DataflowActivityHealthChecker.java │ └── resources │ │ ├── META-INF │ │ ├── services │ │ │ └── net.sf.taverna.t2.workflowmodel.health.HealthChecker │ │ └── spring │ │ │ ├── dataflow-activity-context-osgi.xml │ │ │ └── dataflow-activity-context.xml │ │ └── schema.json │ └── test │ └── java │ └── org │ └── apache │ └── taverna │ └── activities │ └── dataflow │ ├── DataflowActivityFactoryTest.java │ └── DataflowActivityTest.java ├── taverna-execution-api ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── apache │ │ └── taverna │ │ └── platform │ │ └── execution │ │ └── api │ │ ├── AbstractExecution.java │ │ ├── AbstractExecutionEnvironment.java │ │ ├── AbstractExecutionService.java │ │ ├── Execution.java │ │ ├── ExecutionEnvironment.java │ │ ├── ExecutionEnvironmentService.java │ │ ├── ExecutionService.java │ │ ├── InvalidExecutionIdException.java │ │ ├── InvalidWorkflowException.java │ │ └── WorkflowCompiler.java │ └── test │ └── java │ └── org │ └── apache │ └── taverna │ └── platform │ └── execution │ └── api │ └── AbstractExecutionTest.java ├── taverna-execution-hadoop ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ ├── apache │ │ └── taverna │ │ │ └── platform │ │ │ └── execution │ │ │ └── impl │ │ │ └── hadoop │ │ │ ├── CrossProductInputFormat.java │ │ │ ├── CrossProductInputSplit.java │ │ │ ├── CrossProductRecordReader.java │ │ │ ├── CrossProductTest.java │ │ │ ├── DotProductTest.java │ │ │ ├── TavernaInputFormat.java │ │ │ ├── TavernaInputSplit.java │ │ │ ├── TavernaMapper.java │ │ │ ├── TavernaRecordReader.java │ │ │ ├── TavernaReducer.java │ │ │ ├── Test.java │ │ │ └── TextArrayWritable.java │ │ └── pingel │ │ └── util │ │ └── CrossProduct.java │ └── resources │ └── META-INF │ └── LICENSE ├── taverna-execution-impl ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── platform │ │ └── execution │ │ └── impl │ │ └── ExecutionEnvironmentServiceImpl.java │ └── resources │ └── META-INF │ └── spring │ ├── execution-context-osgi.xml │ └── execution-context.xml ├── taverna-execution-local ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── platform │ │ │ └── execution │ │ │ └── impl │ │ │ └── local │ │ │ ├── LocalExecution.java │ │ │ ├── LocalExecutionEnvironment.java │ │ │ ├── LocalExecutionMonitor.java │ │ │ ├── LocalExecutionService.java │ │ │ ├── LocalProcessorReport.java │ │ │ ├── StaticProperty.java │ │ │ └── WorkflowToDataflowMapper.java │ └── resources │ │ └── META-INF │ │ └── spring │ │ ├── execution-local-context-osgi.xml │ │ └── execution-local-context.xml │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── platform │ │ └── execution │ │ └── impl │ │ └── local │ │ └── LocalExecutionTest.java │ └── resources │ ├── log4j.properties │ └── t2flow │ ├── beanshell.t2flow │ └── in-out.t2flow ├── taverna-execution-remote ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── platform │ │ └── execution │ │ └── impl │ │ └── remote │ │ ├── RemoteExecution.java │ │ └── RemoteExecutionService.java │ └── resources │ └── META-INF │ └── spring │ ├── execution-remote-context-osgi.xml │ └── execution-remote-context.xml ├── taverna-observer ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── apache │ │ └── taverna │ │ └── lang │ │ └── observer │ │ ├── MultiCaster.java │ │ ├── Observable.java │ │ ├── Observer.java │ │ ├── SwingAwareObserver.java │ │ └── package-info.java │ └── test │ └── java │ └── org │ └── apache │ └── taverna │ └── lang │ └── observer │ └── ObserverTest.java ├── taverna-prov-owl-bindings ├── .gitignore ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── prov │ │ │ └── owl │ │ │ ├── ProvModel.java │ │ │ ├── TavernaProvModel.java │ │ │ └── WfprovModel.java │ └── resources │ │ └── org │ │ └── apache │ │ └── taverna │ │ └── prov │ │ └── owl │ │ ├── taverna-prov.owl │ │ └── taverna-prov.ttl │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── prov │ │ └── owl │ │ ├── TestProvModel.java │ │ ├── TestTavernaProvModel.java │ │ └── TestWfprovModel.java │ └── resources │ └── handmade.ttl ├── taverna-prov ├── README.md ├── example │ ├── helloanyone.bundle.zip │ ├── helloanyone.bundle │ │ ├── .ro │ │ │ ├── annotations │ │ │ │ ├── a2f03983-8836-4c36-bfb2-d713d9a1928f.ttl │ │ │ │ └── workflow.wfdesc.ttl │ │ │ └── manifest.json │ │ ├── LICENSE │ │ ├── inputs │ │ │ └── name.txt │ │ ├── intermediates │ │ │ └── 3a │ │ │ │ └── 3a82e39d-a537-40cf-91a0-2c89d4a2e62b.txt │ │ ├── mimetype │ │ ├── outputs │ │ │ └── greeting.txt │ │ ├── workflow.wfbundle │ │ └── workflowrun.prov.ttl │ ├── helloanyone.t2flow │ └── test.sparql ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── apache │ └── taverna │ └── prov │ ├── SafeFileOutputStream.java │ ├── Saver.java │ └── W3ProvenanceExport.java ├── taverna-provenanceconnector ├── javadoc.xml ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── provenance │ │ ├── Provenance.java │ │ ├── ProvenanceConnectorFactory.java │ │ ├── api │ │ ├── NativeAnswer.java │ │ ├── ProvenanceAccess.java │ │ ├── ProvenanceConnectorType.java │ │ ├── Query.java │ │ └── QueryAnswer.java │ │ ├── connector │ │ ├── AbstractProvenanceConnector.java │ │ └── ProvenanceSQL.java │ │ ├── lineageservice │ │ ├── AnnotationsLoader.java │ │ ├── Dependencies.java │ │ ├── EventProcessor.java │ │ ├── LineageQueryResultRecord.java │ │ ├── LineageSQLQuery.java │ │ ├── Provenance.java │ │ ├── ProvenanceAnalysis.java │ │ ├── ProvenanceQuery.java │ │ ├── ProvenanceWriter.java │ │ ├── URIGenerator.java │ │ ├── WorkflowDataProcessor.java │ │ ├── types │ │ │ ├── ActivityType.java │ │ │ ├── DataDocumentType.java │ │ │ ├── IterationType.java │ │ │ ├── LiteralType.java │ │ │ ├── PortType.java │ │ │ ├── PortsSequenceType.java │ │ │ ├── ProcessType.java │ │ │ ├── ProcessorType.java │ │ │ └── ProvenanceEventType.java │ │ └── utils │ │ │ ├── Activity.java │ │ │ ├── Collection.java │ │ │ ├── DDRecord.java │ │ │ ├── DataBinding.java │ │ │ ├── DataLink.java │ │ │ ├── DataValueExtractor.java │ │ │ ├── DataflowInvocation.java │ │ │ ├── NestedListNode.java │ │ │ ├── Port.java │ │ │ ├── PortBinding.java │ │ │ ├── ProcessorBinding.java │ │ │ ├── ProcessorEnactment.java │ │ │ ├── ProvenanceProcessor.java │ │ │ ├── ProvenanceUtils.java │ │ │ ├── QueryPort.java │ │ │ ├── ServiceInvocation.java │ │ │ ├── Workflow.java │ │ │ ├── WorkflowRun.java │ │ │ └── WorkflowTree.java │ │ └── opm │ │ ├── OPMImporter.java │ │ └── OPMManager.java │ ├── resources │ └── META-INF │ │ └── spring │ │ └── provenance-connector-context.xml │ └── uml │ ├── database-schema.uml │ └── database-schema.umlclass ├── taverna-reference-api ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── reference │ │ ├── AbstractExternalReference.java │ │ ├── ContextualizedT2Reference.java │ │ ├── DaoException.java │ │ ├── DereferenceException.java │ │ ├── ErrorDocument.java │ │ ├── ErrorDocumentDao.java │ │ ├── ErrorDocumentService.java │ │ ├── ErrorDocumentServiceCallback.java │ │ ├── ErrorDocumentServiceException.java │ │ ├── ExternalReferenceBuilderSPI.java │ │ ├── ExternalReferenceConstructionException.java │ │ ├── ExternalReferenceSPI.java │ │ ├── ExternalReferenceTranslatorSPI.java │ │ ├── ExternalReferenceValidationException.java │ │ ├── Identified.java │ │ ├── IdentifiedList.java │ │ ├── ListDao.java │ │ ├── ListService.java │ │ ├── ListServiceCallback.java │ │ ├── ListServiceException.java │ │ ├── ReferenceContext.java │ │ ├── ReferenceService.java │ │ ├── ReferenceServiceCacheProvider.java │ │ ├── ReferenceServiceException.java │ │ ├── ReferenceServiceResolutionCallback.java │ │ ├── ReferenceSet.java │ │ ├── ReferenceSetAugmentationException.java │ │ ├── ReferenceSetAugmentor.java │ │ ├── ReferenceSetAugmentorCallback.java │ │ ├── ReferenceSetDao.java │ │ ├── ReferenceSetService.java │ │ ├── ReferenceSetServiceCallback.java │ │ ├── ReferenceSetServiceException.java │ │ ├── ReferencedDataNature.java │ │ ├── StackTraceElementBean.java │ │ ├── StreamToValueConverterSPI.java │ │ ├── T2Reference.java │ │ ├── T2ReferenceGenerator.java │ │ ├── T2ReferenceType.java │ │ ├── ValueCarryingExternalReference.java │ │ ├── ValueToReferenceConversionException.java │ │ ├── ValueToReferenceConverterSPI.java │ │ ├── WorkflowRunIdEntity.java │ │ ├── annotations │ │ ├── DeleteIdentifiedOperation.java │ │ ├── GetIdentifiedOperation.java │ │ ├── PutIdentifiedOperation.java │ │ └── package.html │ │ ├── h3 │ │ ├── HibernateComponentClass.java │ │ ├── HibernateMappedEntity.java │ │ └── package.html │ │ └── package.html │ └── resources │ └── org │ └── apache │ └── taverna │ └── reference │ └── AbstractExternalReference.hbm.xml ├── taverna-reference-impl ├── .gitignore ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ ├── platform │ │ │ └── spring │ │ │ │ └── jdbc │ │ │ │ ├── TemporaryJDBC.java │ │ │ │ └── package.html │ │ │ └── reference │ │ │ └── impl │ │ │ ├── AbstractEntityImpl.java │ │ │ ├── AbstractErrorDocumentServiceImpl.java │ │ │ ├── AbstractListServiceImpl.java │ │ │ ├── AbstractReferenceServiceImpl.java │ │ │ ├── AbstractReferenceSetServiceImpl.java │ │ │ ├── AbstractServiceImpl.java │ │ │ ├── AbstractT2ReferenceGenerator.java │ │ │ ├── CacheAspect.java │ │ │ ├── ContextualizedT2ReferenceImpl.java │ │ │ ├── EmptyReferenceContext.java │ │ │ ├── ErrorDocumentImpl.java │ │ │ ├── ErrorDocumentServiceImpl.java │ │ │ ├── IdentifiedArrayList.java │ │ │ ├── InMemoryErrorDocumentDao.java │ │ │ ├── InMemoryListDao.java │ │ │ ├── InMemoryReferenceSetDao.java │ │ │ ├── ListServiceImpl.java │ │ │ ├── ReferenceServiceImpl.java │ │ │ ├── ReferenceSetAugmentorImpl.java │ │ │ ├── ReferenceSetImpl.java │ │ │ ├── ReferenceSetServiceImpl.java │ │ │ ├── SimpleCacheProviderImpl.java │ │ │ ├── SimpleT2ReferenceGenerator.java │ │ │ ├── StackTraceElementBeanImpl.java │ │ │ ├── T2ReferenceImpl.java │ │ │ ├── T2ReferenceListImpl.java │ │ │ ├── TranslationPath.java │ │ │ ├── UUIDT2ReferenceGenerator.java │ │ │ ├── WriteQueueAspect.java │ │ │ └── package.html │ └── resources │ │ ├── META-INF │ │ ├── spring.schemas │ │ └── spring │ │ │ ├── in-memory-reference-impl-context.xml │ │ │ ├── reference-impl-context-osgi.xml │ │ │ └── reference-impl-context.xml │ │ ├── artifact-support.xsd │ │ └── org │ │ └── apache │ │ └── taverna │ │ └── reference │ │ └── impl │ │ ├── ErrorDocumentImpl.hbm.xml │ │ ├── ReferenceSetImpl.hbm.xml │ │ └── T2ReferenceListImpl.hbm.xml │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ ├── platform │ │ └── spring │ │ │ └── jdbc │ │ │ └── TemporaryJDBCTest.java │ │ └── reference │ │ └── impl │ │ ├── AppContextSetup.java │ │ ├── ErrorDocumentDaoTest.java │ │ ├── ErrorDocumentServiceTest.java │ │ ├── ListDaoTest.java │ │ ├── ListServiceTest.java │ │ ├── ReferenceContextImpl.java │ │ ├── ReferenceSetDaoTest.java │ │ ├── ReferenceSetServiceTest.java │ │ └── TranslationPathTest.java │ └── resources │ ├── log4j.xml │ └── vanillaInMemoryAppContext.xml ├── taverna-reference-testhelpers ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── t2referencetest │ │ ├── BlueReference.java │ │ ├── DummyReferenceSet.java │ │ ├── GreenBuilder.java │ │ ├── GreenReference.java │ │ ├── GreenToRed.java │ │ ├── RedReference.java │ │ └── YellowReference.java │ └── resources │ ├── META-INF │ ├── services │ │ ├── org.apache.taverna.reference.ExternalReferenceBuilderSPI │ │ ├── org.apache.taverna.reference.ExternalReferenceSPI │ │ └── org.apache.taverna.reference.ExternalReferenceTranslatorSPI │ └── spring │ │ ├── reference-testhelpers-context-osgi.xml │ │ └── reference-testhelpers-context.xml │ └── org │ └── apache │ └── taverna │ └── t2referencetest │ ├── BlueReference.hbm.xml │ ├── GreenReference.hbm.xml │ ├── RedReference.hbm.xml │ └── YellowReference.hbm.xml ├── taverna-reference-types ├── README.md ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── reference │ │ │ └── impl │ │ │ └── external │ │ │ ├── file │ │ │ ├── FileReference.java │ │ │ ├── FileToFileReference.java │ │ │ └── package.html │ │ │ ├── http │ │ │ ├── HttpReference.java │ │ │ ├── UrlToHttpReference.java │ │ │ └── package.html │ │ │ └── object │ │ │ ├── BooleanToStringReference.java │ │ │ ├── ByteArrayToByteArrayReference.java │ │ │ ├── CharacterToStringReference.java │ │ │ ├── InlineByteArrayReference.java │ │ │ ├── InlineByteArrayReferenceBuilder.java │ │ │ ├── InlineByteToInlineStringTranslator.java │ │ │ ├── InlineStringReference.java │ │ │ ├── InlineStringReferenceBuilder.java │ │ │ ├── InlineStringToInlineByteTranslator.java │ │ │ ├── NumberToStringReference.java │ │ │ ├── StreamToBooleanConverter.java │ │ │ ├── StreamToByteArrayConverter.java │ │ │ ├── StreamToDoubleConverter.java │ │ │ ├── StreamToIntegerConverter.java │ │ │ ├── StreamToStringConverter.java │ │ │ ├── StreamToVMObjectReferenceConverter.java │ │ │ ├── StringToStringReference.java │ │ │ ├── VMObjectReference.java │ │ │ └── package.html │ └── resources │ │ ├── META-INF │ │ ├── services │ │ │ ├── org.apache.taverna.reference.ExternalReferenceBuilderSPI │ │ │ ├── org.apache.taverna.reference.ExternalReferenceSPI │ │ │ ├── org.apache.taverna.reference.ExternalReferenceTranslatorSPI │ │ │ ├── org.apache.taverna.reference.StreamToValueConverterSPI │ │ │ └── org.apache.taverna.reference.ValueToReferenceConverterSPI │ │ └── spring │ │ │ ├── reference-core-extensions-context-osgi.xml │ │ │ └── reference-core-extensions-context.xml │ │ └── org │ │ └── apache │ │ └── taverna │ │ └── reference │ │ └── impl │ │ └── external │ │ ├── file │ │ └── FileReference.hbm.xml │ │ ├── http │ │ └── HttpReference.hbm.xml │ │ └── object │ │ ├── InlineByteArrayReference.hbm.xml │ │ ├── InlineStringReference.hbm.xml │ │ └── VMObjectReference.hbm.xml │ └── test │ └── java │ └── org │ └── apache │ └── taverna │ └── reference │ └── impl │ └── external │ └── object │ └── ByteArrayToStringTest.java ├── taverna-report-api ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── apache │ │ └── taverna │ │ └── platform │ │ └── report │ │ ├── ActivityReport.java │ │ ├── Invocation.java │ │ ├── ProcessorReport.java │ │ ├── ReportListener.java │ │ ├── State.java │ │ ├── StatusReport.java │ │ └── WorkflowReport.java │ └── test │ └── java │ └── org │ └── apache │ └── taverna │ └── platform │ └── report │ └── StatusReportTest.java ├── taverna-run-api ├── pom.xml └── src │ ├── main │ └── java │ │ └── org │ │ └── apache │ │ └── taverna │ │ └── platform │ │ └── run │ │ └── api │ │ ├── InvalidRunIdException.java │ │ ├── RunProfile.java │ │ ├── RunProfileException.java │ │ ├── RunService.java │ │ └── RunStateException.java │ └── test │ └── java │ └── org │ └── apache │ └── taverna │ └── platform │ └── run │ └── api │ └── RunProfileTest.java ├── taverna-run-impl ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── platform │ │ │ └── run │ │ │ └── impl │ │ │ ├── Run.java │ │ │ ├── RunServiceImpl.java │ │ │ └── WorkflowReportJSON.java │ └── resources │ │ └── META-INF │ │ └── spring │ │ ├── run-context-osgi.xml │ │ └── run-context.xml │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── platform │ │ └── run │ │ └── impl │ │ ├── DummyWorkflowReport.java │ │ ├── RunTest.java │ │ └── WorkflowReportJSONTest.java │ └── resources │ ├── hello_anyone.wfbundle │ ├── workflowrun.bundle.zip │ └── workflowrun.json ├── taverna-services-api ├── .project ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── apache │ └── taverna │ └── services │ ├── ActivityTypeNotFoundException.java │ ├── InvalidConfigurationException.java │ └── ServiceRegistry.java ├── taverna-services-impl ├── .project ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ └── services │ │ └── impl │ │ └── ServiceRegistryImpl.java │ └── resources │ └── META-INF │ └── spring │ ├── taverna-services-context-osgi.xml │ └── taverna-services-context.xml ├── taverna-stringconstant-activity ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── activities │ │ │ └── stringconstant │ │ │ ├── StringConstantActivity.java │ │ │ ├── StringConstantActivityFactory.java │ │ │ ├── StringConstantActivityHealthChecker.java │ │ │ ├── StringConstantConfigurationBean.java │ │ │ └── package.html │ └── resources │ │ ├── META-INF │ │ ├── services │ │ │ └── org.apache.taverna.workflowmodel.health.HealthChecker │ │ └── spring │ │ │ ├── stringconstant-activity-context-osgi.xml │ │ │ └── stringconstant-activity-context.xml │ │ └── schema.json │ └── test │ └── java │ └── org │ └── apache │ └── taverna │ └── activities │ └── stringconstant │ ├── StringConstantActivityFactoryTest.java │ └── StringConstantActivityTest.java ├── taverna-workflowmodel-api ├── docs │ ├── MobyCentralCurationUseCasAggregated.uxf │ ├── MobyCentralCurationUseCase.uxf │ └── annotationmodel.uxf ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ ├── annotation │ │ │ ├── AbstractAnnotatedThing.java │ │ │ ├── Annotated.java │ │ │ ├── AnnotationAssertion.java │ │ │ ├── AnnotationBeanSPI.java │ │ │ ├── AnnotationChain.java │ │ │ ├── AnnotationPerspective.java │ │ │ ├── AnnotationRole.java │ │ │ ├── AnnotationSourceSPI.java │ │ │ ├── AppliesTo.java │ │ │ ├── Curateable.java │ │ │ ├── CurationEvent.java │ │ │ ├── CurationEventBeanSPI.java │ │ │ ├── CurationEventType.java │ │ │ ├── HierarchyRole.java │ │ │ ├── HierarchyTraversal.java │ │ │ ├── Person.java │ │ │ ├── annotationbeans │ │ │ │ ├── AbstractNumericRangeAssertion.java │ │ │ │ ├── AbstractNumericValueAssertion.java │ │ │ │ ├── AbstractTextualValueAssertion.java │ │ │ │ ├── Author.java │ │ │ │ ├── DescriptiveTitle.java │ │ │ │ ├── DocumentationUrl.java │ │ │ │ ├── ExampleValue.java │ │ │ │ ├── FreeTextDescription.java │ │ │ │ ├── HostInstitution.java │ │ │ │ ├── IdentificationAssertion.java │ │ │ │ ├── MimeType.java │ │ │ │ ├── Optional.java │ │ │ │ └── SemanticAnnotation.java │ │ │ └── package.html │ │ │ ├── facade │ │ │ ├── FacadeListener.java │ │ │ ├── ResultListener.java │ │ │ ├── WorkflowInstanceFacade.java │ │ │ ├── WorkflowRunCancellation.java │ │ │ └── package.html │ │ │ ├── invocation │ │ │ ├── Completion.java │ │ │ ├── Event.java │ │ │ ├── InvocationContext.java │ │ │ ├── IterationInternalEvent.java │ │ │ ├── ProcessIdentifierException.java │ │ │ ├── TokenOrderException.java │ │ │ ├── TreeCache.java │ │ │ ├── WorkflowDataToken.java │ │ │ └── package.html │ │ │ ├── monitor │ │ │ ├── MonitorManager.java │ │ │ ├── MonitorNode.java │ │ │ ├── MonitorableProperty.java │ │ │ ├── NoSuchPropertyException.java │ │ │ ├── SteerableProperty.java │ │ │ └── package.html │ │ │ ├── provenance │ │ │ ├── item │ │ │ │ ├── AbstractProvenanceItem.java │ │ │ │ ├── ActivityProvenanceItem.java │ │ │ │ ├── DataProvenanceItem.java │ │ │ │ ├── DataflowRunComplete.java │ │ │ │ ├── ErrorProvenanceItem.java │ │ │ │ ├── InputDataProvenanceItem.java │ │ │ │ ├── InvocationStartedProvenanceItem.java │ │ │ │ ├── IterationProvenanceItem.java │ │ │ │ ├── OutputDataProvenanceItem.java │ │ │ │ ├── ProcessProvenanceItem.java │ │ │ │ ├── ProcessorProvenanceItem.java │ │ │ │ ├── ProvenanceItem.java │ │ │ │ ├── WorkflowDataProvenanceItem.java │ │ │ │ └── WorkflowProvenanceItem.java │ │ │ ├── reporter │ │ │ │ └── ProvenanceReporter.java │ │ │ └── vocabulary │ │ │ │ └── SharedVocabulary.java │ │ │ ├── utility │ │ │ ├── TreeModelAdapter.java │ │ │ ├── TypedTreeModel.java │ │ │ ├── TypedTreeModelEvent.java │ │ │ ├── TypedTreeModelListener.java │ │ │ └── package.html │ │ │ ├── visit │ │ │ ├── DataflowCollation.java │ │ │ ├── HierarchyTraverser.java │ │ │ ├── VisitKind.java │ │ │ ├── VisitReport.java │ │ │ └── Visitor.java │ │ │ └── workflowmodel │ │ │ ├── AbstractOutputPort.java │ │ │ ├── AbstractPort.java │ │ │ ├── CompoundEdit.java │ │ │ ├── Condition.java │ │ │ ├── Configurable.java │ │ │ ├── ConfigurationException.java │ │ │ ├── ControlBoundary.java │ │ │ ├── Dataflow.java │ │ │ ├── DataflowInputPort.java │ │ │ ├── DataflowOutputPort.java │ │ │ ├── DataflowPort.java │ │ │ ├── DataflowValidationReport.java │ │ │ ├── Datalink.java │ │ │ ├── Edit.java │ │ │ ├── EditException.java │ │ │ ├── Edits.java │ │ │ ├── EventForwardingOutputPort.java │ │ │ ├── EventHandlingInputPort.java │ │ │ ├── FailureTransmitter.java │ │ │ ├── FilteringInputPort.java │ │ │ ├── InputPort.java │ │ │ ├── InvalidDataflowException.java │ │ │ ├── Merge.java │ │ │ ├── MergeInputPort.java │ │ │ ├── MergeOutputPort.java │ │ │ ├── MergePort.java │ │ │ ├── NamedWorkflowEntity.java │ │ │ ├── NamingException.java │ │ │ ├── OrderedPair.java │ │ │ ├── OutputPort.java │ │ │ ├── Port.java │ │ │ ├── Processor.java │ │ │ ├── ProcessorFinishedEvent.java │ │ │ ├── ProcessorInputPort.java │ │ │ ├── ProcessorOutputPort.java │ │ │ ├── ProcessorPort.java │ │ │ ├── RunDeletionListener.java │ │ │ ├── TokenProcessingEntity.java │ │ │ ├── WorkflowItem.java │ │ │ ├── WorkflowStructureException.java │ │ │ ├── health │ │ │ ├── DisabledActivityHealthChecker.java │ │ │ ├── HealthCheck.java │ │ │ ├── HealthChecker.java │ │ │ ├── RemoteHealthChecker.java │ │ │ ├── UnrecognizedActivityHealthChecker.java │ │ │ └── package.html │ │ │ ├── package.html │ │ │ ├── processor │ │ │ ├── activity │ │ │ │ ├── AbstractActivity.java │ │ │ │ ├── AbstractAsynchronousActivity.java │ │ │ │ ├── Activity.java │ │ │ │ ├── ActivityAndBeanWrapper.java │ │ │ │ ├── ActivityConfigurationException.java │ │ │ │ ├── ActivityFactory.java │ │ │ │ ├── ActivityInputPort.java │ │ │ │ ├── ActivityOutputPort.java │ │ │ │ ├── ActivityPort.java │ │ │ │ ├── AsynchronousActivity.java │ │ │ │ ├── AsynchronousActivityCallback.java │ │ │ │ ├── DisabledActivity.java │ │ │ │ ├── Job.java │ │ │ │ ├── LockedNestedDataflow.java │ │ │ │ ├── MonitorableAsynchronousActivity.java │ │ │ │ ├── NestedDataflow.java │ │ │ │ ├── NestedDataflowSource.java │ │ │ │ ├── NonExecutableActivity.java │ │ │ │ ├── SupersededActivity.java │ │ │ │ ├── UnrecognizedActivity.java │ │ │ │ ├── config │ │ │ │ │ ├── ActivityInputPortDefinitionBean.java │ │ │ │ │ ├── ActivityOutputPortDefinitionBean.java │ │ │ │ │ ├── ActivityPortDefinitionBean.java │ │ │ │ │ ├── ActivityPortsDefinitionBean.java │ │ │ │ │ └── package.html │ │ │ │ └── package.html │ │ │ ├── config │ │ │ │ ├── ConfigurationBean.java │ │ │ │ └── ConfigurationProperty.java │ │ │ ├── dispatch │ │ │ │ ├── AbstractDispatchLayer.java │ │ │ │ ├── AbstractErrorHandlerLayer.java │ │ │ │ ├── DispatchLayer.java │ │ │ │ ├── DispatchLayerFactory.java │ │ │ │ ├── DispatchStack.java │ │ │ │ ├── NotifiableLayer.java │ │ │ │ ├── PropertyContributingDispatchLayer.java │ │ │ │ ├── description │ │ │ │ │ ├── DispatchLayerErrorReaction.java │ │ │ │ │ ├── DispatchLayerJobQueueReaction.java │ │ │ │ │ ├── DispatchLayerJobReaction.java │ │ │ │ │ ├── DispatchLayerResultCompletionReaction.java │ │ │ │ │ ├── DispatchLayerResultReaction.java │ │ │ │ │ ├── DispatchLayerStateEffect.java │ │ │ │ │ ├── DispatchMessageType.java │ │ │ │ │ ├── ReactionTo.java │ │ │ │ │ ├── SupportsStreamedResult.java │ │ │ │ │ └── package.html │ │ │ │ ├── events │ │ │ │ │ ├── AbstractDispatchEvent.java │ │ │ │ │ ├── DispatchCompletionEvent.java │ │ │ │ │ ├── DispatchErrorEvent.java │ │ │ │ │ ├── DispatchErrorType.java │ │ │ │ │ ├── DispatchJobEvent.java │ │ │ │ │ ├── DispatchJobQueueEvent.java │ │ │ │ │ └── DispatchResultEvent.java │ │ │ │ └── package.html │ │ │ └── iteration │ │ │ │ ├── AbstractIterationStrategyNode.java │ │ │ │ ├── CompletionHandlingAbstractIterationStrategyNode.java │ │ │ │ ├── CrossProduct.java │ │ │ │ ├── DotProduct.java │ │ │ │ ├── IterationStrategy.java │ │ │ │ ├── IterationStrategyNode.java │ │ │ │ ├── IterationStrategyStack.java │ │ │ │ ├── IterationTypeMismatchException.java │ │ │ │ ├── MissingIterationInputException.java │ │ │ │ ├── NamedInputPortNode.java │ │ │ │ ├── PrefixDotProduct.java │ │ │ │ ├── TerminalNode.java │ │ │ │ └── package.html │ │ │ ├── serialization │ │ │ ├── DeserializationException.java │ │ │ └── SerializationException.java │ │ │ └── utils │ │ │ ├── AnnotationTools.java │ │ │ ├── NamedWorkflowEntityComparator.java │ │ │ ├── PortComparator.java │ │ │ └── Tools.java │ └── resources │ │ └── META-INF │ │ ├── services │ │ ├── org.apache.taverna.visit.VisitKind │ │ └── org.apache.taverna.workflowmodel.health.HealthChecker │ │ └── spring │ │ ├── workflowmodel-api-context-osgi.xml │ │ └── workflowmodel-api-context.xml │ └── test │ ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ ├── monitor │ │ └── TestMonitorManager.java │ │ └── workflowmodel │ │ ├── health │ │ ├── DummyVisitKind.java │ │ ├── FloatHealthChecker.java │ │ ├── FloatHealthChecker2.java │ │ ├── HealthReportTest.java │ │ └── StringHealthChecker.java │ │ └── processor │ │ └── iteration │ │ └── TestIterationStrategyNodes.java │ └── resources │ └── META-INF │ └── services │ └── org.apache.taverna.workflowmodel.health.HealthChecker ├── taverna-workflowmodel-extensions ├── .gitignore ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── apache │ │ │ └── taverna │ │ │ └── workflowmodel │ │ │ └── processor │ │ │ └── dispatch │ │ │ └── layers │ │ │ ├── CoreDispatchLayerFactory.java │ │ │ ├── ErrorBounce.java │ │ │ ├── Failover.java │ │ │ ├── IntermediateProvenance.java │ │ │ ├── Invoke.java │ │ │ ├── Loop.java │ │ │ ├── LoopConfiguration.java │ │ │ ├── Parallelize.java │ │ │ ├── ParallelizeConfig.java │ │ │ ├── Retry.java │ │ │ ├── RetryConfig.java │ │ │ ├── Stop.java │ │ │ └── package.html │ └── resources │ │ └── META-INF │ │ └── spring │ │ ├── workflowmodel-core-extensions-context-osgi.xml │ │ └── workflowmodel-core-extensions-context.xml │ └── test │ └── java │ └── org │ └── apache │ └── taverna │ └── workflowmodel │ └── processor │ └── dispatch │ └── layers │ └── TestRetry.java └── taverna-workflowmodel-impl ├── pom.xml └── src ├── main ├── java │ └── org │ │ └── apache │ │ └── taverna │ │ ├── annotation │ │ └── impl │ │ │ ├── AnnotationAssertionImpl.java │ │ │ ├── AnnotationChainImpl.java │ │ │ ├── DisputeEvent.java │ │ │ ├── DisputeEventDetails.java │ │ │ ├── PersonImpl.java │ │ │ └── URISource.java │ │ ├── facade │ │ └── impl │ │ │ └── WorkflowInstanceFacadeImpl.java │ │ ├── invocation │ │ └── impl │ │ │ └── InvocationContextImpl.java │ │ ├── monitor │ │ └── impl │ │ │ └── MonitorTreeModel.java │ │ └── workflowmodel │ │ ├── impl │ │ ├── AbstractActivityEdit.java │ │ ├── AbstractAnnotationEdit.java │ │ ├── AbstractBinaryProcessorEdit.java │ │ ├── AbstractCrystalizer.java │ │ ├── AbstractDataflowEdit.java │ │ ├── AbstractDataflowInputPortEdit.java │ │ ├── AbstractDataflowOutputPortEdit.java │ │ ├── AbstractDatalinkEdit.java │ │ ├── AbstractEventHandlingInputPort.java │ │ ├── AbstractFilteringInputPort.java │ │ ├── AbstractMergeEdit.java │ │ ├── AbstractProcessorEdit.java │ │ ├── BasicEventForwardingOutputPort.java │ │ ├── ConditionImpl.java │ │ ├── ConfigureEdit.java │ │ ├── Crystalizer.java │ │ ├── DataflowImpl.java │ │ ├── DataflowInputPortImpl.java │ │ ├── DataflowOutputPortImpl.java │ │ ├── DataflowValidationReportImpl.java │ │ ├── DatalinkImpl.java │ │ ├── EditSupport.java │ │ ├── EditsImpl.java │ │ ├── MergeImpl.java │ │ ├── MergeInputPortImpl.java │ │ ├── MergeOutputPortImpl.java │ │ ├── ProcessorCrystalizerImpl.java │ │ ├── ProcessorImpl.java │ │ ├── ProcessorInputPortImpl.java │ │ ├── ProcessorOutputPortImpl.java │ │ └── package.html │ │ └── processor │ │ ├── activity │ │ └── impl │ │ │ ├── ActivityInputPortImpl.java │ │ │ ├── ActivityOutputPortImpl.java │ │ │ └── package.html │ │ ├── dispatch │ │ └── impl │ │ │ ├── AbstractDispatchLayerEdit.java │ │ │ ├── DispatchStackImpl.java │ │ │ └── package.html │ │ └── iteration │ │ └── impl │ │ ├── IterationStrategyImpl.java │ │ ├── IterationStrategyStackImpl.java │ │ └── package.html └── resources │ ├── META-INF │ ├── services │ │ ├── org.apache.taverna.annotation.AnnotationBeanSPI │ │ ├── org.apache.taverna.annotation.AnnotationSourceSPI │ │ ├── org.apache.taverna.annotation.CurationEventBeanSPI │ │ ├── org.apache.taverna.workflowmodel.Edits │ │ └── org.apache.taverna.workflowmodel.health.HealthChecker │ └── spring │ │ ├── workflowmodel-impl-context-osgi.xml │ │ └── workflowmodel-impl-context.xml │ └── provenanceContext.xml └── test ├── java └── org │ └── apache │ └── taverna │ ├── annotation │ └── TestAnnotations.java │ ├── monitor │ └── impl │ │ └── MonitorTreeModelTest.java │ └── workflowmodel │ ├── impl │ ├── AbstractDatalinkEditTest.java │ ├── AddProcessorEditTest.java │ ├── ChangeDataflowInputPortDepthEditTest.java │ ├── ChangeDataflowInputPortGranularDepthEditTest.java │ ├── ConfigureActivityEditTest.java │ ├── ConnectDatalinkEditTest.java │ ├── ConnectMergedDatalinkEditTest.java │ ├── CreateDataflowInputPortEditTest.java │ ├── CreateDataflowOutputPortEditTest.java │ ├── DataflowImplTest.java │ ├── DefaultDispatchStackEditTest.java │ ├── DummyActivity.java │ ├── DummyDataflow.java │ ├── DummyDataflowInputPort.java │ ├── DummyDataflowOutputPort.java │ ├── DummyProcessor.java │ ├── DummyValidationReport.java │ ├── EditsImplTests.java │ ├── EventKeeper.java │ ├── MapProcessorPortsToActivityEditTest.java │ ├── ProcessorHealthReportTest.java │ ├── RemoveProcessorInputPortEditTest.java │ ├── RemoveProcessorOutputPortEditTest.java │ └── UpdateDataflowInternalIdentifierEditTest.java │ └── processor │ ├── AsynchEchoActivity.java │ ├── DiagnosticEventHandler.java │ ├── EchoConfig.java │ ├── NaiveProcessorConstructionTest.java │ ├── Tools.java │ ├── dispatch │ └── DiagnosticLayer.java │ └── iteration │ ├── DiagnosticIterationStrategyNode.java │ └── impl │ └── IterationTypeCheckerTest.java └── resources ├── log4j.properties └── serialized-fragments ├── 2_port_cross_product.xml ├── activity.xml ├── dataflow_datalinks.xml ├── dataflow_with_condition.xml ├── dataflow_with_merge.xml ├── dataflow_with_unlinked_processor.xml ├── dispatchLayer.xml ├── dispatchStack.xml ├── empty_dataflow_with_ports.xml └── processor.xml /.gitignore: -------------------------------------------------------------------------------- 1 | # ignore project files # 2 | .classpath 3 | .project 4 | .settings/ 5 | catalog-v001.xml 6 | 7 | # ignore target files # 8 | target/ 9 | bin/ 10 | build/ 11 | dist/ 12 | apidoc/ 13 | *.swp 14 | 15 | # ignore svn files if there 16 | .svn 17 | 18 | # ignore log files # 19 | *.log 20 | /logs/* 21 | */logs/* 22 | 23 | 24 | 25 | -------------------------------------------------------------------------------- /.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 | 16 | language: java 17 | -------------------------------------------------------------------------------- /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 Engine 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 2007-2014 University of Manchester, UK 10 | These have been licensed to the Apache Software Foundation under a software grant. 