temporarily empty repository .. as Software Grant is not yet formally on file
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/commit/3ecb1291 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/tree/3ecb1291 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/diff/3ecb1291 Branch: refs/heads/master Commit: 3ecb12916215fa3efdcd9380f55f700d0eb67e95 Parents: fea213a Author: Stian Soiland-Reyes <[email protected]> Authored: Tue Feb 17 20:42:45 2015 +0000 Committer: Stian Soiland-Reyes <[email protected]> Committed: Tue Feb 17 20:42:45 2015 +0000 ---------------------------------------------------------------------- .gitignore | 24 - .travis.yml | 1 - README.md | 3 - pom.xml | 87 - taverna-activity-archetype/pom.xml | 30 - .../META-INF/maven/archetype-metadata.xml | 58 - .../__rootArtifactId__-activity-ui/pom.xml | 47 - .../__classPrefix__ConfigurationPanel.java | 87 - .../config/__classPrefix__ConfigureAction.java | 49 - .../__classPrefix__ConfigureMenuAction.java | 67 - .../__classPrefix__ServiceDesc.java | 106 - .../__classPrefix__ServiceIcon.java | 40 - .../__classPrefix__ServiceProvider.java | 75 - ...classPrefix__ActivityContextViewFactory.java | 62 - .../ui/view/__classPrefix__ContextualView.java | 91 - .../resources/META-INF/spring/context-osgi.xml | 26 - .../main/resources/META-INF/spring/context.xml | 31 - .../src/main/resources/exampleIcon.png | Bin 3654 -> 0 bytes .../__rootArtifactId__-activity/pom.xml | 51 - .../src/main/java/__classPrefix__Activity.java | 135 - .../java/__classPrefix__ActivityFactory.java | 97 - .../__classPrefix__ActivityHealthChecker.java | 66 - .../resources/META-INF/spring/context-osgi.xml | 17 - .../main/resources/META-INF/spring/context.xml | 12 - .../src/main/resources/schema.json | 25 - .../__classPrefix__ActivityFactoryTest.java | 103 - .../test/java/__classPrefix__ActivityTest.java | 76 - .../__rootArtifactId__-plugin/pom.xml | 26 - .../main/resources/archetype-resources/pom.xml | 192 -- taverna-activity-test-utils/pom.xml | 33 - .../activities/testutils/ActivityInvoker.java | 250 -- .../t2/activities/testutils/DummyCallback.java | 106 - .../activities/testutils/LocationConstants.java | 31 - .../context-parts/componentservices.xml | 101 - .../resources/context-parts/dao_hibernate.xml | 102 - .../dao_hibernate_transactional.xml | 120 - .../resources/context-parts/dao_inmemory.xml | 30 - .../context-parts/hibernateprops_derby.xml | 63 - .../resources/context-parts/raven_local.xml | 48 - .../context-parts/referenceservice.xml | 58 - .../resources/inMemoryActivityTestsContext.xml | 29 - taverna-capability-api/pom.xml | 28 - .../api/ActivityConfigurationException.java | 46 - .../api/ActivityNotFoundException.java | 46 - .../capability/api/ActivityService.java | 126 - .../capability/api/ConfigurationException.java | 48 - .../DispatchLayerConfigurationException.java | 46 - .../api/DispatchLayerNotFoundException.java | 46 - .../capability/api/DispatchLayerService.java | 90 - taverna-capability-impl/pom.xml | 59 - .../activity/impl/ActivityServiceImpl.java | 140 - .../dispatch/impl/DispatchLayerServiceImpl.java | 112 - .../spring/taverna-capability-context-osgi.xml | 17 - .../spring/taverna-capability-context.xml | 14 - taverna-credential-manager-impl/pom.xml | 89 - .../impl/CredentialManagerAuthenticator.java | 112 - .../impl/CredentialManagerImpl.java | 2657 ------------------ .../impl/DefaultMasterPasswordProvider.java | 51 - .../impl/DistinguishedNameParserImpl.java | 177 -- .../impl/ParsedDistinguishedNameImpl.java | 265 -- .../credential-manager-impl-context-osgi.xml | 31 - .../spring/credential-manager-impl-context.xml | 25 - .../AddTrustExternalCARoot.crt | 25 - .../trusted-certificates/TERENASSLCA.crt | 27 - .../UTNAddTrustServer_CA.crt | 25 - .../heater.cs.man.ac.uk-not-needed.pem | 26 - .../www.biocatalogue.org-revoked.pem | 26 - .../www.biodiversitycatalogue.org-revoked.pem | 29 - .../impl/CredentialManagerImplIT.java | 339 --- .../impl/CredentialManagerImplTest.java | 872 ------ .../DummyJavaTruststorePasswordProvider.java | 39 - .../impl/DummyMasterPasswordProvider.java | 50 - ...DummyServiceUsernameAndPasswordProvider.java | 50 - .../impl/HTTPAuthenticatorIT.java | 535 ---- ...catorServiceUsernameAndPasswordProvider.java | 73 - .../HTTPSConnectionAndTrustConfirmationIT.java | 336 --- .../impl/PossibleURILookupsTest.java | 254 -- .../TrustAlwaysTrustConfirmationProvider.java | 36 - .../TrustNeverTrustConfimationProvider.java | 36 - .../src/test/resources/html/test.html | 5 - .../security/google-trusted-certificate.pem | 29 - .../src/test/resources/security/t2keystore.ubr | Bin 1888 -> 0 bytes .../test/resources/security/t2truststore.ubr | Bin 199408 -> 0 bytes .../security/test-private-key-cert.p12 | Bin 1902 -> 0 bytes .../security/tomcat_heater_certificate.pem | 20 - taverna-credential-manager/pom.xml | 58 - .../security/credentialmanager/CMException.java | 61 - .../CMNotInitialisedException.java | 45 - .../credentialmanager/CredentialManager.java | 415 --- .../DistinguishedNameParser.java | 61 - .../JavaTruststorePasswordProvider.java | 73 - .../credentialmanager/KeystoreChangedEvent.java | 39 - .../MasterPasswordProvider.java | 112 - .../ParsedDistinguishedName.java | 74 - .../ServiceUsernameAndPasswordProvider.java | 64 - .../TrustConfirmationProvider.java | 56 - .../credentialmanager/UsernamePassword.java | 90 - ...rity.credentialmanager.CredentialProviderSPI | 1 - .../src/test/resources/html/test.html | 5 - .../src/test/resources/realm.properties | 1 - taverna-database-configuration-api/.project | 24 - taverna-database-configuration-api/pom.xml | 18 - .../database/DatabaseConfiguration.java | 124 - .../configuration/database/DatabaseManager.java | 45 - taverna-database-configuration-impl/.project | 24 - taverna-database-configuration-impl/pom.xml | 78 - .../impl/DatabaseConfigurationImpl.java | 252 -- .../database/impl/DatabaseManagerImpl.java | 155 - .../META-INF/spring/database-context-osgi.xml | 18 - .../META-INF/spring/database-context.xml | 20 - taverna-dataflow-activity/pom.xml | 48 - .../activities/dataflow/DataflowActivity.java | 168 -- .../dataflow/DataflowActivityFactory.java | 81 - .../dataflow/DataflowActivityHealthChecker.java | 42 - ...averna.t2.workflowmodel.health.HealthChecker | 1 - .../spring/dataflow-activity-context-osgi.xml | 15 - .../spring/dataflow-activity-context.xml | 12 - .../src/main/resources/schema.json | 19 - .../dataflow/DataflowActivityFactoryTest.java | 65 - .../dataflow/DataflowActivityTest.java | 98 - taverna-execution-api/pom.xml | 45 - .../execution/api/AbstractExecution.java | 139 - .../api/AbstractExecutionEnvironment.java | 79 - .../execution/api/AbstractExecutionService.java | 139 - .../platform/execution/api/Execution.java | 104 - .../execution/api/ExecutionEnvironment.java | 129 - .../api/ExecutionEnvironmentService.java | 52 - .../execution/api/ExecutionService.java | 149 - .../api/InvalidExecutionIdException.java | 48 - .../execution/api/InvalidWorkflowException.java | 48 - .../execution/api/WorkflowCompiler.java | 36 - .../execution/api/AbstractExecutionTest.java | 128 - taverna-execution-hadoop/pom.xml | 33 - .../main/java/org/pingel/util/CrossProduct.java | 159 -- .../impl/hadoop/CrossProductInputFormat.java | 108 - .../impl/hadoop/CrossProductInputSplit.java | 88 - .../impl/hadoop/CrossProductRecordReader.java | 112 - .../execution/impl/hadoop/CrossProductTest.java | 116 - .../execution/impl/hadoop/DotProductTest.java | 106 - .../impl/hadoop/TavernaInputFormat.java | 52 - .../impl/hadoop/TavernaInputSplit.java | 69 - .../execution/impl/hadoop/TavernaMapper.java | 75 - .../impl/hadoop/TavernaRecordReader.java | 106 - .../execution/impl/hadoop/TavernaReducer.java | 24 - .../platform/execution/impl/hadoop/Test.java | 69 - .../impl/hadoop/TextArrayWritable.java | 31 - taverna-execution-impl/pom.xml | 42 - .../impl/ExecutionEnvironmentServiceImpl.java | 354 --- .../META-INF/spring/execution-context-osgi.xml | 13 - .../META-INF/spring/execution-context.xml | 10 - taverna-execution-local/pom.xml | 90 - .../execution/impl/local/LocalExecution.java | 243 -- .../impl/local/LocalExecutionEnvironment.java | 86 - .../impl/local/LocalExecutionMonitor.java | 548 ---- .../impl/local/LocalExecutionService.java | 149 - .../impl/local/LocalProcessorReport.java | 141 - .../execution/impl/local/StaticProperty.java | 66 - .../impl/local/T2ReferenceConverter.java | 41 - .../impl/local/WorkflowToDataflowMapper.java | 527 ---- .../spring/execution-local-context-osgi.xml | 23 - .../META-INF/spring/execution-local-context.xml | 13 - .../impl/local/LocalExecutionTest.java | 166 -- .../src/test/resources/log4j.properties | 1 - .../src/test/resources/t2flow/beanshell.t2flow | 137 - .../src/test/resources/t2flow/in-out.t2flow | 23 - taverna-execution-remote/pom.xml | 48 - .../execution/impl/remote/RemoteExecution.java | 96 - .../impl/remote/RemoteExecutionService.java | 60 - .../spring/execution-remote-context-osgi.xml | 12 - .../spring/execution-remote-context.xml | 8 - taverna-integration-tests/pom.xml | 92 - .../uk/org/taverna/platform/ActivityIT.java | 84 - .../uk/org/taverna/platform/PlatformIT.java | 151 - .../java/uk/org/taverna/platform/RunIT.java | 954 ------- .../t2flow/FetchTodaysXkcdComic.t2flow | 343 --- .../src/test/resources/t2flow/GBSeqTest.t2flow | 518 ---- .../test/resources/t2flow/apiconsumer.t2flow | 178 -- .../src/test/resources/t2flow/beanshell.t2flow | 137 - .../src/test/resources/t2flow/biomart.t2flow | 30 - .../src/test/resources/t2flow/dataflow.t2flow | 217 -- .../src/test/resources/t2flow/in-out.t2flow | 12 - .../src/test/resources/t2flow/input.txt | 1 - .../src/test/resources/t2flow/iteration.t2flow | 474 ---- .../test/resources/t2flow/localworker.t2flow | 67 - .../src/test/resources/t2flow/rest.t2flow | 154 - .../secure-basic-authentication-https.t2flow | 74 - .../t2flow/secure-basic-authentication.t2flow | 74 - .../secure-digest-authentication-https.t2flow | 107 - .../t2flow/secure-digest-authentication.t2flow | 129 - .../resources/t2flow/secure-ws-https.t2flow | 180 -- .../src/test/resources/t2flow/secure-ws.t2flow | 180 -- .../src/test/resources/t2flow/soaplab.t2flow | 95 - .../resources/t2flow/spreadsheetimport.t2flow | 646 ----- .../test/resources/t2flow/stringconstant.t2flow | 32 - .../src/test/resources/t2flow/tool.t2flow | 158 -- .../test/resources/t2flow/wsdl-secure.t2flow | 131 - .../src/test/resources/t2flow/wsdl.t2flow | 22 - .../test/resources/t2flow/xmlSplitter.t2flow | 339 --- .../src/test/resources/t2flow/xpath.t2flow | 127 - taverna-observer/pom.xml | 26 - .../taverna/t2/lang/observer/MultiCaster.java | 93 - .../sf/taverna/t2/lang/observer/Observable.java | 56 - .../sf/taverna/t2/lang/observer/Observer.java | 44 - .../t2/lang/observer/SwingAwareObserver.java | 51 - .../taverna/t2/lang/observer/package-info.java | 73 - .../taverna/t2/lang/observer/ObserverTest.java | 133 - taverna-platform-integration-tests/pom.xml | 635 ----- .../uk/org/taverna/platform/ActivityIT.java | 72 - .../org/taverna/platform/CommandLineToolIT.java | 91 - .../uk/org/taverna/platform/ExecutionIT.java | 134 - .../org/taverna/platform/LocalExecutionIT.java | 120 - .../org/taverna/platform/OSGIFrameworkIT.java | 93 - .../uk/org/taverna/platform/PlatformIT.java | 378 --- .../java/uk/org/taverna/platform/RunIT.java | 1005 ------- .../uk/org/taverna/platform/RunParallelIT.java | 95 - .../uk/org/taverna/platform/RunWorkflowsIT.java | 135 - .../src/test/resources/log4j.properties | 11 - .../security/tomcat_heater_certificate.pem | 20 - .../t2flow/FetchTodaysXkcdComic.t2flow | 343 --- .../src/test/resources/t2flow/GBSeqTest.t2flow | 518 ---- .../test/resources/t2flow/apiconsumer.t2flow | 178 -- .../src/test/resources/t2flow/beanshell.t2flow | 137 - .../src/test/resources/t2flow/biomart.t2flow | 30 - .../src/test/resources/t2flow/dataflow.t2flow | 217 -- .../src/test/resources/t2flow/in-out.t2flow | 23 - .../src/test/resources/t2flow/input.txt | 1 - .../src/test/resources/t2flow/iteration.t2flow | 474 ---- .../test/resources/t2flow/localworker.t2flow | 67 - .../src/test/resources/t2flow/rest.t2flow | 154 - .../secure-basic-authentication-https.t2flow | 74 - .../t2flow/secure-basic-authentication.t2flow | 74 - .../secure-digest-authentication-https.t2flow | 107 - .../t2flow/secure-digest-authentication.t2flow | 129 - .../resources/t2flow/secure-ws-https.t2flow | 180 -- .../src/test/resources/t2flow/secure-ws.t2flow | 180 -- .../src/test/resources/t2flow/soaplab.t2flow | 84 - .../resources/t2flow/spreadsheetimport.t2flow | 646 ----- .../test/resources/t2flow/stringconstant.t2flow | 32 - .../src/test/resources/t2flow/tool.t2flow | 158 -- .../test/resources/t2flow/wsdl-secure.t2flow | 131 - .../src/test/resources/t2flow/wsdl.t2flow | 22 - .../test/resources/t2flow/xmlSplitter.t2flow | 339 --- .../src/test/resources/t2flow/xpath.t2flow | 127 - taverna-prov-owl-bindings/.gitignore | 5 - taverna-prov-owl-bindings/pom.xml | 35 - .../purl/wf4ever/provtaverna/owl/ProvModel.java | 402 --- .../provtaverna/owl/TavernaProvModel.java | 112 - .../wf4ever/provtaverna/owl/WfprovModel.java | 202 -- .../src/main/resources/location-mapping.n3 | 36 - .../org/purl/wf4ever/provtaverna/owl/.gitignore | 1 - .../wf4ever/provtaverna/owl/annotation-core.owl | 399 --- .../purl/wf4ever/provtaverna/owl/annotation.owl | 89 - .../purl/wf4ever/provtaverna/owl/content.owl | 161 -- .../org/purl/wf4ever/provtaverna/owl/dcam.owl | 28 - .../purl/wf4ever/provtaverna/owl/dcterms_od.owl | 584 ---- .../org/purl/wf4ever/provtaverna/owl/foaf.rdf | 606 ---- .../purl/wf4ever/provtaverna/owl/ore-owl.owl | 145 - .../org/purl/wf4ever/provtaverna/owl/pav.rdf | 552 ---- .../purl/wf4ever/provtaverna/owl/prov-aq.rdf | 342 --- .../wf4ever/provtaverna/owl/prov-dictionary.ttl | 246 -- .../org/purl/wf4ever/provtaverna/owl/prov-o.rdf | 1788 ------------ .../org/purl/wf4ever/provtaverna/owl/ro.owl | 203 -- .../org/purl/wf4ever/provtaverna/owl/roevo.owl | 481 ---- .../org/purl/wf4ever/provtaverna/owl/scufl2.rdf | 1567 ----------- .../wf4ever/provtaverna/owl/skos-owl1-dl.rdf | 465 --- .../wf4ever/provtaverna/owl/taverna-prov.owl | 333 --- .../wf4ever/provtaverna/owl/taverna-prov.ttl | 277 -- .../org/purl/wf4ever/provtaverna/owl/terms.rdf | 116 - .../purl/wf4ever/provtaverna/owl/wf4ever.owl | 130 - .../org/purl/wf4ever/provtaverna/owl/wfdesc.owl | 192 -- .../org/purl/wf4ever/provtaverna/owl/wfprov.owl | 212 -- .../wf4ever/provtaverna/owl/TestProvModel.java | 38 - .../provtaverna/owl/TestTavernaProvModel.java | 55 - .../provtaverna/owl/TestWfprovModel.java | 24 - .../src/test/resources/handmade.ttl | 158 -- taverna-prov/README.md | 564 ---- taverna-prov/example/helloanyone.bundle.zip | Bin 12938 -> 0 bytes .../a2f03983-8836-4c36-bfb2-d713d9a1928f.ttl | 5 - .../.ro/annotations/workflow.wfdesc.ttl | 66 - .../helloanyone.bundle/.ro/manifest.json | 68 - .../example/helloanyone.bundle/inputs/name.txt | 1 - .../3a/3a82e39d-a537-40cf-91a0-2c89d4a2e62b.txt | 1 - .../example/helloanyone.bundle/mimetype | 1 - .../helloanyone.bundle/outputs/greeting.txt | 1 - .../helloanyone.bundle/workflow.wfbundle | Bin 9162 -> 0 bytes .../helloanyone.bundle/workflowrun.prov.ttl | 270 -- taverna-prov/example/helloanyone.t2flow | 177 -- taverna-prov/example/test.sparql | 25 - taverna-prov/pom.xml | 81 - .../export/SafeFileOutputStream.java | 119 - .../purl/wf4ever/provtaverna/export/Saver.java | 388 --- .../provtaverna/export/W3ProvenanceExport.java | 1008 ------- taverna-provenanceconnector/javadoc.xml | 6 - taverna-provenanceconnector/pom.xml | 106 - .../sf/taverna/t2/provenance/Provenance.java | 316 --- .../provenance/ProvenanceConnectorFactory.java | 8 - .../taverna/t2/provenance/api/NativeAnswer.java | 66 - .../t2/provenance/api/ProvenanceAccess.java | 725 ----- .../provenance/api/ProvenanceConnectorType.java | 16 - .../net/sf/taverna/t2/provenance/api/Query.java | 105 - .../taverna/t2/provenance/api/QueryAnswer.java | 47 - .../connector/AbstractProvenanceConnector.java | 646 ----- .../t2/provenance/connector/ProvenanceSQL.java | 5 - .../lineageservice/AnnotationsLoader.java | 86 - .../provenance/lineageservice/Dependencies.java | 127 - .../lineageservice/EventProcessor.java | 1547 ---------- .../LineageQueryResultRecord.java | 243 -- .../lineageservice/LineageSQLQuery.java | 82 - .../provenance/lineageservice/Provenance.java | 199 -- .../lineageservice/ProvenanceAnalysis.java | 1200 -------- .../lineageservice/ProvenanceQuery.java | 2069 -------------- .../lineageservice/ProvenanceWriter.java | 676 ----- .../provenance/lineageservice/URIGenerator.java | 58 - .../lineageservice/WorkflowDataProcessor.java | 453 --- .../lineageservice/types/ActivityType.java | 87 - .../lineageservice/types/DataDocumentType.java | 75 - .../lineageservice/types/IterationType.java | 96 - .../lineageservice/types/LiteralType.java | 55 - .../lineageservice/types/PortType.java | 96 - .../lineageservice/types/PortsSequenceType.java | 64 - .../lineageservice/types/ProcessType.java | 105 - .../lineageservice/types/ProcessorType.java | 83 - .../types/ProvenanceEventType.java | 30 - .../lineageservice/utils/Activity.java | 63 - .../lineageservice/utils/Collection.java | 68 - .../lineageservice/utils/DDRecord.java | 149 - .../lineageservice/utils/DataBinding.java | 82 - .../lineageservice/utils/DataLink.java | 127 - .../utils/DataValueExtractor.java | 23 - .../utils/DataflowInvocation.java | 118 - .../lineageservice/utils/NestedListNode.java | 107 - .../provenance/lineageservice/utils/Port.java | 198 -- .../lineageservice/utils/PortBinding.java | 258 -- .../lineageservice/utils/ProcessorBinding.java | 127 - .../utils/ProcessorEnactment.java | 151 - .../utils/ProvenanceProcessor.java | 115 - .../lineageservice/utils/ProvenanceUtils.java | 128 - .../lineageservice/utils/QueryPort.java | 119 - .../lineageservice/utils/ServiceInvocation.java | 161 -- .../lineageservice/utils/Workflow.java | 37 - .../lineageservice/utils/WorkflowRun.java | 72 - .../lineageservice/utils/WorkflowTree.java | 73 - .../taverna/t2/provenance/opm/OPMImporter.java | 541 ---- .../taverna/t2/provenance/opm/OPMManager.java | 414 --- .../spring/provenance-connector-context.xml | 18 - .../src/main/resources/janus.owl | 1 - .../src/main/uml/database-schema.uml | 309 -- .../src/main/uml/database-schema.umlclass | 1880 ------------- taverna-reference-api/pom.xml | 40 - .../t2/reference/AbstractExternalReference.java | 89 - .../t2/reference/ContextualizedT2Reference.java | 47 - .../sf/taverna/t2/reference/DaoException.java | 47 - .../t2/reference/DereferenceException.java | 48 - .../sf/taverna/t2/reference/ErrorDocument.java | 56 - .../taverna/t2/reference/ErrorDocumentDao.java | 64 - .../t2/reference/ErrorDocumentService.java | 152 - .../reference/ErrorDocumentServiceCallback.java | 47 - .../ErrorDocumentServiceException.java | 48 - .../reference/ExternalReferenceBuilderSPI.java | 90 - .../ExternalReferenceConstructionException.java | 50 - .../t2/reference/ExternalReferenceSPI.java | 132 - .../ExternalReferenceTranslatorSPI.java | 96 - .../ExternalReferenceValidationException.java | 50 - .../net/sf/taverna/t2/reference/Identified.java | 36 - .../sf/taverna/t2/reference/IdentifiedList.java | 46 - .../net/sf/taverna/t2/reference/ListDao.java | 67 - .../sf/taverna/t2/reference/ListService.java | 144 - .../t2/reference/ListServiceCallback.java | 47 - .../t2/reference/ListServiceException.java | 48 - .../taverna/t2/reference/ReferenceContext.java | 66 - .../taverna/t2/reference/ReferenceService.java | 294 -- .../ReferenceServiceCacheProvider.java | 52 - .../t2/reference/ReferenceServiceException.java | 47 - .../ReferenceServiceResolutionCallback.java | 47 - .../sf/taverna/t2/reference/ReferenceSet.java | 53 - .../ReferenceSetAugmentationException.java | 47 - .../t2/reference/ReferenceSetAugmentor.java | 92 - .../ReferenceSetAugmentorCallback.java | 53 - .../taverna/t2/reference/ReferenceSetDao.java | 82 - .../t2/reference/ReferenceSetService.java | 181 -- .../reference/ReferenceSetServiceCallback.java | 47 - .../reference/ReferenceSetServiceException.java | 48 - .../t2/reference/ReferencedDataNature.java | 45 - .../t2/reference/StackTraceElementBean.java | 54 - .../t2/reference/StreamToValueConverterSPI.java | 48 - .../sf/taverna/t2/reference/T2Reference.java | 102 - .../t2/reference/T2ReferenceGenerator.java | 81 - .../taverna/t2/reference/T2ReferenceType.java | 47 - .../ValueCarryingExternalReference.java | 44 - .../ValueToReferenceConversionException.java | 48 - .../reference/ValueToReferenceConverterSPI.java | 65 - .../t2/reference/WorkflowRunIdEntity.java | 44 - .../annotations/DeleteIdentifiedOperation.java | 18 - .../annotations/GetIdentifiedOperation.java | 38 - .../annotations/PutIdentifiedOperation.java | 38 - .../t2/reference/annotations/package.html | 4 - .../reference/h3/HibernateComponentClass.java | 38 - .../t2/reference/h3/HibernateMappedEntity.java | 39 - .../net/sf/taverna/t2/reference/h3/package.html | 8 - .../net/sf/taverna/t2/reference/package.html | 43 - .../reference/AbstractExternalReference.hbm.xml | 15 - taverna-reference-impl/.gitignore | 1 - taverna-reference-impl/pom.xml | 134 - .../platform/spring/jdbc/TemporaryJDBC.java | 75 - .../taverna/platform/spring/jdbc/package.html | 6 - .../t2/reference/impl/AbstractEntityImpl.java | 66 - .../impl/AbstractErrorDocumentServiceImpl.java | 119 - .../reference/impl/AbstractListServiceImpl.java | 100 - .../impl/AbstractReferenceServiceImpl.java | 171 -- .../impl/AbstractReferenceSetServiceImpl.java | 160 -- .../t2/reference/impl/AbstractServiceImpl.java | 44 - .../impl/AbstractT2ReferenceGenerator.java | 111 - .../taverna/t2/reference/impl/CacheAspect.java | 127 - .../impl/ContextualizedT2ReferenceImpl.java | 61 - .../reference/impl/EmptyReferenceContext.java | 46 - .../t2/reference/impl/ErrorDocumentImpl.java | 120 - .../impl/ErrorDocumentServiceImpl.java | 163 -- .../impl/HibernateErrorDocumentDao.java | 154 - .../t2/reference/impl/HibernateListDao.java | 151 - .../impl/HibernateReferenceSetDao.java | 197 -- .../t2/reference/impl/IdentifiedArrayList.java | 252 -- .../impl/InMemoryErrorDocumentDao.java | 69 - .../t2/reference/impl/InMemoryListDao.java | 69 - .../reference/impl/InMemoryReferenceSetDao.java | 72 - .../t2/reference/impl/ListServiceImpl.java | 136 - .../t2/reference/impl/ReferenceServiceImpl.java | 731 ----- .../impl/ReferenceSetAugmentorImpl.java | 462 --- .../t2/reference/impl/ReferenceSetImpl.java | 123 - .../reference/impl/ReferenceSetServiceImpl.java | 153 - .../reference/impl/SimpleCacheProviderImpl.java | 57 - .../impl/SimpleT2ReferenceGenerator.java | 63 - .../impl/StackTraceElementBeanImpl.java | 77 - .../t2/reference/impl/T2ReferenceImpl.java | 288 -- .../t2/reference/impl/T2ReferenceListImpl.java | 75 - .../TransactionalHibernateErrorDocumentDao.java | 155 - .../impl/TransactionalHibernateListDao.java | 154 - .../TransactionalHibernateReferenceSetDao.java | 198 -- .../t2/reference/impl/TranslationPath.java | 266 -- .../impl/UUIDT2ReferenceGenerator.java | 56 - .../t2/reference/impl/WriteQueueAspect.java | 142 - .../sf/taverna/t2/reference/impl/package.html | 5 - ...erna.t2.reference.h3.HibernateComponentClass | 2 - ...averna.t2.reference.h3.HibernateMappedEntity | 3 - .../src/main/resources/META-INF/spring.handlers | 1 - .../src/main/resources/META-INF/spring.schemas | 1 - .../spring/hibernate-reference-impl-context.xml | 117 - .../spring/in-memory-reference-impl-context.xml | 46 - .../spring/reference-impl-context-osgi.xml | 25 - .../META-INF/spring/reference-impl-context.xml | 15 - .../src/main/resources/artifact-support.xsd | 57 - .../t2/reference/impl/ErrorDocumentImpl.hbm.xml | 45 - .../t2/reference/impl/ReferenceSetImpl.hbm.xml | 32 - .../reference/impl/T2ReferenceListImpl.hbm.xml | 37 - .../platform/spring/jdbc/TemporaryJDBCTest.java | 60 - .../t2/reference/impl/AppContextSetup.java | 31 - .../t2/reference/impl/DatabaseSetupTest.java | 140 - .../t2/reference/impl/ErrorDocumentDaoTest.java | 151 - .../impl/ErrorDocumentServiceTest.java | 88 - .../taverna/t2/reference/impl/ListDaoTest.java | 121 - .../t2/reference/impl/ListServiceTest.java | 91 - .../t2/reference/impl/ReferenceContextImpl.java | 30 - .../t2/reference/impl/ReferenceSetDaoTest.java | 105 - .../reference/impl/ReferenceSetServiceTest.java | 92 - .../t2/reference/impl/TranslationPathTest.java | 46 - .../src/test/resources/log4j.xml | 44 - .../resources/vanillaHibernateAppContext.xml | 120 - .../vanillaHibernateTransactionalAppContext.xml | 118 - .../resources/vanillaInMemoryAppContext.xml | 29 - taverna-reference-testhelpers/pom.xml | 38 - .../taverna/t2referencetest/BlueReference.java | 129 - .../t2referencetest/DummyReferenceSet.java | 32 - .../taverna/t2referencetest/GreenBuilder.java | 107 - .../taverna/t2referencetest/GreenReference.java | 129 - .../sf/taverna/t2referencetest/GreenToRed.java | 65 - .../taverna/t2referencetest/RedReference.java | 129 - .../t2referencetest/YellowReference.java | 130 - ...rna.t2.reference.ExternalReferenceBuilderSPI | 2 - ...sf.taverna.t2.reference.ExternalReferenceSPI | 5 - ....t2.reference.ExternalReferenceTranslatorSPI | 2 - .../reference-testhelpers-context-osgi.xml | 18 - .../spring/reference-testhelpers-context.xml | 16 - .../t2referencetest/BlueReference.hbm.xml | 16 - .../t2referencetest/GreenReference.hbm.xml | 16 - .../t2referencetest/RedReference.hbm.xml | 16 - .../t2referencetest/YellowReference.hbm.xml | 16 - taverna-reference-types/README.md | 5 - taverna-reference-types/pom.xml | 77 - .../impl/external/file/FileReference.java | 210 -- .../impl/external/file/FileToFileReference.java | 61 - .../reference/impl/external/file/package.html | 4 - .../impl/external/http/HttpReference.java | 217 -- .../impl/external/http/UrlToHttpReference.java | 62 - .../reference/impl/external/http/package.html | 3 - .../object/BooleanToStringReference.java | 53 - .../object/ByteArrayToByteArrayReference.java | 53 - .../object/CharacterToStringReference.java | 53 - .../object/InlineByteArrayReference.java | 93 - .../object/InlineByteArrayReferenceBuilder.java | 67 - .../InlineByteToInlineStringTranslator.java | 51 - .../external/object/InlineStringReference.java | 133 - .../object/InlineStringReferenceBuilder.java | 76 - .../InlineStringToInlineByteTranslator.java | 40 - .../object/NumberToStringReference.java | 52 - .../object/StreamToBooleanConverter.java | 29 - .../object/StreamToByteArrayConverter.java | 62 - .../object/StreamToDoubleConverter.java | 29 - .../object/StreamToIntegerConverter.java | 29 - .../object/StreamToStringConverter.java | 80 - .../StreamToVMObjectReferenceConverter.java | 56 - .../object/StringToStringReference.java | 52 - .../impl/external/object/VMObjectReference.java | 111 - .../reference/impl/external/object/package.html | 4 - ...rna.t2.reference.ExternalReferenceBuilderSPI | 3 - ...sf.taverna.t2.reference.ExternalReferenceSPI | 6 - ....t2.reference.ExternalReferenceTranslatorSPI | 3 - ...verna.t2.reference.StreamToValueConverterSPI | 7 - ...na.t2.reference.ValueToReferenceConverterSPI | 8 - .../reference-core-extensions-context-osgi.xml | 33 - .../reference-core-extensions-context.xml | 31 - .../impl/external/file/FileReference.hbm.xml | 18 - .../impl/external/http/HttpReference.hbm.xml | 16 - .../object/InlineByteArrayReference.hbm.xml | 16 - .../object/InlineStringReference.hbm.xml | 16 - .../external/object/VMObjectReference.hbm.xml | 16 - .../external/object/ByteArrayToStringTest.java | 91 - taverna-report-api/pom.xml | 39 - .../taverna/platform/report/ActivityReport.java | 49 - .../org/taverna/platform/report/Invocation.java | 306 -- .../platform/report/ProcessorReport.java | 164 -- .../taverna/platform/report/ReportListener.java | 32 - .../uk/org/taverna/platform/report/State.java | 30 - .../taverna/platform/report/StatusReport.java | 373 --- .../taverna/platform/report/WorkflowReport.java | 170 -- .../platform/report/StatusReportTest.java | 245 -- taverna-run-api/pom.xml | 46 - .../platform/run/api/InvalidRunIdException.java | 46 - .../taverna/platform/run/api/RunProfile.java | 196 -- .../platform/run/api/RunProfileException.java | 47 - .../taverna/platform/run/api/RunService.java | 235 -- .../platform/run/api/RunStateException.java | 47 - .../platform/run/api/RunProfileTest.java | 233 -- taverna-run-impl/pom.xml | 73 - .../uk/org/taverna/platform/run/impl/Run.java | 279 -- .../platform/run/impl/RunServiceImpl.java | 268 -- .../platform/run/impl/WorkflowReportJSON.java | 328 --- .../META-INF/spring/run-context-osgi.xml | 18 - .../resources/META-INF/spring/run-context.xml | 13 - .../platform/run/impl/DummyWorkflowReport.java | 131 - .../org/taverna/platform/run/impl/RunTest.java | 69 - .../run/impl/WorkflowReportJSONTest.java | 288 -- .../src/test/resources/hello_anyone.wfbundle | Bin 10087 -> 0 bytes .../src/test/resources/workflowrun.bundle.zip | Bin 9167 -> 0 bytes .../src/test/resources/workflowrun.json | 113 - taverna-services-api/.project | 24 - taverna-services-api/pom.xml | 18 - .../services/ActivityTypeNotFoundException.java | 47 - .../services/InvalidConfigurationException.java | 47 - .../commons/services/ServiceRegistry.java | 89 - taverna-services-impl/.project | 24 - taverna-services-impl/pom.xml | 41 - .../services/impl/ServiceRegistryImpl.java | 92 - .../spring/taverna-services-context-osgi.xml | 13 - .../spring/taverna-services-context.xml | 10 - taverna-stringconstant-activity/pom.xml | 43 - .../stringconstant/StringConstantActivity.java | 119 - .../StringConstantActivityFactory.java | 81 - .../StringConstantActivityHealthChecker.java | 58 - .../StringConstantConfigurationBean.java | 45 - .../t2/activities/stringconstant/package.html | 3 - ...averna.t2.workflowmodel.health.HealthChecker | 1 - .../stringconstant-activity-context-osgi.xml | 15 - .../spring/stringconstant-activity-context.xml | 12 - .../src/main/resources/schema.json | 19 - .../StringConstantActivityFactoryTest.java | 64 - .../StringConstantActivityTest.java | 68 - .../MobyCentralCurationUseCasAggregated.uxf | 58 - .../docs/MobyCentralCurationUseCase.uxf | 50 - .../docs/annotationmodel.uxf | 101 - taverna-workflowmodel-api/pom.xml | 52 - .../t2/annotation/AbstractAnnotatedThing.java | 164 -- .../net/sf/taverna/t2/annotation/Annotated.java | 79 - .../t2/annotation/AnnotationAssertion.java | 52 - .../t2/annotation/AnnotationBeanSPI.java | 32 - .../taverna/t2/annotation/AnnotationChain.java | 51 - .../t2/annotation/AnnotationPerspective.java | 62 - .../taverna/t2/annotation/AnnotationRole.java | 51 - .../t2/annotation/AnnotationSourceSPI.java | 35 - .../net/sf/taverna/t2/annotation/AppliesTo.java | 53 - .../sf/taverna/t2/annotation/Curateable.java | 72 - .../sf/taverna/t2/annotation/CurationEvent.java | 52 - .../t2/annotation/CurationEventBeanSPI.java | 35 - .../t2/annotation/CurationEventType.java | 43 - .../sf/taverna/t2/annotation/HierarchyRole.java | 40 - .../t2/annotation/HierarchyTraversal.java | 74 - .../net/sf/taverna/t2/annotation/Person.java | 36 - .../AbstractNumericRangeAssertion.java | 64 - .../AbstractNumericValueAssertion.java | 54 - .../AbstractTextualValueAssertion.java | 53 - .../t2/annotation/annotationbeans/Author.java | 44 - .../annotationbeans/DescriptiveTitle.java | 42 - .../annotationbeans/DocumentationUrl.java | 58 - .../annotationbeans/ExampleValue.java | 43 - .../annotationbeans/FreeTextDescription.java | 48 - .../annotationbeans/HostInstitution.java | 45 - .../IdentificationAssertion.java | 38 - .../t2/annotation/annotationbeans/MimeType.java | 60 - .../t2/annotation/annotationbeans/Optional.java | 44 - .../annotationbeans/SemanticAnnotation.java | 51 - .../net/sf/taverna/t2/annotation/package.html | 17 - .../sf/taverna/t2/facade/FacadeListener.java | 49 - .../sf/taverna/t2/facade/ResultListener.java | 43 - .../t2/facade/WorkflowInstanceFacade.java | 237 -- .../t2/facade/WorkflowRunCancellation.java | 29 - .../java/net/sf/taverna/t2/facade/package.html | 24 - .../sf/taverna/t2/invocation/Completion.java | 107 - .../net/sf/taverna/t2/invocation/Event.java | 168 -- .../t2/invocation/InvocationContext.java | 44 - .../t2/invocation/IterationInternalEvent.java | 103 - .../invocation/ProcessIdentifierException.java | 48 - .../t2/invocation/TokenOrderException.java | 49 - .../net/sf/taverna/t2/invocation/TreeCache.java | 200 -- .../t2/invocation/WorkflowDataToken.java | 91 - .../net/sf/taverna/t2/invocation/package.html | 6 - .../sf/taverna/t2/monitor/MonitorManager.java | 378 --- .../net/sf/taverna/t2/monitor/MonitorNode.java | 76 - .../taverna/t2/monitor/MonitorableProperty.java | 55 - .../t2/monitor/NoSuchPropertyException.java | 50 - .../taverna/t2/monitor/SteerableProperty.java | 37 - .../java/net/sf/taverna/t2/monitor/package.html | 36 - .../provenance/item/AbstractProvenanceItem.java | 77 - .../provenance/item/ActivityProvenanceItem.java | 62 - .../t2/provenance/item/DataProvenanceItem.java | 63 - .../t2/provenance/item/DataflowRunComplete.java | 61 - .../t2/provenance/item/ErrorProvenanceItem.java | 71 - .../item/InputDataProvenanceItem.java | 49 - .../item/InvocationStartedProvenanceItem.java | 41 - .../item/IterationProvenanceItem.java | 108 - .../item/OutputDataProvenanceItem.java | 49 - .../provenance/item/ProcessProvenanceItem.java | 89 - .../item/ProcessorProvenanceItem.java | 57 - .../t2/provenance/item/ProvenanceItem.java | 103 - .../item/WorkflowDataProvenanceItem.java | 101 - .../provenance/item/WorkflowProvenanceItem.java | 101 - .../provenance/reporter/ProvenanceReporter.java | 72 - .../provenance/vocabulary/SharedVocabulary.java | 34 - .../sf/taverna/t2/utility/TreeModelAdapter.java | 174 -- .../sf/taverna/t2/utility/TypedTreeModel.java | 117 - .../taverna/t2/utility/TypedTreeModelEvent.java | 151 - .../t2/utility/TypedTreeModelListener.java | 82 - .../java/net/sf/taverna/t2/utility/package.html | 5 - .../sf/taverna/t2/visit/DataflowCollation.java | 32 - .../sf/taverna/t2/visit/HierarchyTraverser.java | 343 --- .../java/net/sf/taverna/t2/visit/VisitKind.java | 16 - .../net/sf/taverna/t2/visit/VisitReport.java | 346 --- .../java/net/sf/taverna/t2/visit/Visitor.java | 44 - .../t2/workflowmodel/AbstractOutputPort.java | 43 - .../taverna/t2/workflowmodel/AbstractPort.java | 54 - .../taverna/t2/workflowmodel/CompoundEdit.java | 115 - .../sf/taverna/t2/workflowmodel/Condition.java | 52 - .../taverna/t2/workflowmodel/Configurable.java | 56 - .../workflowmodel/ConfigurationException.java | 62 - .../t2/workflowmodel/ControlBoundary.java | 47 - .../sf/taverna/t2/workflowmodel/Dataflow.java | 173 -- .../t2/workflowmodel/DataflowInputPort.java | 52 - .../t2/workflowmodel/DataflowOutputPort.java | 61 - .../taverna/t2/workflowmodel/DataflowPort.java | 34 - .../workflowmodel/DataflowValidationReport.java | 99 - .../sf/taverna/t2/workflowmodel/Datalink.java | 56 - .../net/sf/taverna/t2/workflowmodel/Edit.java | 65 - .../taverna/t2/workflowmodel/EditException.java | 43 - .../net/sf/taverna/t2/workflowmodel/Edits.java | 832 ------ .../EventForwardingOutputPort.java | 46 - .../workflowmodel/EventHandlingInputPort.java | 41 - .../t2/workflowmodel/FailureTransmitter.java | 34 - .../t2/workflowmodel/FilteringInputPort.java | 52 - .../sf/taverna/t2/workflowmodel/InputPort.java | 30 - .../workflowmodel/InvalidDataflowException.java | 63 - .../net/sf/taverna/t2/workflowmodel/Merge.java | 63 - .../t2/workflowmodel/MergeInputPort.java | 52 - .../t2/workflowmodel/MergeOutputPort.java | 35 - .../sf/taverna/t2/workflowmodel/MergePort.java | 35 - .../t2/workflowmodel/NamedWorkflowEntity.java | 45 - .../t2/workflowmodel/NamingException.java | 47 - .../taverna/t2/workflowmodel/OrderedPair.java | 85 - .../sf/taverna/t2/workflowmodel/OutputPort.java | 46 - .../net/sf/taverna/t2/workflowmodel/Port.java | 35 - .../sf/taverna/t2/workflowmodel/Processor.java | 150 - .../workflowmodel/ProcessorFinishedEvent.java | 34 - .../t2/workflowmodel/ProcessorInputPort.java | 30 - .../t2/workflowmodel/ProcessorOutputPort.java | 31 - .../taverna/t2/workflowmodel/ProcessorPort.java | 32 - .../t2/workflowmodel/RunDeletionListener.java | 15 - .../t2/workflowmodel/TokenProcessingEntity.java | 57 - .../taverna/t2/workflowmodel/WorkflowItem.java | 28 - .../WorkflowStructureException.java | 36 - .../health/DisabledActivityHealthChecker.java | 48 - .../t2/workflowmodel/health/HealthCheck.java | 68 - .../t2/workflowmodel/health/HealthChecker.java | 37 - .../health/RemoteHealthChecker.java | 220 -- .../UnrecognizedActivityHealthChecker.java | 48 - .../t2/workflowmodel/health/package.html | 6 - .../sf/taverna/t2/workflowmodel/package.html | 3 - .../processor/activity/AbstractActivity.java | 264 -- .../activity/AbstractAsynchronousActivity.java | 81 - .../processor/activity/Activity.java | 93 - .../activity/ActivityAndBeanWrapper.java | 62 - .../ActivityConfigurationException.java | 62 - .../processor/activity/ActivityFactory.java | 89 - .../processor/activity/ActivityInputPort.java | 78 - .../processor/activity/ActivityOutputPort.java | 32 - .../processor/activity/ActivityPort.java | 34 - .../activity/AsynchronousActivity.java | 50 - .../activity/AsynchronousActivityCallback.java | 137 - .../processor/activity/DisabledActivity.java | 191 -- .../workflowmodel/processor/activity/Job.java | 130 - .../activity/LockedNestedDataflow.java | 11 - .../MonitorableAsynchronousActivity.java | 56 - .../processor/activity/NestedDataflow.java | 36 - .../activity/NestedDataflowSource.java | 18 - .../activity/NonExecutableActivity.java | 80 - .../processor/activity/SupersededActivity.java | 16 - .../activity/UnrecognizedActivity.java | 41 - .../config/ActivityInputPortDefinitionBean.java | 67 - .../ActivityOutputPortDefinitionBean.java | 49 - .../config/ActivityPortDefinitionBean.java | 104 - .../config/ActivityPortsDefinitionBean.java | 82 - .../processor/activity/config/package.html | 7 - .../processor/activity/package.html | 10 - .../processor/config/ConfigurationBean.java | 12 - .../processor/config/ConfigurationProperty.java | 27 - .../dispatch/AbstractDispatchLayer.java | 103 - .../dispatch/AbstractErrorHandlerLayer.java | 283 -- .../processor/dispatch/DispatchLayer.java | 97 - .../dispatch/DispatchLayerFactory.java | 62 - .../processor/dispatch/DispatchStack.java | 100 - .../processor/dispatch/NotifiableLayer.java | 40 - .../PropertyContributingDispatchLayer.java | 64 - .../description/DispatchLayerErrorReaction.java | 44 - .../DispatchLayerJobQueueReaction.java | 45 - .../description/DispatchLayerJobReaction.java | 44 - .../DispatchLayerResultCompletionReaction.java | 44 - .../DispatchLayerResultReaction.java | 44 - .../description/DispatchLayerStateEffect.java | 84 - .../description/DispatchMessageType.java | 61 - .../dispatch/description/ReactionTo.java | 40 - .../description/SupportsStreamedResult.java | 41 - .../processor/dispatch/description/package.html | 3 - .../dispatch/events/AbstractDispatchEvent.java | 45 - .../events/DispatchCompletionEvent.java | 70 - .../dispatch/events/DispatchErrorEvent.java | 119 - .../dispatch/events/DispatchErrorType.java | 54 - .../dispatch/events/DispatchJobEvent.java | 106 - .../dispatch/events/DispatchJobQueueEvent.java | 95 - .../dispatch/events/DispatchResultEvent.java | 108 - .../processor/dispatch/package.html | 19 - .../AbstractIterationStrategyNode.java | 225 -- ...onHandlingAbstractIterationStrategyNode.java | 136 - .../processor/iteration/CrossProduct.java | 164 -- .../processor/iteration/DotProduct.java | 123 - .../processor/iteration/IterationStrategy.java | 54 - .../iteration/IterationStrategyNode.java | 121 - .../iteration/IterationStrategyStack.java | 65 - .../IterationTypeMismatchException.java | 49 - .../MissingIterationInputException.java | 50 - .../processor/iteration/NamedInputPortNode.java | 116 - .../processor/iteration/PrefixDotProduct.java | 111 - .../processor/iteration/TerminalNode.java | 39 - .../processor/iteration/package.html | 4 - .../serialization/DeserializationException.java | 33 - .../serialization/SerializationException.java | 33 - .../t2/workflowmodel/utils/AnnotationTools.java | 151 - .../utils/NamedWorkflowEntityComparator.java | 39 - .../t2/workflowmodel/utils/PortComparator.java | 37 - .../taverna/t2/workflowmodel/utils/Tools.java | 795 ------ .../services/net.sf.taverna.t2.visit.VisitKind | 1 - ...averna.t2.workflowmodel.health.HealthChecker | 2 - .../spring/workflowmodel-api-context-osgi.xml | 25 - .../spring/workflowmodel-api-context.xml | 23 - .../taverna/t2/monitor/TestMonitorManager.java | 173 -- .../t2/workflowmodel/health/DummyVisitKind.java | 26 - .../health/FloatHealthChecker.java | 45 - .../health/FloatHealthChecker2.java | 44 - .../workflowmodel/health/HealthReportTest.java | 88 - .../health/StringHealthChecker.java | 45 - .../iteration/TestIterationStrategyNodes.java | 212 -- ...averna.t2.workflowmodel.health.HealthChecker | 3 - .../.gitignore | 1 - taverna-workflowmodel-core-extensions/pom.xml | 30 - .../layers/CoreDispatchLayerFactory.java | 103 - .../processor/dispatch/layers/ErrorBounce.java | 324 --- .../processor/dispatch/layers/Failover.java | 111 - .../dispatch/layers/IntermediateProvenance.java | 508 ---- .../processor/dispatch/layers/Invoke.java | 369 --- .../processor/dispatch/layers/Loop.java | 424 --- .../dispatch/layers/LoopConfiguration.java | 75 - .../processor/dispatch/layers/Parallelize.java | 463 --- .../dispatch/layers/ParallelizeConfig.java | 50 - .../processor/dispatch/layers/Retry.java | 180 -- .../processor/dispatch/layers/RetryConfig.java | 97 - .../processor/dispatch/layers/Stop.java | 163 -- .../processor/dispatch/layers/package.html | 4 - ...rkflowmodel-core-extensions-context-osgi.xml | 11 - .../workflowmodel-core-extensions-context.xml | 9 - .../processor/dispatch/layers/TestRetry.java | 110 - taverna-workflowmodel-impl/pom.xml | 71 - .../impl/AnnotationAssertionImpl.java | 135 - .../t2/annotation/impl/AnnotationChainImpl.java | 50 - .../t2/annotation/impl/DisputeEvent.java | 74 - .../t2/annotation/impl/DisputeEventDetails.java | 28 - .../taverna/t2/annotation/impl/PersonImpl.java | 32 - .../taverna/t2/annotation/impl/URISource.java | 46 - .../facade/impl/WorkflowInstanceFacadeImpl.java | 631 ----- .../invocation/impl/InvocationContextImpl.java | 72 - .../t2/monitor/impl/MonitorTreeModel.java | 423 --- .../impl/AbstractActivityEdit.java | 69 - .../impl/AbstractAnnotationEdit.java | 70 - .../impl/AbstractBinaryProcessorEdit.java | 95 - .../workflowmodel/impl/AbstractCrystalizer.java | 194 -- .../impl/AbstractDataflowEdit.java | 68 - .../impl/AbstractDataflowInputPortEdit.java | 68 - .../impl/AbstractDataflowOutputPortEdit.java | 70 - .../impl/AbstractDatalinkEdit.java | 67 - .../impl/AbstractEventHandlingInputPort.java | 53 - .../impl/AbstractFilteringInputPort.java | 178 -- .../workflowmodel/impl/AbstractMergeEdit.java | 52 - .../impl/AbstractProcessorEdit.java | 68 - .../impl/BasicEventForwardingOutputPort.java | 93 - .../t2/workflowmodel/impl/ConditionImpl.java | 61 - .../t2/workflowmodel/impl/ConfigureEdit.java | 78 - .../t2/workflowmodel/impl/Crystalizer.java | 66 - .../t2/workflowmodel/impl/DataflowImpl.java | 797 ------ .../impl/DataflowInputPortImpl.java | 93 - .../impl/DataflowOutputPortImpl.java | 112 - .../impl/DataflowValidationReportImpl.java | 94 - .../t2/workflowmodel/impl/DatalinkImpl.java | 68 - .../t2/workflowmodel/impl/EditSupport.java | 46 - .../t2/workflowmodel/impl/EditsImpl.java | 1251 --------- .../t2/workflowmodel/impl/MergeImpl.java | 234 -- .../workflowmodel/impl/MergeInputPortImpl.java | 45 - .../workflowmodel/impl/MergeOutputPortImpl.java | 40 - .../impl/ProcessorCrystalizerImpl.java | 103 - .../t2/workflowmodel/impl/ProcessorImpl.java | 426 --- .../impl/ProcessorInputPortImpl.java | 72 - .../impl/ProcessorOutputPortImpl.java | 59 - .../taverna/t2/workflowmodel/impl/package.html | 3 - .../activity/impl/ActivityInputPortImpl.java | 88 - .../activity/impl/ActivityOutputPortImpl.java | 75 - .../processor/activity/impl/package.html | 3 - .../impl/AbstractDispatchLayerEdit.java | 98 - .../dispatch/impl/DispatchStackImpl.java | 317 --- .../processor/dispatch/impl/package.html | 8 - .../iteration/impl/IterationStrategyImpl.java | 345 --- .../impl/IterationStrategyStackImpl.java | 154 - .../processor/iteration/impl/package.html | 3 - ...t.sf.taverna.t2.annotation.AnnotationBeanSPI | 10 - ...sf.taverna.t2.annotation.AnnotationSourceSPI | 1 - ...f.taverna.t2.annotation.CurationEventBeanSPI | 1 - .../net.sf.taverna.t2.workflowmodel.Edits | 1 - ...averna.t2.workflowmodel.health.HealthChecker | 1 - .../spring/workflowmodel-impl-context-osgi.xml | 15 - .../spring/workflowmodel-impl-context.xml | 13 - .../src/main/resources/provenanceContext.xml | 23 - .../taverna/t2/annotation/TestAnnotations.java | 192 -- .../t2/monitor/impl/MonitorTreeModelTest.java | 56 - .../impl/AbstractDatalinkEditTest.java | 187 -- .../impl/AddProcessorEditTest.java | 90 - .../ChangeDataflowInputPortDepthEditTest.java | 77 - ...eDataflowInputPortGranularDepthEditTest.java | 73 - .../impl/ConfigureActivityEditTest.java | 90 - .../impl/ConnectDatalinkEditTest.java | 88 - .../impl/ConnectMergedDatalinkEditTest.java | 129 - .../impl/CreateDataflowInputPortEditTest.java | 87 - .../impl/CreateDataflowOutputPortEditTest.java | 81 - .../t2/workflowmodel/impl/DataflowImplTest.java | 43 - .../impl/DefaultDispatchStackEditTest.java | 79 - .../t2/workflowmodel/impl/DummyActivity.java | 40 - .../t2/workflowmodel/impl/DummyDataflow.java | 143 - .../impl/DummyDataflowInputPort.java | 39 - .../impl/DummyDataflowOutputPort.java | 37 - .../t2/workflowmodel/impl/DummyProcessor.java | 150 - .../impl/DummyValidationReport.java | 69 - .../t2/workflowmodel/impl/EditsImplTests.java | 61 - .../t2/workflowmodel/impl/EventKeeper.java | 37 - .../MapProcessorPortsToActivityEditTest.java | 133 - .../impl/ProcessorHealthReportTest.java | 140 - .../impl/RemoveProcessorInputPortEditTest.java | 69 - .../impl/RemoveProcessorOutputPortEditTest.java | 71 - ...pdateDataflowInternalIdentifierEditTest.java | 40 - .../processor/AsynchEchoActivity.java | 61 - .../processor/DiagnosticEventHandler.java | 70 - .../t2/workflowmodel/processor/EchoConfig.java | 52 - .../NaiveProcessorConstructionTest.java | 47 - .../t2/workflowmodel/processor/Tools.java | 90 - .../processor/dispatch/DiagnosticLayer.java | 75 - .../DiagnosticIterationStrategyNode.java | 131 - .../impl/IterationTypeCheckerTest.java | 217 -- .../src/test/resources/log4j.properties | 10 - .../2_port_cross_product.xml | 10 - .../resources/serialized-fragments/activity.xml | 14 - .../serialized-fragments/dataflow_datalinks.xml | 84 - .../dataflow_with_condition.xml | 66 - .../dataflow_with_merge.xml | 60 - .../dataflow_with_unlinked_processor.xml | 36 - .../serialized-fragments/dispatchLayer.xml | 11 - .../serialized-fragments/dispatchStack.xml | 51 - .../empty_dataflow_with_ports.xml | 23 - .../serialized-fragments/processor.xml | 28 - 907 files changed, 106850 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/.gitignore ---------------------------------------------------------------------- diff --git a/.gitignore b/.gitignore deleted file mode 100644 index ebe0e5b..0000000 --- a/.gitignore +++ /dev/null @@ -1,24 +0,0 @@ -# ignore project files # -.classpath -.project -.settings/ -catalog-v001.xml - -# ignore target files # -target/ -bin/ -build/ -dist/ -apidoc/ -*.swp - -# ignore svn files if there -.svn - -# ignore log files # -*.log -/logs/* -*/logs/* - - - http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/.travis.yml ---------------------------------------------------------------------- diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index dff5f3a..0000000 --- a/.travis.yml +++ /dev/null @@ -1 +0,0 @@ -language: java http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/README.md ---------------------------------------------------------------------- diff --git a/README.md b/README.md deleted file mode 100644 index 1e4ab4e..0000000 --- a/README.md +++ /dev/null @@ -1,3 +0,0 @@ -# Apache Taverna Engine - -[](https://travis-ci.org/taverna-incubator/incubator-taverna-engine) http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/pom.xml ---------------------------------------------------------------------- diff --git a/pom.xml b/pom.xml deleted file mode 100644 index 74508ca..0000000 --- a/pom.xml +++ /dev/null @@ -1,87 +0,0 @@ -<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" - xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> - <modelVersion>4.0.0</modelVersion> - <parent> - <groupId>org.apache.taverna</groupId> - <artifactId>taverna-parent</artifactId> - <version>1-incubating-SNAPSHOT</version> - </parent> - <groupId>org.apache.taverna.engine</groupId> - <artifactId>taverna-engine</artifactId> - <version>3.1.0-incubating-SNAPSHOT</version> - <packaging>pom</packaging> - <name>Apache Taverna Engine and Platform</name> - <properties> - <taverna.language.version>0.15.0-incubating-SNAPSHOT</taverna.language.version> - <taverna.osgi.version>0.2.0-incubating-SNAPSHOT</taverna.osgi.version> - </properties> - <modules> - <!-- Avoid spaghetti dependencies - <module>taverna-platform-integration-tests</module> - <module>taverna-integration-tests</module> - --> - <module>taverna-activity-archetype</module> - <module>taverna-activity-test-utils</module> - <module>taverna-capability-api</module> - <module>taverna-capability-impl</module> - <module>taverna-credential-manager</module> - <module>taverna-credential-manager-impl</module> - <module>taverna-database-configuration-api</module> - <module>taverna-database-configuration-impl</module> - - <module>taverna-dataflow-activity</module> - <module>taverna-execution-api</module> - <module>taverna-execution-hadoop</module> - <module>taverna-execution-impl</module> - <module>taverna-execution-local</module> - <module>taverna-execution-remote</module> - <module>taverna-observer</module> - - <!-- FIXME: Upgrade to T3 - <module>taverna-prov</module> - --> - <module>taverna-prov-owl-bindings</module> - <!-- - <module>taverna-provenanceconnector</module> - --> - <module>taverna-reference-api</module> - <module>taverna-reference-impl</module> - <module>taverna-reference-testhelpers</module> - <module>taverna-reference-types</module> - <module>taverna-report-api</module> - <module>taverna-run-api</module> - <module>taverna-run-impl</module> - <module>taverna-services-api</module> - <module>taverna-services-impl</module> - <module>taverna-stringconstant-activity</module> - <module>taverna-workflowmodel-api</module> - <module>taverna-workflowmodel-core-extensions</module> - <module>taverna-workflowmodel-impl</module> - </modules> - <dependencyManagement> - <dependencies> - <dependency> - <groupId>log4j</groupId> - <artifactId>log4j</artifactId> - <version>${log4j.version}</version> - </dependency> - <dependency> - <groupId>junit</groupId> - <artifactId>junit</artifactId> - <version>${junit.version}</version> - <scope>test</scope> - </dependency> - </dependencies> - </dependencyManagement> - <repositories> - <repository> - <id>taverna-incubating</id> - <name>Apache Taverna incubating Repository</name> - <url>http://repository.mygrid.org.uk/artifactory/incubator-snapshot-local/</url> - <releases> - <enabled>false</enabled> - </releases> - <snapshots /> - </repository> - </repositories> -</project> http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-activity-archetype/pom.xml ---------------------------------------------------------------------- diff --git a/taverna-activity-archetype/pom.xml b/taverna-activity-archetype/pom.xml deleted file mode 100644 index 72d7468..0000000 --- a/taverna-activity-archetype/pom.xml +++ /dev/null @@ -1,30 +0,0 @@ -<?xml version="1.0"?> -<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"> - <modelVersion>4.0.0</modelVersion> - <parent> - <groupId>org.apache.taverna.engine</groupId> - <artifactId>taverna-engine</artifactId> - <version>3.1.0-incubating-SNAPSHOT</version> - </parent> - <artifactId>taverna-activity-archetype</artifactId> - <packaging>maven-archetype</packaging> - <name>Apache Taverna Activity archetype</name> - <description>Archetype to build a Taverna 3 service activity. - Includes engine and UI parts, and a test class to run the workbench with the new activity. - </description> - <build> - <extensions> - <extension> - <groupId>org.apache.maven.archetype</groupId> - <artifactId>archetype-packaging</artifactId> - <version>2.2</version> - </extension> - </extensions> - <plugins> - <plugin> - <artifactId>maven-archetype-plugin</artifactId> - <version>2.2</version> - </plugin> - </plugins> - </build> -</project> http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-activity-archetype/src/main/resources/META-INF/maven/archetype-metadata.xml ---------------------------------------------------------------------- diff --git a/taverna-activity-archetype/src/main/resources/META-INF/maven/archetype-metadata.xml b/taverna-activity-archetype/src/main/resources/META-INF/maven/archetype-metadata.xml deleted file mode 100644 index 719227f..0000000 --- a/taverna-activity-archetype/src/main/resources/META-INF/maven/archetype-metadata.xml +++ /dev/null @@ -1,58 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<archetype-descriptor - xsi:schemaLocation="http://maven.apache.org/plugins/maven-archetype-plugin/archetype-descriptor/1.0.0 http://maven.apache.org/xsd/archetype-descriptor-1.0.0.xsd" - name="myfancytool" - xmlns="http://maven.apache.org/plugins/maven-archetype-plugin/archetype-descriptor/1.0.0" - xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> - <requiredProperties> - <requiredProperty key="classPrefix"> - <defaultValue>Example</defaultValue> - </requiredProperty> - </requiredProperties> - <modules> - <module id="${rootArtifactId}-activity" dir="__rootArtifactId__-activity" - name="${rootArtifactId}-activity"> - <fileSets> - <fileSet filtered="true" packaged="true" encoding="UTF-8"> - <directory>src/main/java</directory> - <includes> - <include>**/*.java</include> - </includes> - </fileSet> - <fileSet encoding="UTF-8" filtered="true"> - <directory>src/main/resources</directory> - <includes> - <include>**/*.xml</include> - <include>**/*.json</include> - </includes> - </fileSet> - <fileSet filtered="true" packaged="true" encoding="UTF-8"> - <directory>src/test/java</directory> - <includes> - <include>**/*.java</include> - </includes> - </fileSet> - </fileSets> - </module> - <module id="${rootArtifactId}-activity-ui" dir="__rootArtifactId__-activity-ui" - name="${rootArtifactId}-activity-ui"> - <fileSets> - <fileSet filtered="true" packaged="true" encoding="UTF-8"> - <directory>src/main/java</directory> - <includes> - <include>**/*.java</include> - </includes> - </fileSet> - <fileSet encoding="UTF-8" filtered="true"> - <directory>src/main/resources</directory> - <includes> - <include>**/*.xml</include> - <include>**/*.png</include> - </includes> - </fileSet> - </fileSets> - </module> - <module id="${rootArtifactId}-plugin" dir="__rootArtifactId__-plugin" - name="${rootArtifactId}-plugin" /> - </modules> -</archetype-descriptor> http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/pom.xml ---------------------------------------------------------------------- diff --git a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/pom.xml b/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/pom.xml deleted file mode 100644 index 9f01ed6..0000000 --- a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/pom.xml +++ /dev/null @@ -1,47 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" - xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"> - <modelVersion>4.0.0</modelVersion> - <parent> - <groupId>${groupId}</groupId> - <artifactId>${rootArtifactId}</artifactId> - <version>${version}</version> - </parent> - <artifactId>${artifactId}</artifactId> - <packaging>bundle</packaging> - <name>${classPrefix} Taverna activity UI