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Posted to commits@taverna.apache.org by re...@apache.org on 2015/03/23 17:38:35 UTC
[51/51] [partial] incubator-taverna-engine git commit:
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/5f1ddb71
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/tree/5f1ddb71
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/diff/5f1ddb71
Branch: refs/heads/master
Commit: 5f1ddb7158e6e415b3a215e76eb2178041f0e99d
Parents: a368539
Author: redmitry <re...@84.88.50.62>
Authored: Mon Mar 23 17:37:01 2015 +0100
Committer: redmitry <re...@84.88.50.62>
Committed: Mon Mar 23 17:37:01 2015 +0100
----------------------------------------------------------------------
.../resources/META-INF/spring/context-osgi.xml | 22 +-
.../resources/META-INF/spring/context-osgi.xml | 6 +-
.../activities/testutils/ActivityInvoker.java | 250 ----
.../t2/activities/testutils/DummyCallback.java | 106 --
.../activities/testutils/LocationConstants.java | 31 -
.../activities/testutils/ActivityInvoker.java | 249 ++++
.../activities/testutils/DummyCallback.java | 105 ++
.../activities/testutils/LocationConstants.java | 30 +
.../context-parts/componentservices.xml | 32 +-
.../resources/context-parts/dao_hibernate.xml | 28 +-
.../dao_hibernate_transactional.xml | 28 +-
.../resources/context-parts/dao_inmemory.xml | 12 +-
.../context-parts/hibernateprops_derby.xml | 4 +-
.../resources/context-parts/raven_local.xml | 4 +-
.../context-parts/referenceservice.xml | 16 +-
.../capability/api/ActivityService.java | 2 +-
.../capability/api/DispatchLayerService.java | 2 +-
.../activity/impl/ActivityServiceImpl.java | 14 +-
.../dispatch/impl/DispatchLayerServiceImpl.java | 6 +-
.../spring/taverna-capability-context-osgi.xml | 8 +-
.../impl/CredentialManagerImpl.java | 6 +-
.../spring/credential-manager-impl-context.xml | 2 +-
.../impl/CredentialManagerImplIT.java | 4 +-
.../impl/CredentialManagerImplTest.java | 30 +-
.../impl/HTTPAuthenticatorIT.java | 2 +-
.../credentialmanager/CredentialManager.java | 2 +-
.../credentialmanager/KeystoreChangedEvent.java | 2 +-
...rity.credentialmanager.CredentialProviderSPI | 1 -
...rity.credentialmanager.CredentialProviderSPI | 1 +
.../database/DatabaseConfiguration.java | 123 ++
.../configuration/database/DatabaseManager.java | 44 +
.../database/DatabaseConfiguration.java | 124 --
.../configuration/database/DatabaseManager.java | 45 -
.../impl/DatabaseConfigurationImpl.java | 251 ++++
.../database/impl/DatabaseManagerImpl.java | 174 +++
.../impl/DatabaseConfigurationImpl.java | 252 ----
.../database/impl/DatabaseManagerImpl.java | 155 ---
.../META-INF/spring/database-context-osgi.xml | 4 +-
.../activities/dataflow/DataflowActivity.java | 168 ---
.../dataflow/DataflowActivityFactory.java | 81 --
.../dataflow/DataflowActivityHealthChecker.java | 42 -
.../activities/dataflow/DataflowActivity.java | 167 +++
.../dataflow/DataflowActivityFactory.java | 80 ++
.../dataflow/DataflowActivityHealthChecker.java | 41 +
...averna.t2.workflowmodel.health.HealthChecker | 2 +-
.../spring/dataflow-activity-context-osgi.xml | 6 +-
.../spring/dataflow-activity-context.xml | 4 +-
.../dataflow/DataflowActivityFactoryTest.java | 65 -
.../dataflow/DataflowActivityTest.java | 98 --
.../dataflow/DataflowActivityFactoryTest.java | 65 +
.../dataflow/DataflowActivityTest.java | 97 ++
.../execution/api/AbstractExecution.java | 138 ++
.../api/AbstractExecutionEnvironment.java | 78 ++
.../execution/api/AbstractExecutionService.java | 138 ++
.../platform/execution/api/Execution.java | 103 ++
.../execution/api/ExecutionEnvironment.java | 128 ++