11 | 12 | --------------------------------------------------------- 13 | -------------------------------------------------------------------------------- /taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/exampleIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-engine/7318b4319c5e63709c3ea3a3a918f02d3f299130/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/exampleIcon.png -------------------------------------------------------------------------------- /taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/exampleIcon.xcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-engine/7318b4319c5e63709c3ea3a3a918f02d3f299130/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/exampleIcon.xcf -------------------------------------------------------------------------------- /taverna-activity-archetype/src/test/resources/projects/dummyActivity/archetype.properties: -------------------------------------------------------------------------------- 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 | ## 16 | groupId=com.example 17 | artifactId=dummy-taverna-plugin 18 | version=0.1.0-SNAPSHOT 19 | package=com.example.dummy 20 | classPrefix=Dummy 21 | -------------------------------------------------------------------------------- /taverna-activity-archetype/src/test/resources/projects/dummyActivity/goal.txt: -------------------------------------------------------------------------------- 1 | install 2 | -------------------------------------------------------------------------------- /taverna-activity-test-utils/src/main/java/org/apache/taverna/activities/testutils/LocationConstants.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.activities.testutils; 21 | 22 | /** 23 | * A definition of constants for base locations of external resources used for testing. 24 | * 25 | * @author Stuart Owen 26 | * 27 | */ 28 | public interface LocationConstants { 29 | public static final String WSDL_TEST_BASE="http://www.mygrid.org.uk/taverna-tests/testwsdls/"; 30 | } 31 | -------------------------------------------------------------------------------- /taverna-capability-api/src/main/java/org/apache/taverna/platform/capability/api/ActivityNotFoundException.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.platform.capability.api; 21 | 22 | /** 23 | * Thrown when an activity is not found. 24 | * 25 | * @author David Withers 26 | */ 27 | public class ActivityNotFoundException extends Exception { 28 | private static final long serialVersionUID = 1232220199558615801L; 29 | 30 | public ActivityNotFoundException() { 31 | super(); 32 | } 33 | 34 | public ActivityNotFoundException(String message) { 35 | super(message); 36 | } 37 | 38 | public ActivityNotFoundException(String message, Throwable cause) { 39 | super(message, cause); 40 | } 41 | 42 | public ActivityNotFoundException(Throwable cause) { 43 | super(cause); 44 | } 45 | } 46 | -------------------------------------------------------------------------------- /taverna-capability-api/src/main/java/org/apache/taverna/platform/capability/api/DispatchLayerNotFoundException.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.platform.capability.api; 21 | 22 | /** 23 | * Thrown when a dispatch layer is not found. 24 | * 25 | * @author David Withers 26 | */ 27 | public class DispatchLayerNotFoundException extends Exception { 28 | private static final long serialVersionUID = -7227237239711803139L; 29 | 30 | public DispatchLayerNotFoundException() { 31 | super(); 32 | } 33 | 34 | public DispatchLayerNotFoundException(String message) { 35 | super(message); 36 | } 37 | 38 | public DispatchLayerNotFoundException(String message, Throwable cause) { 39 | super(message, cause); 40 | } 41 | 42 | public DispatchLayerNotFoundException(Throwable cause) { 43 | super(cause); 44 | } 45 | } 46 | -------------------------------------------------------------------------------- /taverna-credential-manager-api/src/main/resources/META-INF/services/org.apache.taverna.security.credentialmanager.CredentialProviderSPI: -------------------------------------------------------------------------------- 1 | org.apache.taverna.security.credentialmanager.DefaultMasterPasswordProvider -------------------------------------------------------------------------------- /taverna-credential-manager-api/src/test/resources/html/test.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | 21 | Hello! 22 | 23 | -------------------------------------------------------------------------------- /taverna-credential-manager-api/src/test/resources/realm.properties: -------------------------------------------------------------------------------- 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 | 16 | test: test, user 17 | -------------------------------------------------------------------------------- /taverna-credential-manager-impl/src/test/java/org/apache/taverna/security/credentialmanager/impl/DummyJavaTruststorePasswordProvider.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.security.credentialmanager.impl; 21 | 22 | import org.apache.taverna.security.credentialmanager.JavaTruststorePasswordProvider; 23 | 24 | public class DummyJavaTruststorePasswordProvider implements JavaTruststorePasswordProvider{ 25 | 26 | String javaTruststorePassword; 27 | 28 | @Override 29 | public String getJavaTruststorePassword() { 30 | return javaTruststorePassword; 31 | } 32 | 33 | @Override 34 | public void setJavaTruststorePassword(String password) { 35 | javaTruststorePassword = password; 36 | } 37 | 38 | } 39 | -------------------------------------------------------------------------------- /taverna-credential-manager-impl/src/test/java/org/apache/taverna/security/credentialmanager/impl/TrustAlwaysTrustConfirmationProvider.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.security.credentialmanager.impl; 21 | 22 | import java.security.cert.X509Certificate; 23 | 24 | import org.apache.taverna.security.credentialmanager.TrustConfirmationProvider; 25 | 26 | public class TrustAlwaysTrustConfirmationProvider implements TrustConfirmationProvider{ 27 | 28 | @Override 29 | public Boolean shouldTrustCertificate(X509Certificate[] chain) { 30 | 31 | // Always trust 32 | return Boolean.TRUE; 33 | } 34 | 35 | } 36 | -------------------------------------------------------------------------------- /taverna-credential-manager-impl/src/test/java/org/apache/taverna/security/credentialmanager/impl/TrustNeverTrustConfimationProvider.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.security.credentialmanager.impl; 21 | 22 | import java.security.cert.X509Certificate; 23 | 24 | import org.apache.taverna.security.credentialmanager.TrustConfirmationProvider; 25 | 26 | public class TrustNeverTrustConfimationProvider implements TrustConfirmationProvider{ 27 | 28 | @Override 29 | public Boolean shouldTrustCertificate(X509Certificate[] chain) { 30 | 31 | // Never trust 32 | return Boolean.FALSE; 33 | } 34 | 35 | } 36 | -------------------------------------------------------------------------------- /taverna-credential-manager-impl/src/test/resources/html/test.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | 21 | Hello! 22 | 23 | -------------------------------------------------------------------------------- /taverna-credential-manager-impl/src/test/resources/security/t2keystore.ubr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-engine/7318b4319c5e63709c3ea3a3a918f02d3f299130/taverna-credential-manager-impl/src/test/resources/security/t2keystore.ubr -------------------------------------------------------------------------------- /taverna-credential-manager-impl/src/test/resources/security/t2truststore.ubr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-engine/7318b4319c5e63709c3ea3a3a918f02d3f299130/taverna-credential-manager-impl/src/test/resources/security/t2truststore.ubr -------------------------------------------------------------------------------- /taverna-credential-manager-impl/src/test/resources/security/test-private-key-cert.p12: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-engine/7318b4319c5e63709c3ea3a3a918f02d3f299130/taverna-credential-manager-impl/src/test/resources/security/test-private-key-cert.p12 -------------------------------------------------------------------------------- /taverna-credential-manager-impl/src/test/resources/security/tomcat_heater_certificate.pem: -------------------------------------------------------------------------------- 1 | -----BEGIN CERTIFICATE----- 2 | MIIDyDCCArCgAwIBAgIETlYTBzANBgkqhkiG9w0BAQUFADCBpTELMAkGA1UEBhMCVUsxGzAZBgNV 3 | BAgTEkdyZWF0ZXIgTWFuY2hlc3RlcjETMBEGA1UEBxMKTWFuY2hlc3RlcjEhMB8GA1UEChMYVW5p 4 | dmVyc2l0eSBvZiBNYW5jaGVzdGVyMSMwIQYDVQQLExpTY2hvb2wgb2YgQ29tcHV0ZXIgU2NpZW5j 5 | ZTEcMBoGA1UEAxMTaGVhdGVyLmNzLm1hbi5hYy51azAeFw0xMTA4MjUwOTE2NTVaFw0yMTA4MjIw 6 | OTE2NTVaMIGlMQswCQYDVQQGEwJVSzEbMBkGA1UECBMSR3JlYXRlciBNYW5jaGVzdGVyMRMwEQYD 7 | VQQHEwpNYW5jaGVzdGVyMSEwHwYDVQQKExhVbml2ZXJzaXR5IG9mIE1hbmNoZXN0ZXIxIzAhBgNV 8 | BAsTGlNjaG9vbCBvZiBDb21wdXRlciBTY2llbmNlMRwwGgYDVQQDExNoZWF0ZXIuY3MubWFuLmFj 9 | LnVrMIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA1/TuezSNYFpD2NTtw5UGECCPwClV 10 | Om08Nca1aanOVxv5rcn4eUVbu6Btm/dqgiCeV8nCyu7nEPvWP+Kvktseikx3LZ08qKdDRLpNa68/ 11 | WrjcbS6ICs2hphhqftHSpl0OPnWkQicbI7Z4uUdqmF6DsLDOLpRfiYhh9lZ0FM7PD3yt42GR5E2B 12 | j465IJQweZxLCsRKwuZlvOsWJxnx1MHVj7ZFBYl7HSBfEpvThyqKL5R7FOZW0zpG3+Y+S9HmfQYk 13 | BipXrrNS1+lsIwPU8jD31PBzVPBNxIeKYHxXCKLf+EBah/tAKSxIzUihxhh1pdNEPvUyy2zY9vyv 14 | 1PfXd8Uk0wIDAQABMA0GCSqGSIb3DQEBBQUAA4IBAQAtiPDBRlmjhFd9DP1NvbyfMApdjLufMLvr 15 | mzze3W6A4XUZj+kXR/Z3KYj84pWOnhe+Benvw5bIf2JM+sqIiSUA+TB8losx+SeY5hZ3lqEFY1wZ 16 | 1qy47hH3rY98RdSAXlAhvGCEL/CktvIEHgaSlCmrOvK76ySwRCTYA9DJTWeB81R7bP7le2ewSg5c 17 | MY/Hy3VBkMGbVnZQoHhkUd7TIsPqD1SvYQDCug49JFsKsyrfep3nANAQO7uR8FYrCYtXj66z9ziO 18 | m0gZm+h/Rq8StgMrNwmi+3mGAgRJ6JKj4vAWJfyUSaOjLLf9u3BvrxVtQKCMSDGx25dBFlZXHIhE 19 | rONf 20 | -----END CERTIFICATE----- 21 | -------------------------------------------------------------------------------- /taverna-database-configuration-api/.project: -------------------------------------------------------------------------------- 1 | 2 | 3 | taverna-database-configuration-api 4 | 5 | 6 | 7 | 8 | 9 | org.eclipse.jdt.core.javabuilder 10 | 11 | 12 | 13 | 14 | org.eclipse.m2e.core.maven2Builder 15 | 16 | 17 | 18 | 19 | 20 | org.eclipse.pde.PluginNature 21 | org.eclipse.jdt.core.javanature 22 | org.eclipse.m2e.core.maven2Nature 23 | 24 | 25 | -------------------------------------------------------------------------------- /taverna-database-configuration-api/src/main/java/org/apache/taverna/configuration/database/DatabaseManager.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.configuration.database; 21 | 22 | import java.sql.Connection; 23 | import java.sql.SQLException; 24 | 25 | import javax.sql.DataSource; 26 | 27 | /** 28 | * 29 | * 30 | * @author David Withers 31 | */ 32 | public interface DatabaseManager { 33 | 34 | public Connection getConnection() throws SQLException; 35 | 36 | public DataSource getDataSource(); 37 | 38 | public void startDerbyNetworkServer(); 39 | 40 | public void stopDerbyNetworkServer(); 41 | 42 | public boolean isRunning(); 43 | 44 | } -------------------------------------------------------------------------------- /taverna-database-configuration-impl/.project: -------------------------------------------------------------------------------- 1 | 2 | 3 | taverna-database-configuration-impl 4 | 5 | 6 | 7 | 8 | 9 | org.eclipse.jdt.core.javabuilder 10 | 11 | 12 | 13 | 14 | org.eclipse.m2e.core.maven2Builder 15 | 16 | 17 | 18 | 19 | 20 | org.eclipse.pde.PluginNature 21 | org.eclipse.jdt.core.javanature 22 | org.eclipse.m2e.core.maven2Nature 23 | 24 | 25 | -------------------------------------------------------------------------------- /taverna-dataflow-activity/src/main/java/org/apache/taverna/activities/dataflow/DataflowActivityHealthChecker.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.activities.dataflow; 21 | 22 | import java.util.List; 23 | 24 | import org.apache.taverna.visit.VisitReport; 25 | import org.apache.taverna.workflowmodel.health.HealthChecker; 26 | 27 | public class DataflowActivityHealthChecker implements HealthChecker { 28 | 29 | public boolean canVisit(Object subject) { 30 | return false; 31 | } 32 | 33 | public VisitReport visit(DataflowActivity activity, List ancestors) { 34 | return null; 35 | } 36 | 37 | public boolean isTimeConsuming() { 38 | return true; 39 | } 40 | 41 | } 42 | -------------------------------------------------------------------------------- /taverna-dataflow-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker: -------------------------------------------------------------------------------- 1 | org.apache.taverna.activities.dataflow.DataflowActivityHealthChecker -------------------------------------------------------------------------------- /taverna-dataflow-activity/src/main/resources/META-INF/spring/dataflow-activity-context.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /taverna-dataflow-activity/src/main/resources/schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "http://purl.org/dc/terms/rights": "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.", 3 | "http://purl.org/dc/terms/license": {"@id": "http://www.apache.org/licenses/LICENSE-2.0"}, 4 | "$schema": "http://json-schema.org/draft-03/schema#", 5 | "id": "http://ns.taverna.org.uk/2010/activity/dataflow.schema.json", 6 | "title": "Dataflow activity configuration", 7 | "type": "object", 8 | "properties": { 9 | "@context": { 10 | "description": "JSON-LD context for interpreting the configuration as RDF", 11 | "required": true, 12 | "enum": ["http://ns.taverna.org.uk/2010/activity/dataflow.context.json"] 13 | }, 14 | "nestedWorkflow": { 15 | "title": "Nested Workflow", 16 | "description": "Name of the nested workflow", 17 | "type": "string", 18 | "required": true 19 | } 20 | } 21 | } 22 | -------------------------------------------------------------------------------- /taverna-execution-api/src/main/java/org/apache/taverna/platform/execution/api/InvalidWorkflowException.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.platform.execution.api; 21 | 22 | /** 23 | * Thrown when a Workflow fails to validate. 24 | * 25 | * @author David Withers 26 | */ 27 | public class InvalidWorkflowException extends Exception { 28 | 29 | private static final long serialVersionUID = 7491175798204912590L; 30 | 31 | public InvalidWorkflowException() { 32 | super(); 33 | } 34 | 35 | public InvalidWorkflowException(String message, Throwable cause) { 36 | super(message, cause); 37 | } 38 | 39 | public InvalidWorkflowException(String message) { 40 | super(message); 41 | } 42 | 43 | public InvalidWorkflowException(Throwable cause) { 44 | super(cause); 45 | } 46 | 47 | } 48 | -------------------------------------------------------------------------------- /taverna-execution-hadoop/src/main/java/org/apache/taverna/platform/execution/impl/hadoop/TavernaReducer.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.platform.execution.impl.hadoop; 21 | 22 | import java.io.IOException; 23 | import java.util.Map; 24 | 25 | import org.apache.hadoop.fs.Path; 26 | 27 | public class TavernaReducer extends 28 | org.apache.hadoop.mapreduce.Reducer, Object, Object> { 29 | 30 | private Context context; 31 | 32 | @Override 33 | protected void setup(Context context) throws IOException, 34 | InterruptedException { 35 | this.context = context; 36 | } 37 | 38 | @Override 39 | protected void reduce(int[] key, Iterable> values, 40 | Context context) throws IOException, InterruptedException { 41 | } 42 | 43 | } 44 | -------------------------------------------------------------------------------- /taverna-execution-hadoop/src/main/java/org/apache/taverna/platform/execution/impl/hadoop/TextArrayWritable.