bindings</name> - - <dependencies> - <dependency> - <groupId>${project.groupId}</groupId> - <artifactId>${rootArtifactId}-activity</artifactId> - <version>${version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>activity-palette-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>menu-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>contextual-views-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>activity-tools</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - - <dependency> - <groupId>com.fasterxml.jackson.core</groupId> - <artifactId>jackson-databind</artifactId> - <version>2.3.0</version> - </dependency> - </dependencies> -</project> http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/config/__classPrefix__ConfigurationPanel.java ---------------------------------------------------------------------- diff --git a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/config/__classPrefix__ConfigurationPanel.java b/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/config/__classPrefix__ConfigurationPanel.java deleted file mode 100644 index d92efb7..0000000 --- a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/config/__classPrefix__ConfigurationPanel.java +++ /dev/null @@ -1,87 +0,0 @@ -#set( $symbol_pound = '#' ) -#set( $symbol_dollar = '$' ) -#set( $symbol_escape = '\' ) -package ${package}.ui.config; - -import java.awt.GridLayout; -import java.net.URI; - -import javax.swing.JLabel; -import javax.swing.JOptionPane; -import javax.swing.JTextField; - -import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel; - -import uk.org.taverna.commons.services.ServiceRegistry; -import uk.org.taverna.scufl2.api.activity.Activity; - -@SuppressWarnings("serial") -public class ${classPrefix}ConfigurationPanel extends ActivityConfigurationPanel { - - private final ServiceRegistry serviceRegistry; - - private JTextField fieldString; - private JTextField fieldURI; - - public ${classPrefix}ConfigurationPanel(Activity activity, ServiceRegistry serviceRegistry) { - super(activity); - this.serviceRegistry = serviceRegistry; - initialise(); - } - - protected void initialise() { - // call super.initialise() to initialise the configuration - super.initialise(); - - removeAll(); - setLayout(new GridLayout(0, 2)); - - // FIXME: Create GUI depending on activity configuration bean - JLabel labelString = new JLabel("Example string:"); - add(labelString); - fieldString = new JTextField(20); - add(fieldString); - labelString.setLabelFor(fieldString); - - JLabel labelURI = new JLabel("Example URI:"); - add(labelURI); - fieldURI = new JTextField(25); - add(fieldURI); - labelURI.setLabelFor(fieldURI); - - // Populate fields from activity configuration - fieldString.setText(getProperty("exampleString")); - fieldURI.setText(getProperty("exampleUri")); - } - - /** - * Check that user values in UI are valid - */ - @Override - public boolean checkValues() { - try { - URI.create(fieldURI.getText()); - } catch (IllegalArgumentException ex) { - JOptionPane.showMessageDialog(this, ex.getCause().getMessage(), - "Invalid URI", JOptionPane.ERROR_MESSAGE); - // Not valid, return false - return false; - } - // All valid, return true - return true; - } - - /** - * Set the configuration properties from the UI - */ - @Override - public void noteConfiguration() { - // FIXME: Update bean fields from your UI elements - setProperty("exampleString", fieldString.getText()); - setProperty("exampleUri", fieldURI.getText()); - - configureInputPorts(serviceRegistry); - configureOutputPorts(serviceRegistry); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/config/__classPrefix__ConfigureAction.java ---------------------------------------------------------------------- diff --git a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/config/__classPrefix__ConfigureAction.java b/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/config/__classPrefix__ConfigureAction.java deleted file mode 100644 index c7d5d10..0000000 --- a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/config/__classPrefix__ConfigureAction.java +++ /dev/null @@ -1,49 +0,0 @@ -#set( $symbol_pound = '#' ) -#set( $symbol_dollar = '$' ) -#set( $symbol_escape = '\' ) -package ${package}.ui.config; - -import java.awt.event.ActionEvent; - -import uk.org.taverna.commons.services.ServiceRegistry; -import uk.org.taverna.scufl2.api.activity.Activity; - -import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry; -import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager; -import net.sf.taverna.t2.workbench.edits.EditManager; -import net.sf.taverna.t2.workbench.file.FileManager; -import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog; - -@SuppressWarnings("serial") -public class ${classPrefix}ConfigureAction extends ActivityConfigurationAction { - - private final EditManager editManager; - private final FileManager fileManager; - private final ServiceRegistry serviceRegistry; - - public ${classPrefix}ConfigureAction(Activity activity, - EditManager editManager, FileManager fileManager, - ActivityIconManager activityIconManager, - ServiceDescriptionRegistry serviceDescriptionRegistry, - ServiceRegistry serviceRegistry) { - super(activity, activityIconManager, serviceDescriptionRegistry); - this.editManager = editManager; - this.fileManager = fileManager; - this.serviceRegistry = serviceRegistry; - } - - public void actionPerformed(ActionEvent e) { - ActivityConfigurationDialog currentDialog = getDialog(getActivity()); - if (currentDialog != null) { - currentDialog.toFront(); - return; - } - - ${classPrefix}ConfigurationPanel panel = new ${classPrefix}ConfigurationPanel(getActivity(), serviceRegistry); - ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(getActivity(), panel, editManager); - - setDialog(getActivity(), dialog, fileManager); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/menu/__classPrefix__ConfigureMenuAction.java ---------------------------------------------------------------------- diff --git a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/menu/__classPrefix__ConfigureMenuAction.java b/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/menu/__classPrefix__ConfigureMenuAction.java deleted file mode 100644 index a257a4e..0000000 --- a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/menu/__classPrefix__ConfigureMenuAction.java +++ /dev/null @@ -1,67 +0,0 @@ -#set( $symbol_pound = '#' ) -#set( $symbol_dollar = '$' ) -#set( $symbol_escape = '\' ) -package ${package}.ui.menu; - -import java.net.URI; - -import javax.swing.Action; - -import uk.org.taverna.commons.services.ServiceRegistry; - -import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry; -import net.sf.taverna.t2.ui.menu.ContextualMenuComponent; -import net.sf.taverna.t2.ui.menu.MenuComponent; -import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager; -import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction; -import net.sf.taverna.t2.workbench.edits.EditManager; -import net.sf.taverna.t2.workbench.file.FileManager; - -import ${package}.ui.config.${classPrefix}ConfigureAction; - -public class ${classPrefix}ConfigureMenuAction extends AbstractConfigureActivityMenuAction implements - MenuComponent, ContextualMenuComponent { - - private static final URI ACTIVITY_TYPE = URI - .create("http://example.com/2013/activity/${rootArtifactId}"); - - private EditManager editManager; - private FileManager fileManager; - private ActivityIconManager activityIconManager; - private ServiceDescriptionRegistry serviceDescriptionRegistry; - private ServiceRegistry serviceRegistry; - - public ${classPrefix}ConfigureMenuAction() { - super(ACTIVITY_TYPE); - } - - @Override - protected Action createAction() { - Action result = new ${classPrefix}ConfigureAction(findActivity(), editManager, fileManager, - activityIconManager, serviceDescriptionRegistry, serviceRegistry); - result.putValue(Action.NAME, "Configure example service"); - addMenuDots(result); - return result; - } - - public void setEditManager(EditManager editManager) { - this.editManager = editManager; - } - - public void setFileManager(FileManager fileManager) { - this.fileManager = fileManager; - } - - public void setActivityIconManager(ActivityIconManager activityIconManager) { - this.activityIconManager = activityIconManager; - } - - public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) { - this.serviceDescriptionRegistry = serviceDescriptionRegistry; - } - - public void setServiceRegistry(ServiceRegistry serviceRegistry) { - this.serviceRegistry = serviceRegistry; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/serviceprovider/__classPrefix__ServiceDesc.java ---------------------------------------------------------------------- diff --git a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/serviceprovider/__classPrefix__ServiceDesc.java b/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/serviceprovider/__classPrefix__ServiceDesc.java deleted file mode 100644 index 5de7bc4..0000000 --- a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/serviceprovider/__classPrefix__ServiceDesc.java +++ /dev/null @@ -1,106 +0,0 @@ -#set( $symbol_pound = '#' ) -#set( $symbol_dollar = '$' ) -#set( $symbol_escape = '\' ) -package ${package}.ui.serviceprovider; - -import java.net.URI; -import java.util.Arrays; -import java.util.List; - -import javax.swing.Icon; - -import uk.org.taverna.scufl2.api.configurations.Configuration; - -import com.fasterxml.jackson.databind.node.ObjectNode; - -import net.sf.taverna.t2.servicedescriptions.ServiceDescription; - -public