.../api/ExecutionEnvironmentService.java | 51 +
.../execution/api/ExecutionService.java | 148 +++
.../api/InvalidExecutionIdException.java | 47 +
.../execution/api/InvalidWorkflowException.java | 47 +
.../execution/api/WorkflowCompiler.java | 55 +
.../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 | 127 ++
.../execution/api/AbstractExecutionTest.java | 128 --
.../impl/hadoop/CrossProductInputFormat.java | 107 ++
.../impl/hadoop/CrossProductInputSplit.java | 87 ++
.../impl/hadoop/CrossProductRecordReader.java | 131 ++
.../execution/impl/hadoop/CrossProductTest.java | 115 ++
.../execution/impl/hadoop/DotProductTest.java | 105 ++
.../impl/hadoop/TavernaInputFormat.java | 51 +
.../impl/hadoop/TavernaInputSplit.java | 68 +
.../execution/impl/hadoop/TavernaMapper.java | 94 ++
.../impl/hadoop/TavernaRecordReader.java | 105 ++
.../execution/impl/hadoop/TavernaReducer.java | 43 +
.../platform/execution/impl/hadoop/Test.java | 68 +
.../impl/hadoop/TextArrayWritable.java | 30 +
.../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 -
.../impl/ExecutionEnvironmentServiceImpl.java | 353 +++++
.../impl/ExecutionEnvironmentServiceImpl.java | 354 -----
.../META-INF/spring/execution-context-osgi.xml | 4 +-
.../META-INF/spring/execution-context.xml | 2 +-
.../execution/impl/local/LocalExecution.java | 242 ++++
.../impl/local/LocalExecutionEnvironment.java | 86 ++
.../impl/local/LocalExecutionMonitor.java | 547 ++++++++
.../impl/local/LocalExecutionService.java | 148 +++
.../impl/local/LocalProcessorReport.java | 160 +++
.../execution/impl/local/StaticProperty.java | 65 +
.../impl/local/T2ReferenceConverter.java | 57 +
.../impl/local/WorkflowToDataflowMapper.java | 526 ++++++++
.../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 | 8 +-
.../META-INF/spring/execution-local-context.xml | 2 +-
.../impl/local/LocalExecutionTest.java | 165 +++
.../impl/local/LocalExecutionTest.java | 166 ---
.../src/test/resources/t2flow/beanshell.t2flow | 76 +-
.../src/test/resources/t2flow/in-out.t2flow | 18 +-
.../execution/impl/remote/RemoteExecution.java | 95 ++
.../impl/remote/RemoteExecutionService.java | 59 +
.../execution/impl/remote/RemoteExecution.java | 96 --
.../impl/remote/RemoteExecutionService.java | 60 -
.../spring/execution-remote-context-osgi.xml | 2 +-
.../spring/execution-remote-context.xml | 2 +-
.../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/lang/observer/MultiCaster.java | 92 ++
.../taverna/lang/observer/Observable.java | 55 +
.../apache/taverna/lang/observer/Observer.java | 43 +
.../lang/observer/SwingAwareObserver.java | 50 +
.../taverna/lang/observer/package-info.java | 72 +
.../taverna/t2/lang/observer/ObserverTest.java | 133 --
.../taverna/lang/observer/ObserverTest.java | 128 ++
.../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.java | 88 ++
.../reference/ContextualizedT2Reference.java | 46 +
.../apache/taverna/reference/DaoException.java | 46 +
.../taverna/reference/DereferenceException.java | 47 +
.../apache/taverna/reference/ErrorDocument.java | 55 +
.../taverna/reference/ErrorDocumentDao.java | 63 +
.../taverna/reference/ErrorDocumentService.java | 151 +++
.../reference/ErrorDocumentServiceCallback.java | 46 +
.../ErrorDocumentServiceException.java | 47 +
.../reference/ExternalReferenceBuilderSPI.java | 89 ++
.../ExternalReferenceConstructionException.java | 49 +
.../taverna/reference/ExternalReferenceSPI.java | 131 ++
.../ExternalReferenceTranslatorSPI.java | 95 ++
.../ExternalReferenceValidationException.java | 49 +
.../apache/taverna/reference/Identified.java | 35 +
.../taverna/reference/IdentifiedList.java | 45 +