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.platform.execution.impl.hadoop; 21 | 22 | import org.apache.hadoop.io.ArrayWritable; 23 | import org.apache.hadoop.io.Text; 24 | 25 | public class TextArrayWritable extends ArrayWritable { 26 | public TextArrayWritable() { 27 | super(Text.class); 28 | } 29 | 30 | } -------------------------------------------------------------------------------- /taverna-execution-impl/src/main/resources/META-INF/spring/execution-context.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /taverna-execution-local/src/test/resources/log4j.properties: -------------------------------------------------------------------------------- 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 | 16 | log4j.logger.net.sf.taverna=INFO 17 | -------------------------------------------------------------------------------- /taverna-execution-remote/src/main/resources/META-INF/spring/execution-remote-context.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 23 | 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /taverna-observer/src/main/java/org/apache/taverna/lang/observer/Observer.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.lang.observer; 21 | 22 | /** 23 | * Implement if you want to register with an {@link Observable} 24 | * 25 | * @author Ian Dunlop 26 | * @author Stian Soiland 27 | * 28 | * @param 29 | */ 30 | public interface Observer { 31 | /** 32 | * Called by the {@link Observable} to notify the implementing class of 33 | * changes 34 | * 35 | * @param sender 36 | * the class where the changes have happened 37 | * @param message 38 | * what has changed 39 | * @throws Exception 40 | */ 41 | public void notify(Observable sender, Message message) 42 | throws Exception; 43 | } 44 | -------------------------------------------------------------------------------- /taverna-prov-owl-bindings/.gitignore: -------------------------------------------------------------------------------- 1 | target 2 | .classpath 3 | .project 4 | .settings 5 | .Settings 6 | -------------------------------------------------------------------------------- /taverna-prov-owl-bindings/src/test/java/org/apache/taverna/prov/owl/TestWfprovModel.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 | package org.apache.taverna.prov.owl; 20 | import static org.junit.Assert.assertEquals; 21 | 22 | import java.net.URI; 23 | import java.util.UUID; 24 | 25 | import org.junit.Test; 26 | 27 | import org.apache.jena.ontology.Individual; 28 | 29 | 30 | public class TestWfprovModel { 31 | @Test 32 | public void dummy() throws Exception { 33 | ProvModel provModel = new WfprovModel(); 34 | Individual bundle = provModel.createBundle(uuid()); 35 | assertEquals("Bundle", bundle.getOntClass().getLocalName()); 36 | 37 | } 38 | 39 | private URI uuid() { 40 | return URI.create("urn:uuid:" + UUID.randomUUID()); 41 | } 42 | } 43 | -------------------------------------------------------------------------------- /taverna-prov/example/helloanyone.bundle.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-engine/7318b4319c5e63709c3ea3a3a918f02d3f299130/taverna-prov/example/helloanyone.bundle.zip -------------------------------------------------------------------------------- /taverna-prov/example/helloanyone.bundle/.ro/annotations/a2f03983-8836-4c36-bfb2-d713d9a1928f.ttl: -------------------------------------------------------------------------------- 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 | @prefix wfdesc: . 18 | 19 | 20 | wfdesc:hasWorkflowDefinition 21 | <../../workflow.wfbundle> . 22 | -------------------------------------------------------------------------------- /taverna-prov/example/helloanyone.bundle/inputs/name.txt: -------------------------------------------------------------------------------- 1 | fred -------------------------------------------------------------------------------- /taverna-prov/example/helloanyone.bundle/intermediates/3a/3a82e39d-a537-40cf-91a0-2c89d4a2e62b.txt: -------------------------------------------------------------------------------- 1 | Hello, -------------------------------------------------------------------------------- /taverna-prov/example/helloanyone.bundle/mimetype: -------------------------------------------------------------------------------- 1 | application/vnd.wf4ever.robundle+zip -------------------------------------------------------------------------------- /taverna-prov/example/helloanyone.bundle/outputs/greeting.txt: -------------------------------------------------------------------------------- 1 | Hello, fred -------------------------------------------------------------------------------- /taverna-prov/example/helloanyone.bundle/workflow.wfbundle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-engine/7318b4319c5e63709c3ea3a3a918f02d3f299130/taverna-prov/example/helloanyone.bundle/workflow.wfbundle -------------------------------------------------------------------------------- /taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/ProvenanceConnectorFactory.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 | package org.apache.taverna.provenance; 20 | 21 | import org.apache.taverna.provenance.connector.AbstractProvenanceConnector; 22 | 23 | public interface ProvenanceConnectorFactory { 24 | public AbstractProvenanceConnector getProvenanceConnector(); 25 | public String getConnectorType(); 26 | } 27 | -------------------------------------------------------------------------------- /taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/api/ProvenanceConnectorType.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 | package org.apache.taverna.provenance.api; 20 | 21 | /** 22 | * Defines names for the common Provenance Connector types 23 | * 24 | * @author Stuart Owen 25 | */ 26 | public class ProvenanceConnectorType { 27 | public static final String MYSQL = "mysql"; 28 | public static final String DERBY = "derby"; 29 | } 30 | -------------------------------------------------------------------------------- /taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/connector/ProvenanceSQL.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.provenance.connector; 21 | 22 | public class ProvenanceSQL { 23 | 24 | } 25 | -------------------------------------------------------------------------------- /taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/types/LiteralType.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 | package org.apache.taverna.provenance.lineageservice.types; 20 | 21 | /** 22 | * 23 | * @author Paolo Missier 24 | * 25 | */ 26 | public class LiteralType implements ProvenanceEventType { 27 | private String id; // attribute 28 | 29 | public LiteralType() { 30 | } 31 | 32 | public LiteralType(String id) { 33 | this.id = id; 34 | } 35 | 36 | /** 37 | * Gets the id value for this LiteralType. 38 | * 39 | * @return id 40 | */ 41 | public String getId() { 42 | return id; 43 | } 44 | 45 | /** 46 | * Sets the id value for this LiteralType. 47 | * 48 | * @param id 49 | */ 50 | public void setId(String id) { 51 | this.id = id; 52 | } 53 | } 54 | -------------------------------------------------------------------------------- /taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/types/ProvenanceEventType.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.provenance.lineageservice.types; 21 | 22 | /** 23 | * Used by an implementation of Provenance to identify the item type 24 | * 25 | * @author Paolo Missier 26 | */ 27 | public interface ProvenanceEventType { 28 | 29 | } 30 | -------------------------------------------------------------------------------- /taverna-provenanceconnector/src/main/java/org/apache/taverna/provenance/lineageservice/utils/DataValueExtractor.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 | package org.apache.taverna.provenance.lineageservice.utils; 20 | 21 | public interface DataValueExtractor { 22 | 23 | /** 24 | * extracts a printable string from a more complex object. This is not the 25 | * same as toString() as it is applied to an object, rather than being a 26 | * method on the object itself 27 | * 28 | * @param complexContent 29 | * should really be a byte array FIXME 30 | * @return 31 | */ 32 | public String extractString(Object complexContent); 33 | 34 | } 35 | -------------------------------------------------------------------------------- /taverna-reference-api/src/main/java/org/apache/taverna/reference/DaoException.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.reference; 21 | 22 | /** 23 | * Thrown by the Data Access Object interface methods, wrapping any underlying 24 | * exception. 25 | * 26 | * @author Tom Oinn 27 | */ 28 | public class DaoException extends RuntimeException { 29 | static final long serialVersionUID = 8496141798637577803L; 30 | 31 | public DaoException() { 32 | super(); 33 | } 34 | 35 | public DaoException(String message) { 36 | super(message); 37 | } 38 | 39 | public DaoException(Throwable cause) { 40 | super(cause); 41 | } 42 | 43 | public DaoException(String message, Throwable cause) { 44 | super(message, cause); 45 | } 46 | } 47 | -------------------------------------------------------------------------------- /taverna-reference-api/src/main/java/org/apache/taverna/reference/Identified.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.reference; 21 | 22 | /** 23 | * Interface for any object that has an associated {@link T2Reference} 24 | * 25 | * @author Tom Oinn 26 | */ 27 | public interface Identified { 28 | /** 29 | * Return an appropriately configured instance of T2Reference for this 30 | * identified object. 31 | * 32 | * @return the id of this object in the form of a T2Reference 33 | */ 34 | T2Reference getId(); 35 | } 36 | -------------------------------------------------------------------------------- /taverna-reference-api/src/main/java/org/apache/taverna/reference/ReferencedDataNature.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.reference; 21 | 22 | /** 23 | * Where possible ExternalReferenceSPI implementations should be able to 24 | * determine whether the data they refer to is textual or binary in nature. This 25 | * enumeration contains values for textual, binary and unknown data natures. 26 | * 27 | * @author Tom Oinn 28 | */ 29 | public enum ReferencedDataNature { 30 | /** 31 | * The data is binary, no character encoding will be specified. 32 | */ 33 | BINARY, 34 | 35 | /** 36 | * The data is textual, character encoding may be defined. 37 | */ 38 | TEXT, 39 | 40 | /** 41 | * Unknown data nature. 42 | */ 43 | UNKNOWN; 44 | } 45 | -------------------------------------------------------------------------------- /taverna-reference-api/src/main/java/org/apache/taverna/reference/WorkflowRunIdEntity.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.reference; 21 | 22 | /** 23 | * Entity that wraps workflow run id and can be passed through ( 24 | * {@link ReferenceContext} to be used by {@link T2ReferenceGenerator} to 25 | * generate references that are specific for a workflow run. 26 | * 27 | * @author Alex Nenadic 28 | */ 29 | public class WorkflowRunIdEntity { 30 | private String workflowRunId; 31 | 32 | public WorkflowRunIdEntity(String workflowRunId) { 33 | this.setWorkflowRunId(workflowRunId); 34 | } 35 | 36 | public void setWorkflowRunId(String workflowRunId) { 37 | this.workflowRunId = workflowRunId; 38 | } 39 | 40 | public String getWorkflowRunId() { 41 | return workflowRunId; 42 | } 43 | } 44 | -------------------------------------------------------------------------------- /taverna-reference-api/src/main/java/org/apache/taverna/reference/annotations/DeleteIdentifiedOperation.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.reference.annotations; 21 | 22 | import static java.lang.annotation.ElementType.METHOD; 23 | import static java.lang.annotation.RetentionPolicy.RUNTIME; 24 | 25 | import java.lang.annotation.Retention; 26 | import java.lang.annotation.Target; 27 | 28 | /** 29 | * Applied to methods in Dao implementations which delete data in the backing 30 | * store. 31 | * 32 | * @author Stuart Owen 33 | */ 34 | @Retention(RUNTIME) 35 | @Target(METHOD) 36 | public @interface DeleteIdentifiedOperation { 37 | } -------------------------------------------------------------------------------- /taverna-reference-api/src/main/java/org/apache/taverna/reference/annotations/GetIdentifiedOperation.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.reference.annotations; 21 | 22 | import static java.lang.annotation.ElementType.METHOD; 23 | import static java.lang.annotation.RetentionPolicy.RUNTIME; 24 | 25 | import java.lang.annotation.Retention; 26 | import java.lang.annotation.Target; 27 | 28 | /** 29 | * Applied to methods in Dao implementations which fetch data from the backing 30 | * store by ID 31 | * 32 | * @author Tom Oinn 33 | */ 34 | @Retention(RUNTIME) 35 | @Target(METHOD) 36 | public @interface GetIdentifiedOperation { 37 | } 38 | -------------------------------------------------------------------------------- /taverna-reference-api/src/main/java/org/apache/taverna/reference/annotations/PutIdentifiedOperation.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.reference.annotations; 21 | 22 | import static java.lang.annotation.ElementType.METHOD; 23 | import static java.lang.annotation.RetentionPolicy.RUNTIME; 24 | 25 | import java.lang.annotation.Retention; 26 | import java.lang.annotation.Target; 27 | 28 | /** 29 | * Applied to methods in Dao implementations which store or update data in the 30 | * backing store. 31 | * 32 | * @author Tom Oinn 33 | */ 34 | @Retention(RUNTIME) 35 | @Target(METHOD) 36 | public @interface PutIdentifiedOperation { 37 | } 38 | -------------------------------------------------------------------------------- /taverna-reference-api/src/main/java/org/apache/taverna/reference/annotations/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Annotations to make methods in the data access object implementations 21 | for cache injection. 22 | -------------------------------------------------------------------------------- /taverna-reference-api/src/main/java/org/apache/taverna/reference/h3/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Contains the marker interfaces used by the implementation package to 21 | ensure that all appropriate classes are mapped in hibernate 22 | before 23 | implementations of classes that depend upon them, and to ensure that 24 | 'static' classes such as the implementations of reference set etc are 25 | mapped correctly. 26 | -------------------------------------------------------------------------------- /taverna-reference-api/src/main/resources/org/apache/taverna/reference/AbstractExternalReference.hbm.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /taverna-reference-impl/.gitignore: -------------------------------------------------------------------------------- 1 | derby.log 2 | -------------------------------------------------------------------------------- /taverna-reference-impl/src/main/java/org/apache/taverna/platform/spring/jdbc/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Extensions to the JDBC parts of Spring, and support for proxying of JDBC 21 | drivers so we can load them dynamically from raven artifacts. The proxy 22 | approach is inspired by http://www.jroller.com/tackline/entry/dynamically_loading_jdbc_drivers 23 | with additions to build from raven rather than from existing jar files. 