class ${classPrefix}ServiceDesc extends ServiceDescription { - - private static final URI ACTIVITY_TYPE = URI - .create("http://example.com/2013/activity/${rootArtifactId}"); - - // FIXME: Replace example fields and getters/setters with any required - // and optional fields. (All fields are searchable in the Service palette, - // for instance try a search for exampleString:3) - private String exampleString; - private String exampleUri; - - public String getExampleString() { - return exampleString; - } - public void setExampleString(String exampleString) { - this.exampleString = exampleString; - } - - public String getExampleUri() { - return exampleUri; - } - public void setExampleUri(String exampleUri) { - this.exampleUri = exampleUri; - } - - /** - * The type of Activity which should be instantiated when adding a service - * for this description - */ - @Override - public URI getActivityType() { - return ACTIVITY_TYPE; - } - - /** - * The configuration which is to be used for configuring the instantiated activity. - * Making this configuration will typically require some of the fields set on this service - * description, like an endpoint URL or method name. - * - */ - @Override - public Configuration getActivityConfiguration() { - Configuration configuration = new Configuration(); - configuration.setType(ACTIVITY_TYPE.resolve("#Config")); - ObjectNode json = configuration.getJsonAsObjectNode(); - json.put("exampleString", exampleString); - json.put("exampleUri", exampleUri); - return configuration; - } - - /** - * An icon to represent this service description in the service palette. - */ - @Override - public Icon getIcon() { - return ${classPrefix}ServiceIcon.getIcon(); - } - - /** - * The display name that will be shown in service palette and will - * be used as a template for processor name when added to workflow. - */ - @Override - public String getName() { - return exampleString; - } - - /** - * The path to this service description in the service palette. Folders - * will be created for each element of the returned path. - */ - @Override - public List<String> getPath() { - // For deeper paths you may return several strings - return Arrays.asList("${classPrefix}s " + exampleUri); - } - - /** - * Return a list of data values uniquely identifying this service - * description (to avoid duplicates). Include only primary key like fields, - * ie. ignore descriptions, icons, etc. - */ - @Override - protected List<? extends Object> getIdentifyingData() { - // FIXME: Use your fields instead of example fields - return Arrays.<Object>asList(exampleString, exampleUri); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/serviceprovider/__classPrefix__ServiceIcon.java ---------------------------------------------------------------------- diff --git a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/serviceprovider/__classPrefix__ServiceIcon.java b/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/serviceprovider/__classPrefix__ServiceIcon.java deleted file mode 100644 index 023edcb..0000000 --- a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/serviceprovider/__classPrefix__ServiceIcon.java +++ /dev/null @@ -1,40 +0,0 @@ -#set( $symbol_pound = '#' ) -#set( $symbol_dollar = '$' ) -#set( $symbol_escape = '\' ) -package ${package}.ui.serviceprovider; - -import java.net.URI; - -import javax.swing.Icon; -import javax.swing.ImageIcon; - -import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI; - -public class ${classPrefix}ServiceIcon implements ActivityIconSPI { - - private static final URI ACTIVITY_TYPE = URI - .create("http://example.com/2013/activity/${rootArtifactId}"); - - private static Icon icon; - - @Override - public int canProvideIconScore(URI activityType) { - if (ACTIVITY_TYPE.equals(activityType)) { - return DEFAULT_ICON + 1; - } - return NO_ICON; - } - - @Override - public Icon getIcon(URI activityType) { - return getIcon(); - } - - public static Icon getIcon() { - if (icon == null) { - icon = new ImageIcon(${classPrefix}ServiceIcon.class.getResource("/exampleIcon.png")); - } - return icon; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/serviceprovider/__classPrefix__ServiceProvider.java ---------------------------------------------------------------------- diff --git a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/serviceprovider/__classPrefix__ServiceProvider.java b/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/serviceprovider/__classPrefix__ServiceProvider.java deleted file mode 100644 index 8a30c6f..0000000 --- a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/serviceprovider/__classPrefix__ServiceProvider.java +++ /dev/null @@ -1,75 +0,0 @@ -#set( $symbol_pound = '#' ) -#set( $symbol_dollar = '$' ) -#set( $symbol_escape = '\' ) -package ${package}.ui.serviceprovider; - -import java.net.URI; -import java.util.ArrayList; -import java.util.List; - -import javax.swing.Icon; - -import net.sf.taverna.t2.servicedescriptions.ServiceDescription; -import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider; - -public class ${classPrefix}ServiceProvider implements ServiceDescriptionProvider { - - private static final URI providerId = URI - .create("http://example.com/2011/service-provider/${rootArtifactId}"); - - /** - * Do the actual search for services. Return using the callBack parameter. - */ - public void findServiceDescriptionsAsync( - FindServiceDescriptionsCallBack callBack) { - // Use callback.status() for long-running searches - // callBack.status("Resolving example services"); - - List<ServiceDescription> results = new ArrayList<ServiceDescription>(); - - // FIXME: Implement the actual service search/lookup instead - // of dummy for-loop - for (int i = 1; i <= 5; i++) { - ${classPrefix}ServiceDesc service = new ${classPrefix}ServiceDesc(); - // Populate the service description bean - service.setExampleString("Example " + i); - service.setExampleUri("http://localhost:8192/service"); - - // Optional: set description - service.setDescription("Service example number " + i); - results.add(service); - } - - // partialResults() can also be called several times from inside - // for-loop if the full search takes a long time - callBack.partialResults(results); - - // No more results will be coming - callBack.finished(); - } - - /** - * Icon for service provider - */ - public Icon getIcon() { - return ${classPrefix}ServiceIcon.getIcon(); - } - - /** - * Name of service provider, appears in right click for 'Remove service - * provider' - */ - public String getName() { - return "My example service"; - } - - @Override - public String toString() { - return getName(); - } - - public String getId() { - return providerId.toASCIIString(); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/view/__classPrefix__ActivityContextViewFactory.java ---------------------------------------------------------------------- diff --git a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/view/__classPrefix__ActivityContextViewFactory.java b/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/view/__classPrefix__ActivityContextViewFactory.java deleted file mode 100644 index de87ef3..0000000 --- a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/java/ui/view/__classPrefix__ActivityContextViewFactory.java +++ /dev/null @@ -1,62 +0,0 @@ -#set( $symbol_pound = '#' ) -#set( $symbol_dollar = '$' ) -#set( $symbol_escape = '\' ) -package ${package}.ui.view; - -import java.net.URI; -import java.util.Arrays; -import java.util.List; - -import uk.org.taverna.commons.services.ServiceRegistry; -import uk.org.taverna.scufl2.api.activity.Activity; - -import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry; -import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager; -import net.sf.taverna.t2.workbench.edits.EditManager; -import net.sf.taverna.t2.workbench.file.FileManager; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory; - -public class ${classPrefix}ActivityContextViewFactory implements ContextualViewFactory<Activity> { - - private static final URI ACTIVITY_TYPE = URI - .create("http://example.com/2013/activity/${rootArtifactId}"); - - private EditManager editManager; - private FileManager fileManager; - private ActivityIconManager activityIconManager; - private ServiceDescriptionRegistry serviceDescriptionRegistry; - private ServiceRegistry serviceRegistry; - - @Override - public boolean canHandle(Object object) { - return object instanceof Activity && ((Activity) object).getType().equals(ACTIVITY_TYPE); - } - - @Override - public List<ContextualView> getViews(Activity selection) { - return Arrays.<ContextualView>asList(new ${classPrefix}ContextualView(selection, editManager, - fileManager, activityIconManager, serviceDescriptionRegistry, serviceRegistry)); - } - - public void setEditManager(EditManager editManager) { - this.editManager = editManager; - } - - public void setFileManager(FileManager fileManager) { - this.fileManager = fileManager; - } - - public void setActivityIconManager(ActivityIconManager activityIconManager) { - this.activityIconManager = activityIconManager; - } - - public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) { - this.serviceDescriptionRegistry = serviceDescriptionRegistry; - } - - public void setServiceRegistry(ServiceRegistry serviceRegistry) { - this.serviceRegistry = serviceRegistry; - } - -}