.../org/apache/taverna/reference/ListDao.java | 66 +
.../apache/taverna/reference/ListService.java | 143 ++
.../taverna/reference/ListServiceCallback.java | 46 +
.../taverna/reference/ListServiceException.java | 47 +
.../taverna/reference/ReferenceContext.java | 65 +
.../taverna/reference/ReferenceService.java | 293 ++++
.../ReferenceServiceCacheProvider.java | 51 +
.../reference/ReferenceServiceException.java | 46 +
.../ReferenceServiceResolutionCallback.java | 46 +
.../apache/taverna/reference/ReferenceSet.java | 52 +
.../ReferenceSetAugmentationException.java | 46 +
.../reference/ReferenceSetAugmentor.java | 91 ++
.../ReferenceSetAugmentorCallback.java | 52 +
.../taverna/reference/ReferenceSetDao.java | 81 ++
.../taverna/reference/ReferenceSetService.java | 180 +++
.../reference/ReferenceSetServiceCallback.java | 46 +
.../reference/ReferenceSetServiceException.java | 47 +
.../taverna/reference/ReferencedDataNature.java | 44 +
.../reference/StackTraceElementBean.java | 53 +
.../reference/StreamToValueConverterSPI.java | 47 +
.../apache/taverna/reference/T2Reference.java | 101 ++
.../taverna/reference/T2ReferenceGenerator.java | 80 ++
.../taverna/reference/T2ReferenceType.java | 46 +
.../ValueCarryingExternalReference.java | 43 +
.../ValueToReferenceConversionException.java | 47 +
.../reference/ValueToReferenceConverterSPI.java | 64 +
.../taverna/reference/WorkflowRunIdEntity.java | 43 +
.../annotations/DeleteIdentifiedOperation.java | 37 +
.../annotations/GetIdentifiedOperation.java | 37 +
.../annotations/PutIdentifiedOperation.java | 37 +
.../taverna/reference/annotations/package.html | 4 +
.../reference/h3/HibernateComponentClass.java | 37 +
.../reference/h3/HibernateMappedEntity.java | 38 +
.../apache/taverna/reference/h3/package.html | 8 +
.../org/apache/taverna/reference/package.html | 43 +
.../reference/AbstractExternalReference.hbm.xml | 15 -
.../reference/AbstractExternalReference.hbm.xml | 12 +
.../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 -
.../platform/spring/jdbc/TemporaryJDBC.java | 74 ++
.../taverna/platform/spring/jdbc/package.html | 6 +
.../reference/impl/AbstractEntityImpl.java | 65 +
.../impl/AbstractErrorDocumentServiceImpl.java | 118 ++
.../reference/impl/AbstractListServiceImpl.java | 99 ++
.../impl/AbstractReferenceServiceImpl.java | 170 +++
.../impl/AbstractReferenceSetServiceImpl.java | 159 +++
.../reference/impl/AbstractServiceImpl.java | 43 +
.../impl/AbstractT2ReferenceGenerator.java | 110 ++
.../taverna/reference/impl/CacheAspect.java | 126 ++
.../impl/ContextualizedT2ReferenceImpl.java | 60 +
.../reference/impl/EmptyReferenceContext.java | 45 +
.../reference/impl/ErrorDocumentImpl.java | 119 ++
.../impl/ErrorDocumentServiceImpl.java | 162 +++
.../impl/HibernateErrorDocumentDao.java | 153 +++
.../reference/impl/HibernateListDao.java | 150 +++
.../impl/HibernateReferenceSetDao.java | 197 +++
.../reference/impl/IdentifiedArrayList.java | 252 ++++
.../impl/InMemoryErrorDocumentDao.java | 69 +
.../taverna/reference/impl/InMemoryListDao.java | 68 +
.../reference/impl/InMemoryReferenceSetDao.java | 71 +
.../taverna/reference/impl/ListServiceImpl.java | 135 ++
.../reference/impl/ReferenceServiceImpl.java | 730 ++++++++++
.../impl/ReferenceSetAugmentorImpl.java | 461 +++++++
.../reference/impl/ReferenceSetImpl.java | 122 ++
.../reference/impl/ReferenceSetServiceImpl.java | 152 +++
.../reference/impl/SimpleCacheProviderImpl.java | 56 +
.../impl/SimpleT2ReferenceGenerator.java | 62 +
.../impl/StackTraceElementBeanImpl.java | 76 ++
.../taverna/reference/impl/T2ReferenceImpl.java | 287 ++++
.../reference/impl/T2ReferenceListImpl.java | 74 ++