24 | -------------------------------------------------------------------------------- /taverna-reference-impl/src/main/java/org/apache/taverna/reference/impl/EmptyReferenceContext.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.reference.impl; 21 | 22 | import java.util.ArrayList; 23 | import java.util.List; 24 | 25 | import org.apache.taverna.reference.ReferenceContext; 26 | 27 | /** 28 | * A trivial implementation of ReferenceContext, used if the context parameter 29 | * to any service method is null. 30 | * 31 | * @author Tom Oinn 32 | */ 33 | public class EmptyReferenceContext implements ReferenceContext { 34 | /** 35 | * Return an empty entity set for all queries. 36 | */ 37 | @Override 38 | public List getEntities(Class arg0) { 39 | return new ArrayList<>(); 40 | } 41 | 42 | @Override 43 | public void addEntity(Object entity) { 44 | } 45 | } 46 | -------------------------------------------------------------------------------- /taverna-reference-impl/src/main/java/org/apache/taverna/reference/impl/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Implementation of the reference manager APIs backed by Hibernate. These 21 | classes are intended to be used with Spring, so have their dependencies 22 | injected through set methods rather than constructor arguments. 23 | -------------------------------------------------------------------------------- /taverna-reference-impl/src/main/resources/META-INF/spring.schemas: -------------------------------------------------------------------------------- 1 | http\://taverna.sf.net/schema/artifact-support/artifact-support.xsd=artifact-support.xsd -------------------------------------------------------------------------------- /taverna-reference-testhelpers/src/main/resources/META-INF/services/org.apache.taverna.reference.ExternalReferenceBuilderSPI: -------------------------------------------------------------------------------- 1 | # Implementation classes of ExternalReferenceBuilderSPI go here, one per line 2 | org.apache.taverna.t2referencetest.GreenBuilder -------------------------------------------------------------------------------- /taverna-reference-testhelpers/src/main/resources/META-INF/services/org.apache.taverna.reference.ExternalReferenceSPI: -------------------------------------------------------------------------------- 1 | # Implementation classes of ExternalReferenceSPI go here, one per line 2 | org.apache.taverna.t2referencetest.GreenReference 3 | org.apache.taverna.t2referencetest.BlueReference 4 | org.apache.taverna.t2referencetest.RedReference 5 | org.apache.taverna.t2referencetest.YellowReference -------------------------------------------------------------------------------- /taverna-reference-testhelpers/src/main/resources/META-INF/services/org.apache.taverna.reference.ExternalReferenceTranslatorSPI: -------------------------------------------------------------------------------- 1 | # Implementation classes of ExternalReferenceTranslatorSPI go here, one per line 2 | org.apache.taverna.t2referencetest.GreenToRed -------------------------------------------------------------------------------- /taverna-reference-testhelpers/src/main/resources/org/apache/taverna/t2referencetest/BlueReference.hbm.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /taverna-reference-testhelpers/src/main/resources/org/apache/taverna/t2referencetest/GreenReference.hbm.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /taverna-reference-testhelpers/src/main/resources/org/apache/taverna/t2referencetest/RedReference.hbm.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /taverna-reference-testhelpers/src/main/resources/org/apache/taverna/t2referencetest/YellowReference.hbm.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /taverna-reference-types/README.md: -------------------------------------------------------------------------------- 1 | Taverna Workflow system Execution Engine data reference management implementation. 2 | 3 | Implements certain SPIs to provide a core functionality for the reference management framework. This includes ExternalReference implementations to reference data held in local files and URLs along with the appropriate translate / publish logic. Implementations in this package are tied only to the API, although certain metadata files (such as Hibernate mappings) are also included, where appropriate. (These will be silently ignored if using a backing store that is not Hibernate-based.) 4 | 5 | This code was previously hosted at 6 | http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.core.reference-core-extensions - 7 | for historical references (e.g. for Taverna 2.x), see 8 | [taverna-svn on GitHub](https://github.com/taverna/taverna-svn/tree/master/taverna/engine/net.sf.taverna.t2.core.reference-core-extensions) 9 | and the `old/` git tags in this repository, e.g. 10 | [old/reference-core-extension-1.5](https://github.com/apache/incubator-taverna-engine/tree/old/reference-core-extensions-1.5) 11 | -------------------------------------------------------------------------------- /taverna-reference-types/src/main/java/org/apache/taverna/reference/impl/external/file/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Support for references to a file on a local (or otherwise mounted) 21 | filesystem 22 | -------------------------------------------------------------------------------- /taverna-reference-types/src/main/java/org/apache/taverna/reference/impl/external/http/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Support for references to a URL with the HTTP protocol 21 | -------------------------------------------------------------------------------- /taverna-reference-types/src/main/java/org/apache/taverna/reference/impl/external/object/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Support for representation of inlined objects as references. Replaces 21 | the old Literal support 22 | -------------------------------------------------------------------------------- /taverna-reference-types/src/main/resources/META-INF/services/org.apache.taverna.reference.ExternalReferenceBuilderSPI: -------------------------------------------------------------------------------- 1 | # Implementation classes of ExternalReferenceBuilderSPI go here, one per line 2 | org.apache.taverna.reference.impl.external.object.InlineStringReferenceBuilder 3 | org.apache.taverna.reference.impl.external.object.InlineByteArrayReferenceBuilder -------------------------------------------------------------------------------- /taverna-reference-types/src/main/resources/META-INF/services/org.apache.taverna.reference.ExternalReferenceSPI: -------------------------------------------------------------------------------- 1 | # Implementation classes of ExternalReferenceSPI go here, one per line 2 | org.apache.taverna.reference.impl.external.file.FileReference 3 | org.apache.taverna.reference.impl.external.http.HttpReference 4 | org.apache.taverna.reference.impl.external.object.InlineStringReference 5 | org.apache.taverna.reference.impl.external.object.InlineByteArrayReference 6 | org.apache.taverna.reference.impl.external.object.VMObjectReference -------------------------------------------------------------------------------- /taverna-reference-types/src/main/resources/META-INF/services/org.apache.taverna.reference.ExternalReferenceTranslatorSPI: -------------------------------------------------------------------------------- 1 | # Implementation classes of ExternalReferenceTranslatorSPI go here, one per line 2 | org.apache.taverna.reference.impl.external.object.InlineByteToInlineStringTranslator 3 | org.apache.taverna.reference.impl.external.object.InlineStringToInlineByteTranslator 4 | -------------------------------------------------------------------------------- /taverna-reference-types/src/main/resources/META-INF/services/org.apache.taverna.reference.StreamToValueConverterSPI: -------------------------------------------------------------------------------- 1 | # Implementation classes of StreamToValueConverterSPI go here, one per line 2 | org.apache.taverna.reference.impl.external.object.StreamToStringConverter 3 | org.apache.taverna.reference.impl.external.object.StreamToByteArrayConverter 4 | org.apache.taverna.reference.impl.external.object.StreamToVMObjectReferenceConverter 5 | org.apache.taverna.reference.impl.external.object.StreamToDoubleConverter 6 | org.apache.taverna.reference.impl.external.object.StreamToBooleanConverter 7 | org.apache.taverna.reference.impl.external.object.StreamToIntegerConverter 8 | -------------------------------------------------------------------------------- /taverna-reference-types/src/main/resources/META-INF/services/org.apache.taverna.reference.ValueToReferenceConverterSPI: -------------------------------------------------------------------------------- 1 | # Implementation classes of ValueToReferenceConverterSPI go here, one per line 2 | org.apache.taverna.reference.impl.external.file.FileToFileReference 3 | org.apache.taverna.reference.impl.external.http.UrlToHttpReference 4 | org.apache.taverna.reference.impl.external.object.StringToStringReference 5 | org.apache.taverna.reference.impl.external.object.ByteArrayToByteArrayReference 6 | org.apache.taverna.reference.impl.external.object.NumberToStringReference 7 | org.apache.taverna.reference.impl.external.object.CharacterToStringReference 8 | org.apache.taverna.reference.impl.external.object.BooleanToStringReference 9 | -------------------------------------------------------------------------------- /taverna-report-api/src/main/java/org/apache/taverna/platform/report/ReportListener.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.platform.report; 21 | 22 | import java.nio.file.Path; 23 | 24 | /** 25 | * @author David Withers 26 | */ 27 | public interface ReportListener { 28 | void outputAdded(Path path, String portName, int[] index); 29 | 30 | void stateChanged(State oldState, State newState); 31 | } 32 | -------------------------------------------------------------------------------- /taverna-report-api/src/main/java/org/apache/taverna/platform/report/State.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.platform.report; 21 | 22 | /** 23 | * Valid states for status reports. 24 | * 25 | * @author David Withers 26 | */ 27 | public enum State { 28 | CREATED, RUNNING, COMPLETED, PAUSED, CANCELLED, FAILED 29 | } 30 | -------------------------------------------------------------------------------- /taverna-run-api/src/main/java/org/apache/taverna/platform/run/api/InvalidRunIdException.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.platform.run.api; 21 | 22 | /** 23 | * Thrown when a runID is not valid for the RunService. 24 | * 25 | * @author David Withers 26 | */ 27 | public class InvalidRunIdException extends Exception { 28 | private static final long serialVersionUID = -8524012164316151704L; 29 | 30 | public InvalidRunIdException() { 31 | super(); 32 | } 33 | 34 | public InvalidRunIdException(String message) { 35 | super(message); 36 | } 37 | 38 | public InvalidRunIdException(String message, Throwable cause) { 39 | super(message, cause); 40 | } 41 | 42 | public InvalidRunIdException(Throwable cause) { 43 | super(cause); 44 | } 45 | } 46 | -------------------------------------------------------------------------------- /taverna-run-api/src/main/java/org/apache/taverna/platform/run/api/RunProfileException.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.platform.run.api; 21 | 22 | /** 23 | * Thrown when a RunProfile doesn't contain the correct components 24 | * to run a workflow. 25 | * 26 | * @author David Withers 27 | */ 28 | public class RunProfileException extends Exception { 29 | private static final long serialVersionUID = 4717267498382223527L; 30 | 31 | public RunProfileException() { 32 | super(); 33 | } 34 | 35 | public RunProfileException(String message, Throwable cause) { 36 | super(message, cause); 37 | } 38 | 39 | public RunProfileException(String message) { 40 | super(message); 41 | } 42 | 43 | public RunProfileException(Throwable cause) { 44 | super(cause); 45 | } 46 | } 47 | -------------------------------------------------------------------------------- /taverna-run-api/src/main/java/org/apache/taverna/platform/run/api/RunStateException.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.platform.run.api; 21 | 22 | /** 23 | * Thrown when an operation is attempted when a workflow is in the wrong state, 24 | * e.g., resuming a workflow that is not paused. 25 | * 26 | * @author David Withers 27 | */ 28 | public class RunStateException extends Exception { 29 | private static final long serialVersionUID = 6759341273715906131L; 30 | 31 | public RunStateException() { 32 | super(); 33 | } 34 | 35 | public RunStateException(String message, Throwable cause) { 36 | super(message, cause); 37 | } 38 | 39 | public RunStateException(String message) { 40 | super(message); 41 | } 42 | 43 | public RunStateException(Throwable cause) { 44 | super(cause); 45 | } 46 | } 47 | -------------------------------------------------------------------------------- /taverna-run-impl/src/main/resources/META-INF/spring/run-context.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /taverna-run-impl/src/test/resources/hello_anyone.wfbundle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-engine/7318b4319c5e63709c3ea3a3a918f02d3f299130/taverna-run-impl/src/test/resources/hello_anyone.wfbundle -------------------------------------------------------------------------------- /taverna-run-impl/src/test/resources/workflowrun.bundle.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/apache/incubator-taverna-engine/7318b4319c5e63709c3ea3a3a918f02d3f299130/taverna-run-impl/src/test/resources/workflowrun.bundle.zip -------------------------------------------------------------------------------- /taverna-services-api/.project: -------------------------------------------------------------------------------- 1 | 2 | 3 | taverna-services-api 4 | 5 | 6 | 7 | 8 | 9 | org.eclipse.jdt.core.javabuilder 10 | 11 | 12 | 13 | 14 | org.eclipse.m2e.core.maven2Builder 15 | 16 | 17 | 18 | 19 | 20 | org.eclipse.pde.PluginNature 21 | org.eclipse.jdt.core.javanature 22 | org.eclipse.m2e.core.maven2Nature 23 | 24 | 25 | -------------------------------------------------------------------------------- /taverna-services-api/src/main/java/org/apache/taverna/services/ActivityTypeNotFoundException.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.services; 21 | 22 | /** 23 | * Thrown when an activity type is not found. 24 | * 25 | * @author David Withers 26 | */ 27 | @SuppressWarnings("serial") 28 | public class ActivityTypeNotFoundException extends Exception { 29 | 30 | public ActivityTypeNotFoundException() { 31 | super(); 32 | } 33 | 34 | public ActivityTypeNotFoundException(String message) { 35 | super(message); 36 | } 37 | 38 | public ActivityTypeNotFoundException(String message, Throwable cause) { 39 | super(message, cause); 40 | } 41 | 42 | public ActivityTypeNotFoundException(Throwable cause) { 43 | super(cause); 44 | } 45 | 46 | } 47 | -------------------------------------------------------------------------------- /taverna-services-api/src/main/java/org/apache/taverna/services/InvalidConfigurationException.