.../TransactionalHibernateErrorDocumentDao.java | 154 +++
.../impl/TransactionalHibernateListDao.java | 153 +++
.../TransactionalHibernateReferenceSetDao.java | 197 +++
.../taverna/reference/impl/TranslationPath.java | 285 ++++
.../impl/UUIDT2ReferenceGenerator.java | 55 +
.../reference/impl/WriteQueueAspect.java | 141 ++
.../apache/taverna/reference/impl/package.html | 5 +
...erna.t2.reference.h3.HibernateComponentClass | 2 -
...averna.t2.reference.h3.HibernateMappedEntity | 3 -
...taverna.reference.h3.HibernateComponentClass | 2 +
...e.taverna.reference.h3.HibernateMappedEntity | 3 +
.../src/main/resources/META-INF/spring.handlers | 2 +-
.../spring/hibernate-reference-impl-context.xml | 22 +-
.../spring/in-memory-reference-impl-context.xml | 14 +-
.../spring/reference-impl-context-osgi.xml | 14 +-
.../META-INF/spring/reference-impl-context.xml | 4 +-
.../t2/reference/impl/ErrorDocumentImpl.hbm.xml | 45 -
.../t2/reference/impl/ReferenceSetImpl.hbm.xml | 32 -
.../reference/impl/T2ReferenceListImpl.hbm.xml | 37 -
.../reference/impl/ErrorDocumentImpl.hbm.xml | 39 +
.../reference/impl/ReferenceSetImpl.hbm.xml | 24 +
.../reference/impl/T2ReferenceListImpl.hbm.xml | 32 +
.../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 -
.../platform/spring/jdbc/TemporaryJDBCTest.java | 59 +
.../taverna/reference/impl/AppContextSetup.java | 50 +
.../reference/impl/DatabaseSetupTest.java | 139 ++
.../reference/impl/ErrorDocumentDaoTest.java | 170 +++
.../impl/ErrorDocumentServiceTest.java | 107 ++
.../taverna/reference/impl/ListDaoTest.java | 140 ++
.../taverna/reference/impl/ListServiceTest.java | 110 ++
.../reference/impl/ReferenceContextImpl.java | 49 +
.../reference/impl/ReferenceSetDaoTest.java | 124 ++
.../reference/impl/ReferenceSetServiceTest.java | 111 ++
.../reference/impl/TranslationPathTest.java | 65 +
.../src/test/resources/log4j.xml | 4 +-
.../resources/vanillaHibernateAppContext.xml | 16 +-
.../vanillaHibernateTransactionalAppContext.xml | 16 +-
.../resources/vanillaInMemoryAppContext.xml | 6 +-
.../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 --
.../taverna/t2referencetest/BlueReference.java | 128 ++
.../t2referencetest/DummyReferenceSet.java | 51 +
.../taverna/t2referencetest/GreenBuilder.java | 106 ++
.../taverna/t2referencetest/GreenReference.java | 128 ++
.../taverna/t2referencetest/GreenToRed.java | 64 +
.../taverna/t2referencetest/RedReference.java | 128 ++
.../t2referencetest/YellowReference.java | 129 ++
...rna.t2.reference.ExternalReferenceBuilderSPI | 2 -
...sf.taverna.t2.reference.ExternalReferenceSPI | 5 -
....t2.reference.ExternalReferenceTranslatorSPI | 2 -
...averna.reference.ExternalReferenceBuilderSPI | 2 +
...pache.taverna.reference.ExternalReferenceSPI | 5 +
...rna.reference.ExternalReferenceTranslatorSPI | 2 +
.../reference-testhelpers-context-osgi.xml | 12 +-
.../spring/reference-testhelpers-context.xml | 12 +-
.../t2referencetest/BlueReference.hbm.xml | 16 -
.../t2referencetest/GreenReference.hbm.xml | 16 -
.../t2referencetest/RedReference.hbm.xml | 16 -
.../t2referencetest/YellowReference.hbm.xml | 16 -
.../t2referencetest/BlueReference.hbm.xml | 11 +
.../t2referencetest/GreenReference.hbm.xml | 11 +
.../t2referencetest/RedReference.hbm.xml | 11 +
.../t2referencetest/YellowReference.hbm.xml | 11 +
.../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 -
.../impl/external/file/FileReference.java | 210 +++
.../impl/external/file/FileToFileReference.java | 60 +
.../reference/impl/external/file/package.html | 4 +
.../impl/external/http/HttpReference.java | 216 +++
.../impl/external/http/UrlToHttpReference.java | 61 +
.../reference/impl/external/http/package.html | 3 +
.../object/BooleanToStringReference.java | 52 +
.../object/ByteArrayToByteArrayReference.java | 52 +
.../object/CharacterToStringReference.java | 52 +
.../object/InlineByteArrayReference.java | 92 ++
.../object/InlineByteArrayReferenceBuilder.java | 66 +
.../InlineByteToInlineStringTranslator.java | 70 +
.../external/object/InlineStringReference.java | 132 ++
.../object/InlineStringReferenceBuilder.java | 75 ++
.../InlineStringToInlineByteTranslator.java | 59 +
.../object/NumberToStringReference.java | 51 +
.../object/StreamToBooleanConverter.java | 45 +
.../object/StreamToByteArrayConverter.java | 61 +
.../object/StreamToDoubleConverter.java | 45 +
.../object/StreamToIntegerConverter.java | 45 +
.../object/StreamToStringConverter.java | 79 ++
.../StreamToVMObjectReferenceConverter.java | 55 +
.../object/StringToStringReference.java | 51 +
.../impl/external/object/VMObjectReference.java | 110 ++
.../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 -
...averna.reference.ExternalReferenceBuilderSPI | 3 +
...pache.taverna.reference.ExternalReferenceSPI | 6 +
...rna.reference.ExternalReferenceTranslatorSPI | 3 +
....taverna.reference.StreamToValueConverterSPI | 7 +
...verna.reference.ValueToReferenceConverterSPI | 8 +
.../reference-core-extensions-context-osgi.xml | 40 +-
.../reference-core-extensions-context.xml | 40 +-
.../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 -
.../impl/external/file/FileReference.hbm.xml | 13 +
.../impl/external/http/HttpReference.hbm.xml | 11 +
.../object/InlineByteArrayReference.hbm.xml | 11 +
.../object/InlineStringReference.hbm.xml | 11 +
.../external/object/VMObjectReference.hbm.xml | 11 +
.../external/object/ByteArrayToStringTest.java | 91 --
.../external/object/ByteArrayToStringTest.java | 110 ++
.../taverna/platform/report/ActivityReport.java | 48 +
.../taverna/platform/report/Invocation.java | 305 +++++
.../platform/report/ProcessorReport.java | 163 +++
.../taverna/platform/report/ReportListener.java | 31 +
.../apache/taverna/platform/report/State.java | 29 +
.../taverna/platform/report/StatusReport.java | 372 ++++++
.../taverna/platform/report/WorkflowReport.java | 168 +++
.../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 | 169 ---
.../platform/report/StatusReportTest.java | 244 ++++
.../platform/report/StatusReportTest.java | 245 ----
.../platform/run/api/InvalidRunIdException.java | 45 +
.../taverna/platform/run/api/RunProfile.java | 215 +++
.../platform/run/api/RunProfileException.java | 46 +
.../taverna/platform/run/api/RunService.java | 254 ++++
.../platform/run/api/RunStateException.java | 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 | 232 ++++
.../platform/run/api/RunProfileTest.java | 233 ----
.../apache/taverna/platform/run/impl/Run.java | 278 ++++
.../platform/run/impl/RunServiceImpl.java | 267 ++++
.../platform/run/impl/WorkflowReportJSON.java | 347 +++++
.../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 | 4 +-
.../resources/META-INF/spring/run-context.xml | 2 +-
.../platform/run/impl/DummyWorkflowReport.java | 131 ++
.../taverna/platform/run/impl/RunTest.java | 69 +
.../run/impl/WorkflowReportJSONTest.java | 285 ++++
.../platform/run/impl/DummyWorkflowReport.java | 131 --
.../org/taverna/platform/run/impl/RunTest.java | 69 -
.../run/impl/WorkflowReportJSONTest.java | 288 ----
.../services/ActivityTypeNotFoundException.java | 46 +
.../services/InvalidConfigurationException.java | 46 +
.../commons/services/ServiceRegistry.java | 88 ++
.../services/ActivityTypeNotFoundException.java | 47 -