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.services; 21 | 22 | /** 23 | * Thrown when a Configuration is not valid for a Configurable. 24 | * 25 | * @author David Withers 26 | */ 27 | @SuppressWarnings("serial") 28 | public class InvalidConfigurationException extends Exception { 29 | 30 | public InvalidConfigurationException() { 31 | super(); 32 | } 33 | 34 | public InvalidConfigurationException(String message) { 35 | super(message); 36 | } 37 | 38 | public InvalidConfigurationException(String message, Throwable cause) { 39 | super(message, cause); 40 | } 41 | 42 | public InvalidConfigurationException(Throwable cause) { 43 | super(cause); 44 | } 45 | 46 | } 47 | -------------------------------------------------------------------------------- /taverna-services-impl/.project: -------------------------------------------------------------------------------- 1 | 2 | 3 | taverna-services-impl 4 | 5 | 6 | 7 | 8 | 9 | org.eclipse.jdt.core.javabuilder 10 | 11 | 12 | 13 | 14 | org.eclipse.m2e.core.maven2Builder 15 | 16 | 17 | 18 | 19 | 20 | org.eclipse.pde.PluginNature 21 | org.eclipse.jdt.core.javanature 22 | org.eclipse.m2e.core.maven2Nature 23 | 24 | 25 | -------------------------------------------------------------------------------- /taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Contains the activity classes required in the execution of Beanshell scripts. 21 | -------------------------------------------------------------------------------- /taverna-stringconstant-activity/src/main/resources/META-INF/services/org.apache.taverna.workflowmodel.health.HealthChecker: -------------------------------------------------------------------------------- 1 | org.apache.taverna.activities.stringconstant.StringConstantActivityHealthChecker -------------------------------------------------------------------------------- /taverna-stringconstant-activity/src/main/resources/META-INF/spring/stringconstant-activity-context.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/annotation/AnnotationBeanSPI.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.annotation; 21 | 22 | /** 23 | * Marker interface to denote that a bean class is a container for the 24 | * information encapsulated by an InformationAssertion object 25 | * 26 | * @author Tom Oinn 27 | * 28 | */ 29 | public interface AnnotationBeanSPI { 30 | 31 | } 32 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/annotation/AnnotationSourceSPI.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.annotation; 21 | 22 | /** 23 | * A marker interface that specified that the implementation is a bean 24 | * containing information about a source of annotations. These might be 25 | * publications, web URIs, a free text container, a person (etc). We should be 26 | * able to use existing schemes for identification of sources, publications etc 27 | * here. 28 | * 29 | * @author Tom Oinn 30 | * 31 | */ 32 | public interface AnnotationSourceSPI { 33 | 34 | } 35 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/annotation/CurationEventBeanSPI.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.annotation; 21 | 22 | /** 23 | * Contains the detail for a single curation event. In many cases this will be a 24 | * plain base curation object with very little information but it allows for us 25 | * to specify additional parameters to the curation event which can then be used 26 | * by the AnnotationPerspective instance to determine whether it believes the 27 | * curator. 28 | * 29 | * @author Tom Oinn 30 | * 31 | */ 32 | public interface CurationEventBeanSPI { 33 | 34 | } 35 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/annotation/CurationEventType.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.annotation; 21 | 22 | public enum CurationEventType { 23 | 24 | /** 25 | * The curation event asserts that the event it is attached to was correct, 26 | * effectively signing off an approval on the attached event. 27 | */ 28 | VALIDATION, 29 | 30 | /** 31 | * The curation event repudiates the information in the attached event, 32 | * denying its validity. 33 | */ 34 | REPUDIATION, 35 | 36 | /** 37 | * The curation event neither validates nor repudiates the information in 38 | * the attached event. 39 | */ 40 | NEUTRAL; 41 | 42 | } 43 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/annotation/HierarchyRole.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.annotation; 21 | 22 | /** 23 | * Possible relationships between entities in a hierarchical context. This is 24 | * used as a property of the HierarchyTraversal annotation on members which 25 | * traverse a conceptual object hierarchy such as a parent-child containment 26 | * relationship. As an example the getProcessors() method in Dataflow is 27 | * annotated with &HierarchyRole(role=CHILD) to indicate that 28 | * it accesses child members of the workflow model containment hierarchy. 29 | * 30 | * @author Tom Oinn 31 | * 32 | */ 33 | public enum HierarchyRole { 34 | 35 | CHILD, 36 | 37 | PARENT; 38 | 39 | } 40 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/annotation/Person.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.annotation; 21 | 22 | /** 23 | * All metadata assertions and curation assertions have a person who is 24 | * ultimately responsible for the assertion (although this may not necessarily 25 | * imply that the assertion was created interactively). 26 | * 27 | * TODO this needs to have some members! Cross reference with myExperiment user 28 | * model I suspect. 29 | * 30 | * @author Tom Oinn 31 | * 32 | */ 33 | public interface Person { 34 | 35 | } 36 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/annotation/annotationbeans/Author.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.annotation.annotationbeans; 21 | 22 | import org.apache.taverna.annotation.AppliesTo; 23 | import org.apache.taverna.workflowmodel.Dataflow; 24 | 25 | /** 26 | * The name of an author of a dataflow held as a String 27 | * 28 | * It should allow many but currently only allows one 29 | * 30 | * @author Alan R Williams 31 | * 32 | */ 33 | @AppliesTo(targetObjectType = { Dataflow.class }, many = false) 34 | public class Author extends AbstractTextualValueAssertion { 35 | 36 | /** 37 | * Default constructor as mandated by java bean specification 38 | */ 39 | public Author() { 40 | // 41 | } 42 | 43 | } 44 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/annotation/annotationbeans/DescriptiveTitle.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.annotation.annotationbeans; 21 | 22 | import org.apache.taverna.annotation.AppliesTo; 23 | import org.apache.taverna.workflowmodel.Dataflow; 24 | 25 | /** 26 | * The descriptive title of a dataflow held as a String 27 | * 28 | * @author Alan R Williams 29 | * 30 | */ 31 | @AppliesTo(targetObjectType = { Dataflow.class }, many = false) 32 | public class DescriptiveTitle extends AbstractTextualValueAssertion { 33 | 34 | /** 35 | * Default constructor as mandated by java bean specification 36 | */ 37 | public DescriptiveTitle() { 38 | // 39 | } 40 | 41 | } 42 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/annotation/annotationbeans/ExampleValue.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.annotation.annotationbeans; 21 | 22 | import org.apache.taverna.annotation.AppliesTo; 23 | import org.apache.taverna.workflowmodel.DataflowInputPort; 24 | import org.apache.taverna.workflowmodel.DataflowOutputPort; 25 | 26 | /** 27 | * A String containing an example or a description of an example 28 | * 29 | * @author Alan R Williams 30 | * 31 | */ 32 | @AppliesTo(targetObjectType = { DataflowInputPort.class , DataflowOutputPort.class }, many = false) 33 | public class ExampleValue extends AbstractTextualValueAssertion { 34 | 35 | /** 36 | * Default constructor as mandated by java bean specification 37 | */ 38 | public ExampleValue() { 39 | // 40 | } 41 | 42 | } 43 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/annotation/annotationbeans/HostInstitution.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.annotation.annotationbeans; 21 | 22 | import org.apache.taverna.annotation.AppliesTo; 23 | import org.apache.taverna.workflowmodel.processor.activity.Activity; 24 | 25 | /** 26 | * The host institution for an activity implementation 27 | * 28 | * @author Tom Oinn 29 | * @author Alan Williams 30 | */ 31 | @AppliesTo(targetObjectType = { Activity.class }, many = false) 32 | public class HostInstitution extends AbstractTextualValueAssertion { 33 | 34 | /** 35 | * Default constructor as mandated by java bean specification 36 | */ 37 | public HostInstitution() { 38 | super(); 39 | } 40 | 41 | } 42 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/facade/WorkflowRunCancellation.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.facade; 21 | 22 | /** 23 | * A WorkflowRunCancellation is passed to listeners when a workflow run is 24 | * cancelled. 25 | * 26 | * @author alanrw 27 | */ 28 | @SuppressWarnings("serial") 29 | public class WorkflowRunCancellation extends Throwable { 30 | /** 31 | * The id of the workflow run that was cancelled 32 | */ 33 | private String cancelledWorkflowRunId; 34 | 35 | public WorkflowRunCancellation (String runId) { 36 | cancelledWorkflowRunId = runId; 37 | } 38 | 39 | /** 40 | * @return the id of the workflow run that was cancelled. 41 | */ 42 | public String getCancelledWorkflowRunId() { 43 | return cancelledWorkflowRunId; 44 | } 45 | } 46 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/invocation/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Contains classes supporting workflow invocation. Other packages may have 21 | dependencies on this one but classes here will only be accessed by 22 | non-taverna code in an invocation context. Nothing in here should be 23 | critical to the definition and manipulation of the workflow defintion. 24 | 25 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/monitor/SteerableProperty.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.monitor; 21 | 22 | /** 23 | * Some monitorable properties are mutable and can be written to by steering 24 | * agents or other clients. 25 | * 26 | * @author Tom Oinn 27 | */ 28 | public interface SteerableProperty extends MonitorableProperty { 29 | /** 30 | * Set the property value 31 | * 32 | * @param newValue 33 | * @throws NoSuchPropertyException 34 | */ 35 | void setProperty(T newValue) throws NoSuchPropertyException; 36 | } 37 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/provenance/vocabulary/SharedVocabulary.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.provenance.vocabulary; 21 | 22 | import org.apache.taverna.provenance.item.ProvenanceItem; 23 | 24 | /** 25 | * Static strings which identify all the {@link ProvenanceItem}s and 26 | * {@link ProvenanceEventType}s 27 | * 28 | * @author Paolo Missier 29 | * @author Ian Dunlop 30 | */ 31 | public enum SharedVocabulary { 32 | DATAFLOW_EVENT_TYPE, PROCESS_EVENT_TYPE, PROVENANCE_EVENT_TYPE, ACTIVITY_EVENT_TYPE, DATA_EVENT_TYPE, ERROR_EVENT_TYPE, INMEMORY_EVENT_TYPE, INPUTDATA_EVENT_TYPE, ITERATION_EVENT_TYPE, OUTPUTDATA_EVENT_TYPE, PROCESSOR_EVENT_TYPE, WEBSERVICE_EVENT_TYPE, WORKFLOW_DATA_EVENT_TYPE, WORKFLOW_EVENT_TYPE, END_WORKFLOW_EVENT_TYPE, INVOCATION_STARTED_EVENT_TYPE; 33 | } 34 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/utility/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Utility classes, currently consists of a generic type safe alternative 21 | to TreeModel along with an adapter class to allow it to be used where a 22 | TreeModel is required (i.e. JTree) 23 | 24 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/visit/VisitKind.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.visit; 21 | 22 | /** 23 | * A type of visit that can be made e.g. a health check. 24 | * 25 | * @author alanrw 26 | */ 27 | public abstract class VisitKind { 28 | /** 29 | * The class that all visitors that extend/implement if they make this type 30 | * of visit. 31 | * 32 | * @return 33 | */ 34 | public abstract Class> getVisitorClass(); 35 | } 36 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/AbstractOutputPort.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.workflowmodel; 21 | 22 | /** 23 | * Simple implementation of OutputPort, extends AbstractPort and adds the 24 | * granular depth bean getter. 25 | * 26 | * @author Tom Oinn 27 | */ 28 | public abstract class AbstractOutputPort extends AbstractPort implements 29 | OutputPort { 30 | protected int granularDepth; 31 | 32 | protected AbstractOutputPort(String portName, int portDepth, 33 | int granularDepth) { 34 | super(portName, portDepth); 35 | this.granularDepth = granularDepth; 36 | } 37 | 38 | @Override 39 | public int getGranularDepth() { 40 | return granularDepth; 41 | } 42 | } 43 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/DataflowPort.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.workflowmodel; 21 | 22 | /** 23 | * Defines that the implementing port belongs to a Dataflow 24 | * 25 | * @author Tom Oinn 26 | * @author Stian Soiland-Reyes 27 | */ 28 | public interface DataflowPort extends Port { 29 | /** 30 | * Get the parent DataFlow to which this port belongs 31 | */ 32 | public Dataflow getDataflow(); 33 | } 34 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/EditException.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.workflowmodel; 21 | 22 | /** 23 | * Superclass of all exceptions thrown when altering the workflow model through 24 | * the edit manager. 25 | * 26 | * @author Tom Oinn 27 | */ 28 | public class EditException extends Exception { 29 | public EditException(String string) { 30 | super(string); 31 | } 32 | 33 | public EditException(String string, Throwable cause) { 34 | super(string, cause); 35 | } 36 | 37 | public EditException(Throwable t) { 38 | super(t); 39 | } 40 | 41 | private static final long serialVersionUID = 1L; 42 | } 43 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/EventHandlingInputPort.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.workflowmodel; 21 | 22 | import org.apache.taverna.invocation.WorkflowDataToken; 23 | 24 | /** 25 | * Input port capable of receiving and reacting to workflow events. 26 | * 27 | * @author Tom Oinn 28 | */ 29 | public interface EventHandlingInputPort extends InputPort { 30 | /** 31 | * Receive an arbitrary workflow event. 32 | */ 33 | void receiveEvent(WorkflowDataToken t); 34 | 35 | /** 36 | * If this port is connected to a Datalink return the link, otherwise return 37 | * null 38 | */ 39 | Datalink getIncomingLink(); 40 | } 41 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/FailureTransmitter.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.workflowmodel; 21 | 22 | /** 23 | * Used to message interested parties when a top level failure occurs within a 24 | * {@link Dataflow} 25 | *

26 | * Not implemented in the current code, this is a placeholder for the failure 27 | * handling system. 28 | * 29 | * @author Tom Oinn 30 | */ 31 | public interface FailureTransmitter { 32 | 33 | } 34 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/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.workflowmodel; 21 | 22 | /** 23 | * Marker interface denoting that the instance is an input port. 24 | * 25 | * @author Tom Oinn 26 | */ 27 | public interface InputPort extends Port { 28 | 29 | } 30 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/MergeOutputPort.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.workflowmodel; 21 | 22 | /** 23 | * An EventForwardingOutputPort that is associated with Merge instances. 24 | * In particular it provides access to the Merge instance it is associated with. 25 | * 26 | * @see Merge 27 | * @see MergePort 28 | * @see EventForwardingOutputPort 29 | * 30 | * @author Stuart Owen 31 | * @author Stian Soiland-Reyes 32 | */ 33 | public interface MergeOutputPort extends EventForwardingOutputPort, MergePort { 34 | } 35 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/MergePort.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.workflowmodel; 21 | 22 | /** 23 | * An input or output {@link Port} for a {@link Merge}. 24 | * 25 | * @see MergeInputPort 26 | * @see MergeOutputPort 27 | * @author Stian Soiland-Reyes 28 | */ 29 | public interface MergePort extends Port { 30 | /** 31 | * @return the Merge instance the port is associated with. 32 | */ 33 | Merge getMerge(); 34 | } 35 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/Port.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.workflowmodel; 21 | 22 | import org.apache.taverna.annotation.Annotated; 23 | 24 | /** 25 | * Named port which receives events from some other entity and handles them 26 | * appropriately. 27 | * 28 | * @author Tom Oinn 29 | */ 30 | public interface Port extends Annotated, WorkflowItem { 31 | String getName(); 32 | 33 | int getDepth(); 34 | } 35 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/ProcessorInputPort.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.workflowmodel; 21 | 22 | /** 23 | * Input port on a Processor, is both a filtering input port and a processor 24 | * port 25 | * 26 | * @author Tom Oinn 27 | */ 28 | public interface ProcessorInputPort extends FilteringInputPort, ProcessorPort { 29 | } 30 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/ProcessorOutputPort.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.workflowmodel; 21 | 22 | /** 23 | * Input port on a Processor, is both an event forwarding output port and a 24 | * processor port 25 | * 26 | * @author Tom Oinn 27 | */ 28 | public interface ProcessorOutputPort extends EventForwardingOutputPort, 29 | ProcessorPort { 30 | } 31 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/ProcessorPort.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.workflowmodel; 21 | 22 | /** 23 | * An {@link ProcessorInputPort} or {@link ProcessorOutputPort} belonging to a 24 | * {@link Processor}. 25 | */ 26 | public interface ProcessorPort extends Port { 27 | /** 28 | * Get the Processor to which this port belongs 29 | */ 30 | public Processor getProcessor(); 31 | } 32 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/RunDeletionListener.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.workflowmodel; 21 | 22 | /** 23 | * A RunDeletionListener is notified when a run is deleted. It is then able to 24 | * take any specific action needed to deal with the deletion of the run, for 25 | * example deleting data that is not held within Taverna. 26 | * 27 | * @author alanrw 28 | */ 29 | public interface RunDeletionListener { 30 | void deleteRun(String runToDelete); 31 | } 32 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/WorkflowStructureException.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.workflowmodel; 21 | 22 | /** 23 | * Thrown predominantly at runtime under circumstances that suggest an 24 | * inconsistancy in the workflow model. This might include attempting to feed 25 | * data into a port that doesn't exist or has an unknown name or similar errors. 26 | * 27 | * @author Tom OInn 28 | */ 29 | public class WorkflowStructureException extends RuntimeException { 30 | private static final long serialVersionUID = 1L; 31 | 32 | public WorkflowStructureException(String string) { 33 | super(string); 34 | } 35 | } 36 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/health/HealthChecker.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.workflowmodel.health; 21 | 22 | import org.apache.taverna.visit.Visitor; 23 | 24 | /** 25 | * An SPI interface whose implementation performs a health check on an arbitrary 26 | * instance. 27 | * 28 | * @author Stuart Owen 29 | * @author David Withers 30 | * 31 | * @param 32 | * the type of the item being checked 33 | */ 34 | public interface HealthChecker extends Visitor { 35 | 36 | } 37 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/health/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | 21 | A package that contains a set of classes to be used in testing a Dataflow prior to invocation.
22 | These can carry our various tests such as a service endpoint being accessible. HealthChecker provides an 23 | SPI extension point to allow 3rd party developers to implement their own Activity checkers. 24 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Defines classes and interfaces for workflow level entities and events. 21 | 22 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/processor/activity/ActivityOutputPort.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.workflowmodel.processor.activity; 21 | 22 | import org.apache.taverna.workflowmodel.OutputPort; 23 | 24 | /** 25 | * The output port of an {@link Activity}. 26 | * 27 | * @author Stian Soiland-Reyes 28 | */ 29 | public interface ActivityOutputPort extends OutputPort, ActivityPort { 30 | 31 | } 32 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/processor/activity/ActivityPort.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.workflowmodel.processor.activity; 21 | 22 | import org.apache.taverna.workflowmodel.Port; 23 | 24 | /** 25 | * The input or output port of an {@link Activity}. 26 | * 27 | * @see ActivityInputPort 28 | * @see ActivityOutputPort 29 | * @author Stian Soiland-Reyes 30 | */ 31 | public interface ActivityPort extends Port { 32 | 33 | } 34 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/processor/activity/LockedNestedDataflow.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.workflowmodel.processor.activity; 21 | 22 | /** 23 | * A LockedNestedDataflow is intended to be unchangeable. It is normally defined 24 | * elsewhere to the workflow. 25 | * 26 | * @author alanrw 27 | */ 28 | public interface LockedNestedDataflow extends NestedDataflow { 29 | 30 | } 31 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/processor/activity/NestedDataflow.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.workflowmodel.processor.activity; 21 | 22 | import org.apache.taverna.workflowmodel.Dataflow; 23 | 24 | /** 25 | * Nested workflows/dataflows can come in many shapes and sizes - in-line, url 26 | * etc. However, they are all {@link Dataflow}s. Implement this in any 27 | * implementation of a Nested dataflow 28 | * 29 | * @author Ian Dunlop 30 | */ 31 | public interface NestedDataflow { 32 | Dataflow getNestedDataflow(); 33 | 34 | void setNestedDataflow(Dataflow dataflow); 35 | } 36 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/processor/activity/NestedDataflowSource.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.workflowmodel.processor.activity; 21 | 22 | import org.apache.taverna.workflowmodel.Dataflow; 23 | 24 | /** 25 | * @author alanrw 26 | */ 27 | public interface NestedDataflowSource { 28 | T getNestedDataflow(); 29 | 30 | Dataflow getParentDataflow(); 31 | 32 | @Override 33 | String toString(); 34 | } 35 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/processor/activity/SupersededActivity.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.workflowmodel.processor.activity; 21 | 22 | /** 23 | * 24 | * A superseded activity is one which has been replaced be another activity type 25 | * of similar functionality but different configuration and name 26 | * 27 | * @author alanrw 28 | */ 29 | public interface SupersededActivity extends 30 | Activity { 31 | Activity getReplacementActivity() throws ActivityConfigurationException; 32 | } 33 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/processor/activity/config/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | A set of helper classes to aid in defining how Activities are configured. 21 | An Activity class is associated with a ConfigurationType, which is an arbitrary Java object defining 22 | how the Activity should be configured.
23 | This package provides classes and interfaces that help in creating these ConfigurationTypes with details that are common 24 | across different Activities, but there use is in no way enforced. 25 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/processor/activity/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Provides definitions for a single Activity to be contained within a 21 | Processor. Activity was previously called 'Service' but this was 22 | somewhat misleading as there wasn't always a service backing it. The 23 | Activity may be abstract, it may be synchronous or asynchronous in which 24 | case it uses a callback mechanism. It doesn't carry around annotation 25 | itself instead using an activity annotation container to handle this 26 | (this avoids third parties having to manage annotation containment 27 | themselves). 28 | 29 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/processor/config/ConfigurationBean.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.workflowmodel.processor.config; 21 | 22 | import java.lang.annotation.ElementType; 23 | import java.lang.annotation.Retention; 24 | import java.lang.annotation.RetentionPolicy; 25 | import java.lang.annotation.Target; 26 | 27 | @Retention(RetentionPolicy.RUNTIME) 28 | @Target(ElementType.TYPE) 29 | public @interface ConfigurationBean { 30 | String uri(); 31 | } 32 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/processor/dispatch/NotifiableLayer.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.workflowmodel.processor.dispatch; 21 | 22 | import org.apache.taverna.invocation.Completion; 23 | import org.apache.taverna.workflowmodel.processor.activity.Job; 24 | 25 | /** 26 | * If a layer requires notification of the arrival of new items to the event 27 | * queues within the dispatcher it should implement this interface. 28 | * 29 | * @author Tom Oinn 30 | */ 31 | public interface NotifiableLayer { 32 | /** 33 | * Called when a new {@link Job} or {@link Completion} is added to a queue 34 | * within the dispatch stack 35 | * 36 | * @param owningProcess 37 | */ 38 | void eventAdded(String owningProcess); 39 | } 40 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/processor/dispatch/description/ReactionTo.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.workflowmodel.processor.dispatch.description; 21 | 22 | import java.lang.annotation.Documented; 23 | import java.lang.annotation.ElementType; 24 | import java.lang.annotation.Retention; 25 | import java.lang.annotation.RetentionPolicy; 26 | import java.lang.annotation.Target; 27 | 28 | /** 29 | * Describes the type of message to which the various DispatchLayerFooReaction 30 | * classes are referring 31 | * 32 | * @author Tom Oinn 33 | */ 34 | @Documented 35 | @Target(ElementType.ANNOTATION_TYPE) 36 | @Retention(RetentionPolicy.RUNTIME) 37 | public @interface ReactionTo { 38 | public DispatchMessageType messageType(); 39 | } 40 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/processor/dispatch/description/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Annotations and enumerations used to describe dispatch layers, specifically the types of messages they can consume and their reactions to those messages. 21 | 22 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/processor/iteration/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Object model and enactment logic for the iteration strategy component of 21 | a Processor 22 | 23 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/serialization/DeserializationException.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.workflowmodel.serialization; 21 | 22 | public class DeserializationException extends Exception { 23 | public DeserializationException(String msg) { 24 | super(msg); 25 | } 26 | 27 | public DeserializationException(String msg, Exception cause) { 28 | super(msg, cause); 29 | } 30 | 31 | private static final long serialVersionUID = -5905705659863088259L; 32 | } 33 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/serialization/SerializationException.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.workflowmodel.serialization; 21 | 22 | public class SerializationException extends Exception { 23 | public SerializationException(String msg, Exception cause) { 24 | super(msg, cause); 25 | } 26 | 27 | public SerializationException(String msg) { 28 | super(msg); 29 | } 30 | 31 | private static final long serialVersionUID = -218787623524401819L; 32 | } 33 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/utils/NamedWorkflowEntityComparator.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.workflowmodel.utils; 21 | 22 | import java.util.Comparator; 23 | 24 | import org.apache.taverna.workflowmodel.NamedWorkflowEntity; 25 | 26 | /** 27 | * Compare two named workflow entities (such as a Processor) by their local 28 | * name. 29 | * 30 | * @author Stian Soiland-Reyes 31 | */ 32 | public class NamedWorkflowEntityComparator implements 33 | Comparator { 34 | @Override 35 | public int compare(NamedWorkflowEntity o1, NamedWorkflowEntity o2) { 36 | return o1.getLocalName().compareToIgnoreCase(o2.getLocalName()); 37 | } 38 | } -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/java/org/apache/taverna/workflowmodel/utils/PortComparator.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.workflowmodel.utils; 21 | 22 | import java.util.Comparator; 23 | 24 | import org.apache.taverna.workflowmodel.Port; 25 | 26 | /** 27 | * Compare two workflow ports by their name. 28 | * 29 | * @author Stian Soiland-Reyes 30 | */ 31 | public class PortComparator implements Comparator { 32 | @Override 33 | public int compare(Port o1, Port o2) { 34 | return o1.getName().compareToIgnoreCase(o2.getName()); 35 | } 36 | } 37 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/resources/META-INF/services/org.apache.taverna.visit.VisitKind: -------------------------------------------------------------------------------- 1 | org.apache.taverna.workflowmodel.health.HealthCheck 2 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/main/resources/META-INF/services/org.apache.taverna.workflowmodel.health.HealthChecker: -------------------------------------------------------------------------------- 1 | org.apache.taverna.workflowmodel.health.DisabledActivityHealthChecker 2 | org.apache.taverna.workflowmodel.health.UnrecognizedActivityHealthChecker 3 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/test/java/org/apache/taverna/workflowmodel/health/DummyVisitKind.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.workflowmodel.health; 21 | 22 | import org.apache.taverna.visit.VisitKind; 23 | import org.apache.taverna.visit.Visitor; 24 | 25 | /** 26 | * @author alanrw 27 | * 28 | */ 29 | public class DummyVisitKind extends VisitKind { 30 | @Override 31 | public Class> getVisitorClass() { 32 | return null; 33 | } 34 | 35 | private static class Singleton { 36 | private static DummyVisitKind instance = new DummyVisitKind(); 37 | } 38 | 39 | public static DummyVisitKind getInstance() { 40 | return Singleton.instance; 41 | } 42 | } 43 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/test/java/org/apache/taverna/workflowmodel/health/FloatHealthChecker.