.../services/InvalidConfigurationException.java | 47 -
.../commons/services/ServiceRegistry.java | 89 --
.../services/impl/ServiceRegistryImpl.java | 91 ++
.../services/impl/ServiceRegistryImpl.java | 92 --
.../spring/taverna-services-context-osgi.xml | 2 +-
.../spring/taverna-services-context.xml | 2 +-
.../stringconstant/StringConstantActivity.java | 119 --
.../StringConstantActivityFactory.java | 81 --
.../StringConstantActivityHealthChecker.java | 58 -
.../StringConstantConfigurationBean.java | 45 -
.../t2/activities/stringconstant/package.html | 3 -
.../stringconstant/StringConstantActivity.java | 118 ++
.../StringConstantActivityFactory.java | 80 ++
.../StringConstantActivityHealthChecker.java | 57 +
.../StringConstantConfigurationBean.java | 44 +
.../activities/stringconstant/package.html | 3 +
...averna.t2.workflowmodel.health.HealthChecker | 1 -
...e.taverna.workflowmodel.health.HealthChecker | 1 +
.../stringconstant-activity-context-osgi.xml | 6 +-
.../spring/stringconstant-activity-context.xml | 4 +-
.../StringConstantActivityFactoryTest.java | 64 -
.../StringConstantActivityTest.java | 68 -
.../StringConstantActivityFactoryTest.java | 63 +
.../StringConstantActivityTest.java | 58 +
.../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 -----------
.../annotation/AbstractAnnotatedThing.java | 163 +++
.../apache/taverna/annotation/Annotated.java | 78 ++
.../taverna/annotation/AnnotationAssertion.java | 51 +
.../taverna/annotation/AnnotationBeanSPI.java | 31 +
.../taverna/annotation/AnnotationChain.java | 50 +
.../annotation/AnnotationPerspective.java | 61 +
.../taverna/annotation/AnnotationRole.java | 50 +
.../taverna/annotation/AnnotationSourceSPI.java | 34 +
.../apache/taverna/annotation/AppliesTo.java | 52 +
.../apache/taverna/annotation/Curateable.java | 71 +
.../taverna/annotation/CurationEvent.java | 51 +
.../annotation/CurationEventBeanSPI.java | 34 +
.../taverna/annotation/CurationEventType.java | 42 +
.../taverna/annotation/HierarchyRole.java | 39 +
.../taverna/annotation/HierarchyTraversal.java | 73 +
.../org/apache/taverna/annotation/Person.java | 35 +
.../AbstractNumericRangeAssertion.java | 63 +
.../AbstractNumericValueAssertion.java | 53 +
.../AbstractTextualValueAssertion.java | 52 +
.../annotation/annotationbeans/Author.java | 43 +
.../annotationbeans/DescriptiveTitle.java | 41 +
.../annotationbeans/DocumentationUrl.java | 57 +
.../annotationbeans/ExampleValue.java | 42 +
.../annotationbeans/FreeTextDescription.java | 47 +
.../annotationbeans/HostInstitution.java | 41 +
.../IdentificationAssertion.java | 54 +
.../annotation/annotationbeans/MimeType.java | 59 +
.../annotation/annotationbeans/Optional.java | 43 +
.../annotationbeans/SemanticAnnotation.java | 67 +
.../org/apache/taverna/annotation/package.html | 17 +
.../apache/taverna/facade/FacadeListener.java | 48 +
.../apache/taverna/facade/ResultListener.java | 42 +
.../taverna/facade/WorkflowInstanceFacade.java | 236 ++++
.../taverna/facade/WorkflowRunCancellation.java | 45 +
.../java/org/apache/taverna/facade/package.html | 24 +
.../apache/taverna/invocation/Completion.java | 106 ++
.../org/apache/taverna/invocation/Event.java | 167 +++
.../taverna/invocation/InvocationContext.java | 43 +
.../invocation/IterationInternalEvent.java | 102 ++
.../invocation/ProcessIdentifierException.java | 47 +
.../taverna/invocation/TokenOrderException.java | 48 +
.../apache/taverna/invocation/TreeCache.java | 199 +++
.../taverna/invocation/WorkflowDataToken.java | 90 ++
.../org/apache/taverna/invocation/package.html | 6 +
.../apache/taverna/monitor/MonitorManager.java | 377 ++++++
.../org/apache/taverna/monitor/MonitorNode.java | 75 ++
.../taverna/monitor/MonitorableProperty.java | 54 +
.../monitor/NoSuchPropertyException.java | 49 +
.../taverna/monitor/SteerableProperty.java | 36 +
.../org/apache/taverna/monitor/package.html | 36 +
.../provenance/item/AbstractProvenanceItem.java | 96 ++
.../provenance/item/ActivityProvenanceItem.java | 61 +
.../provenance/item/DataProvenanceItem.java | 62 +
.../provenance/item/DataflowRunComplete.java | 60 +
.../provenance/item/ErrorProvenanceItem.java | 70 +
.../item/InputDataProvenanceItem.java | 48 +
.../item/InvocationStartedProvenanceItem.java | 60 +
.../item/IterationProvenanceItem.java | 107 ++
.../item/OutputDataProvenanceItem.java | 48 +
.../provenance/item/ProcessProvenanceItem.java | 88 ++
.../item/ProcessorProvenanceItem.java | 56 +
.../taverna/provenance/item/ProvenanceItem.java | 102 ++
.../item/WorkflowDataProvenanceItem.java | 100 ++
.../provenance/item/WorkflowProvenanceItem.java | 100 ++
.../provenance/reporter/ProvenanceReporter.java | 91 ++
.../provenance/vocabulary/SharedVocabulary.java | 33 +
.../taverna/utility/TreeModelAdapter.java | 173 +++
.../apache/taverna/utility/TypedTreeModel.java | 116 ++
.../taverna/utility/TypedTreeModelEvent.java | 150 +++
.../taverna/utility/TypedTreeModelListener.java | 81 ++
.../org/apache/taverna/utility/package.html | 5 +
.../apache/taverna/visit/DataflowCollation.java | 51 +
.../taverna/visit/HierarchyTraverser.java | 362 +++++
.../org/apache/taverna/visit/VisitKind.java | 35 +
.../org/apache/taverna/visit/VisitReport.java | 362 +++++
.../java/org/apache/taverna/visit/Visitor.java | 63 +
.../workflowmodel/AbstractOutputPort.java | 42 +
.../taverna/workflowmodel/AbstractPort.java | 53 +
.../taverna/workflowmodel/CompoundEdit.java | 114 ++
.../apache/taverna/workflowmodel/Condition.java | 51 +
.../taverna/workflowmodel/Configurable.java | 54 +
.../workflowmodel/ConfigurationException.java | 61 +
.../taverna/workflowmodel/ControlBoundary.java | 46 +
.../apache/taverna/workflowmodel/Dataflow.java | 172 +++
.../workflowmodel/DataflowInputPort.java | 51 +
.../workflowmodel/DataflowOutputPort.java | 61 +
.../taverna/workflowmodel/DataflowPort.java | 33 +
.../workflowmodel/DataflowValidationReport.java | 98 ++
.../apache/taverna/workflowmodel/Datalink.java | 55 +
.../org/apache/taverna/workflowmodel/Edit.java | 64 +
.../taverna/workflowmodel/EditException.java | 42 +
.../org/apache/taverna/workflowmodel/Edits.java | 831 ++++++++++++
.../EventForwardingOutputPort.java | 45 +
.../workflowmodel/EventHandlingInputPort.java | 40 +
.../workflowmodel/FailureTransmitter.java | 33 +
.../workflowmodel/FilteringInputPort.java | 51 +
.../apache/taverna/workflowmodel/InputPort.java | 29 +
.../workflowmodel/InvalidDataflowException.java | 62 +
.../org/apache/taverna/workflowmodel/Merge.java | 62 +
.../taverna/workflowmodel/MergeInputPort.java | 51 +
.../taverna/workflowmodel/MergeOutputPort.java | 34 +
.../apache/taverna/workflowmodel/MergePort.java | 34 +
.../workflowmodel/NamedWorkflowEntity.java | 44 +
.../taverna/workflowmodel/NamingException.java | 46 +
.../taverna/workflowmodel/OrderedPair.java | 84 ++
.../taverna/workflowmodel/OutputPort.java | 45 +
.../org/apache/taverna/workflowmodel/Port.java | 34 +
.../apache/taverna/workflowmodel/Processor.java | 149 +++
.../workflowmodel/ProcessorFinishedEvent.java | 53 +
.../workflowmodel/ProcessorInputPort.java | 29 +
.../workflowmodel/ProcessorOutputPort.java | 30 +
.../taverna/workflowmodel/ProcessorPort.java | 31 +
.../workflowmodel/RunDeletionListener.java | 31 +
.../workflowmodel/TokenProcessingEntity.java | 56 +