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.workflowmodel.health; 21 | 22 | import java.util.List; 23 | 24 | import org.apache.taverna.visit.VisitReport; 25 | 26 | public class FloatHealthChecker implements HealthChecker { 27 | 28 | @Override 29 | public boolean canVisit(Object subject) { 30 | return subject!=null && subject instanceof Float; 31 | } 32 | 33 | @Override 34 | public VisitReport visit(Float o, List ancestry) { 35 | return null; 36 | } 37 | 38 | @Override 39 | public boolean isTimeConsuming() { 40 | return false; 41 | } 42 | 43 | } 44 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/test/java/org/apache/taverna/workflowmodel/health/FloatHealthChecker2.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.workflowmodel.health; 21 | 22 | import java.util.List; 23 | 24 | import org.apache.taverna.visit.VisitReport; 25 | 26 | public class FloatHealthChecker2 implements HealthChecker { 27 | 28 | @Override 29 | public boolean canVisit(Object subject) { 30 | return subject!=null && subject instanceof Float; 31 | } 32 | 33 | @Override 34 | public VisitReport visit(Float o, List ancestry) { 35 | return null; 36 | } 37 | 38 | @Override 39 | public boolean isTimeConsuming() { 40 | return false; 41 | } 42 | 43 | } 44 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/test/java/org/apache/taverna/workflowmodel/health/StringHealthChecker.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.workflowmodel.health; 21 | 22 | import java.util.List; 23 | 24 | import org.apache.taverna.visit.VisitReport; 25 | 26 | public class StringHealthChecker implements HealthChecker { 27 | 28 | @Override 29 | public boolean canVisit(Object subject) { 30 | return subject!=null && subject instanceof String; 31 | } 32 | 33 | @Override 34 | public VisitReport visit(String o, List ancestry) { 35 | return null; 36 | } 37 | 38 | @Override 39 | public boolean isTimeConsuming() { 40 | return false; 41 | } 42 | 43 | } 44 | -------------------------------------------------------------------------------- /taverna-workflowmodel-api/src/test/resources/META-INF/services/org.apache.taverna.workflowmodel.health.HealthChecker: -------------------------------------------------------------------------------- 1 | org.apache.taverna.workflowmodel.health.StringHealthChecker 2 | org.apache.taverna.workflowmodel.health.FloatHealthChecker 3 | org.apache.taverna.workflowmodel.health.FloatHealthChecker2 -------------------------------------------------------------------------------- /taverna-workflowmodel-extensions/.gitignore: -------------------------------------------------------------------------------- 1 | /target/ 2 | -------------------------------------------------------------------------------- /taverna-workflowmodel-extensions/src/main/java/org/apache/taverna/workflowmodel/processor/dispatch/layers/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Contains implementations of DispatchLayer defined by the core Taverna 2 21 | specification. 22 | 23 | -------------------------------------------------------------------------------- /taverna-workflowmodel-extensions/src/main/resources/META-INF/spring/workflowmodel-core-extensions-context.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 24 | 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/main/java/org/apache/taverna/annotation/impl/DisputeEventDetails.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.annotation.impl; 21 | 22 | import org.apache.taverna.annotation.CurationEventBeanSPI; 23 | 24 | public class DisputeEventDetails implements CurationEventBeanSPI { 25 | public DisputeEventDetails() { 26 | } 27 | } 28 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/main/java/org/apache/taverna/annotation/impl/PersonImpl.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.annotation.impl; 21 | 22 | import org.apache.taverna.annotation.Person; 23 | 24 | public class PersonImpl implements Person { 25 | @SuppressWarnings("unused") 26 | private String name; 27 | 28 | public PersonImpl(String name) { 29 | this.name = name; 30 | } 31 | } 32 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/main/java/org/apache/taverna/annotation/impl/URISource.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.annotation.impl; 21 | 22 | import java.net.URI; 23 | 24 | import org.apache.taverna.annotation.AnnotationSourceSPI; 25 | 26 | public class URISource implements AnnotationSourceSPI{ 27 | private URI uri; 28 | 29 | public URISource() { 30 | } 31 | 32 | public URISource(URI uri) { 33 | this.uri = uri; 34 | } 35 | 36 | public void setUri(URI uri) { 37 | // if (uri != null) 38 | // throw new RuntimeException("URI has already been set"); 39 | this.uri = uri; 40 | } 41 | 42 | public URI getUri() { 43 | return uri; 44 | } 45 | } 46 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/main/java/org/apache/taverna/workflowmodel/impl/MergeOutputPortImpl.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.workflowmodel.impl; 21 | 22 | import org.apache.taverna.workflowmodel.Merge; 23 | import org.apache.taverna.workflowmodel.MergeOutputPort; 24 | 25 | class MergeOutputPortImpl extends BasicEventForwardingOutputPort 26 | implements MergeOutputPort { 27 | private Merge merge; 28 | 29 | public MergeOutputPortImpl(Merge merge, String portName, int portDepth, 30 | int granularDepth) { 31 | super(portName, portDepth, granularDepth); 32 | this.merge = merge; 33 | } 34 | 35 | @Override 36 | public Merge getMerge() { 37 | return merge; 38 | } 39 | } 40 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/main/java/org/apache/taverna/workflowmodel/impl/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Implementation package for workflow entities 21 | 22 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/main/java/org/apache/taverna/workflowmodel/processor/activity/impl/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Contains specific implementations of the Activity Ports, together with an implementation of ActivityPortBuilder which is responsible for building them. 21 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/main/java/org/apache/taverna/workflowmodel/processor/dispatch/impl/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Implementation package for the dispatch stack interfaces. Contains 21 | DispatchStack implementation and edit objects to modify it, actual 22 | dispatch layer implementations are held elsewhere (in third party 23 | plugins and in the 24 | net.sf.taverna.t2.workflowmodel.processor.dispatch.layers package for 25 | internal layers) 26 | 27 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/main/java/org/apache/taverna/workflowmodel/processor/iteration/impl/package.html: -------------------------------------------------------------------------------- 1 | 19 | 20 | Implementation logic for the iteration system. 21 | 22 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/main/resources/META-INF/services/org.apache.taverna.annotation.AnnotationBeanSPI: -------------------------------------------------------------------------------- 1 | org.apache.taverna.annotation.impl.annotationbeans.Author 2 | org.apache.taverna.annotation.impl.annotationbeans.DescriptiveTitle 3 | org.apache.taverna.annotation.impl.annotationbeans.FreeTextDescription 4 | org.apache.taverna.annotation.impl.annotationbeans.HostInstitution 5 | #org.apache.taverna.annotation.impl.annotationbeans.MimeType 6 | org.apache.taverna.annotation.impl.annotationbeans.DocumentationUrl 7 | org.apache.taverna.annotation.impl.annotationbeans.Optional 8 | org.apache.taverna.annotation.impl.annotationbeans.ExampleValue 9 | org.apache.taverna.annotation.impl.annotationbeans.SemanticAnnotation 10 | org.apache.taverna.annotation.impl.annotationbeans.IdentificationAssertion 11 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/main/resources/META-INF/services/org.apache.taverna.annotation.AnnotationSourceSPI: -------------------------------------------------------------------------------- 1 | org.apache.taverna.annotation.impl.URISource -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/main/resources/META-INF/services/org.apache.taverna.annotation.CurationEventBeanSPI: -------------------------------------------------------------------------------- 1 | org.apache.taverna.annotation.impl.DisputeEventDetails -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/main/resources/META-INF/services/org.apache.taverna.workflowmodel.Edits: -------------------------------------------------------------------------------- 1 | org.apache.taverna.workflowmodel.impl.EditsImpl -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/main/resources/META-INF/services/org.apache.taverna.workflowmodel.health.HealthChecker: -------------------------------------------------------------------------------- 1 | org.apache.taverna.workflowmodel.processor.dispatch.layers.health.LoopHealthChecker 2 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/main/resources/META-INF/spring/workflowmodel-impl-context.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/test/java/org/apache/taverna/workflowmodel/impl/DummyActivity.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.workflowmodel.impl; 21 | 22 | import org.apache.taverna.workflowmodel.processor.activity.AbstractActivity; 23 | import org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException; 24 | 25 | public class DummyActivity extends AbstractActivity { 26 | 27 | private Integer bean=null; 28 | 29 | @Override 30 | public void configure(Integer conf) throws ActivityConfigurationException { 31 | bean=conf; 32 | } 33 | 34 | @Override 35 | public Integer getConfiguration() { 36 | return bean; 37 | } 38 | 39 | } -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/test/java/org/apache/taverna/workflowmodel/impl/DummyDataflowInputPort.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.workflowmodel.impl; 21 | 22 | import org.apache.taverna.invocation.WorkflowDataToken; 23 | import org.apache.taverna.workflowmodel.Dataflow; 24 | 25 | public class DummyDataflowInputPort extends DataflowInputPortImpl { 26 | 27 | public String tokenOwningProcess; 28 | 29 | public DummyDataflowInputPort(String name, int depth, int granularDepth, 30 | Dataflow df) { 31 | super(name, depth, granularDepth, df); 32 | } 33 | 34 | @Override 35 | public void receiveEvent(WorkflowDataToken t) { 36 | tokenOwningProcess=t.getOwningProcess(); 37 | } 38 | } 39 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/test/java/org/apache/taverna/workflowmodel/impl/DummyDataflowOutputPort.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.workflowmodel.impl; 21 | 22 | import java.util.List; 23 | 24 | import org.apache.taverna.facade.ResultListener; 25 | import org.apache.taverna.workflowmodel.Dataflow; 26 | 27 | public class DummyDataflowOutputPort extends DataflowOutputPortImpl { 28 | 29 | public DummyDataflowOutputPort(String portName, Dataflow dataflow) { 30 | super(portName, dataflow); 31 | } 32 | 33 | public List getResultListeners() { 34 | return resultListeners; 35 | } 36 | } 37 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/test/java/org/apache/taverna/workflowmodel/impl/EventKeeper.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.workflowmodel.impl; 21 | 22 | import java.util.ArrayList; 23 | import java.util.List; 24 | 25 | import org.apache.taverna.invocation.WorkflowDataToken; 26 | import org.apache.taverna.workflowmodel.processor.DiagnosticEventHandler; 27 | 28 | public final class EventKeeper extends DiagnosticEventHandler { 29 | public List events = new ArrayList(); 30 | 31 | @Override 32 | public synchronized void receiveEvent(WorkflowDataToken token) { 33 | super.receiveEvent(token); 34 | events.add(token); 35 | } 36 | } -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/test/java/org/apache/taverna/workflowmodel/impl/UpdateDataflowInternalIdentifierEditTest.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.workflowmodel.impl; 21 | 22 | import static org.junit.Assert.assertEquals; 23 | import org.apache.taverna.workflowmodel.Dataflow; 24 | import org.apache.taverna.workflowmodel.Edits; 25 | 26 | import org.junit.Test; 27 | 28 | 29 | public class UpdateDataflowInternalIdentifierEditTest { 30 | private static Edits edits = new EditsImpl(); 31 | 32 | @Test 33 | public void testDoEdit() throws Exception { 34 | Dataflow df = edits.createDataflow(); 35 | edits.getUpdateDataflowInternalIdentifierEdit(df, "123").doEdit(); 36 | assertEquals("The internal id should be 123","123",df.getIdentifier()); 37 | } 38 | } 39 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/test/java/org/apache/taverna/workflowmodel/processor/EchoConfig.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.workflowmodel.processor; 21 | 22 | /** 23 | * Trivial property class to configure the echo activity. As the echo activity 24 | * actually has no configuration whatsoever I've put some dummy properties 25 | * in here to test the serialization framework. 26 | * 27 | * @author Tom 28 | * 29 | */ 30 | public class EchoConfig { 31 | 32 | private String foo = "wibble!"; 33 | 34 | public String getFoo() { 35 | return this.foo; 36 | } 37 | 38 | public void setFoo(String newFoo) { 39 | this.foo = newFoo; 40 | } 41 | 42 | public EchoConfig() { 43 | // 44 | } 45 | 46 | public EchoConfig(String newFoo) { 47 | super(); 48 | this.foo = newFoo; 49 | } 50 | 51 | } 52 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/test/resources/log4j.properties: -------------------------------------------------------------------------------- 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 | 16 | log4j.rootLogger=WARN, CONSOLE 17 | log4j.logger.net.sf.taverna.t2=DEBUG 18 | #log4j.logger.net.sf.taverna.t2.ui=DEBUG 19 | 20 | #log4j.logger.org.apache.commons.httpclient=ERROR 21 | 22 | # Default output to console 23 | log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender 24 | log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout 25 | log4j.appender.CONSOLE.layout.ConversionPattern=%-5p %d{ISO8601} (%c:%L) - %m%n 26 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/test/resources/serialized-fragments/2_port_cross_product.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/test/resources/serialized-fragments/activity.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | 22 | org.apache.taverna.workflowmodel.serialization.DummyActivity 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 5 32 | 33 | 34 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/test/resources/serialized-fragments/dispatchLayer.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | 22 | org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize 23 | 24 | 25 | 27 | 7 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/test/resources/serialized-fragments/empty_dataflow_with_ports.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | george 22 | 23 | 24 | input1 25 | 0 26 | 0 27 | 28 | 29 | input2 30 | 1 31 | 1 32 | 33 | 34 | 35 | 36 | output 37 | 38 | 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /taverna-workflowmodel-impl/src/test/resources/serialized-fragments/processor.xml: -------------------------------------------------------------------------------- 1 | 2 | 20 | 21 | george 22 | 23 | 24 | input 25 | 0 26 | 27 | 28 | 29 | 30 | output 31 | 1 32 | 0 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | --------------------------------------------------------------------------------