.../taverna/workflowmodel/WorkflowItem.java | 47 +
.../WorkflowStructureException.java | 35 +
.../health/DisabledActivityHealthChecker.java | 64 +
.../workflowmodel/health/HealthCheck.java | 84 ++
.../workflowmodel/health/HealthChecker.java | 36 +
.../health/RemoteHealthChecker.java | 236 ++++
.../UnrecognizedActivityHealthChecker.java | 64 +
.../taverna/workflowmodel/health/package.html | 6 +
.../apache/taverna/workflowmodel/package.html | 3 +
.../processor/activity/AbstractActivity.java | 263 ++++
.../activity/AbstractAsynchronousActivity.java | 80 ++
.../processor/activity/Activity.java | 92 ++
.../activity/ActivityAndBeanWrapper.java | 61 +
.../ActivityConfigurationException.java | 61 +
.../processor/activity/ActivityFactory.java | 88 ++
.../processor/activity/ActivityInputPort.java | 77 ++
.../processor/activity/ActivityOutputPort.java | 31 +
.../processor/activity/ActivityPort.java | 33 +
.../activity/AsynchronousActivity.java | 49 +
.../activity/AsynchronousActivityCallback.java | 136 ++
.../processor/activity/DisabledActivity.java | 190 +++
.../workflowmodel/processor/activity/Job.java | 129 ++
.../activity/LockedNestedDataflow.java | 30 +
.../MonitorableAsynchronousActivity.java | 55 +
.../processor/activity/NestedDataflow.java | 35 +
.../activity/NestedDataflowSource.java | 34 +
.../activity/NonExecutableActivity.java | 96 ++
.../processor/activity/SupersededActivity.java | 32 +
.../activity/UnrecognizedActivity.java | 57 +
.../config/ActivityInputPortDefinitionBean.java | 66 +
.../ActivityOutputPortDefinitionBean.java | 48 +
.../config/ActivityPortDefinitionBean.java | 103 ++
.../config/ActivityPortsDefinitionBean.java | 81 ++
.../processor/activity/config/package.html | 7 +
.../processor/activity/package.html | 10 +
.../processor/config/ConfigurationBean.java | 31 +
.../processor/config/ConfigurationProperty.java | 46 +
.../dispatch/AbstractDispatchLayer.java | 102 ++
.../dispatch/AbstractErrorHandlerLayer.java | 282 ++++
.../processor/dispatch/DispatchLayer.java | 96 ++
.../dispatch/DispatchLayerFactory.java | 61 +
.../processor/dispatch/DispatchStack.java | 99 ++
.../processor/dispatch/NotifiableLayer.java | 39 +
.../PropertyContributingDispatchLayer.java | 63 +
.../description/DispatchLayerErrorReaction.java | 43 +
.../DispatchLayerJobQueueReaction.java | 44 +
.../description/DispatchLayerJobReaction.java | 43 +
.../DispatchLayerResultCompletionReaction.java | 43 +
.../DispatchLayerResultReaction.java | 43 +
.../description/DispatchLayerStateEffect.java | 83 ++
.../description/DispatchMessageType.java | 60 +
.../dispatch/description/ReactionTo.java | 39 +
.../description/SupportsStreamedResult.java | 40 +
.../processor/dispatch/description/package.html | 3 +
.../dispatch/events/AbstractDispatchEvent.java | 44 +
.../events/DispatchCompletionEvent.java | 69 +
.../dispatch/events/DispatchErrorEvent.java | 118 ++
.../dispatch/events/DispatchErrorType.java | 53 +
.../dispatch/events/DispatchJobEvent.java | 105 ++
.../dispatch/events/DispatchJobQueueEvent.java | 94 ++
.../dispatch/events/DispatchResultEvent.java | 107 ++
.../processor/dispatch/package.html | 19 +
.../AbstractIterationStrategyNode.java | 224 ++++
...onHandlingAbstractIterationStrategyNode.java | 135 ++
.../processor/iteration/CrossProduct.java | 163 +++
.../processor/iteration/DotProduct.java | 122 ++
.../processor/iteration/IterationStrategy.java | 53 +
.../iteration/IterationStrategyNode.java | 120 ++
.../iteration/IterationStrategyStack.java | 64 +
.../IterationTypeMismatchException.java | 48 +
.../MissingIterationInputException.java | 49 +
.../processor/iteration/NamedInputPortNode.java | 115 ++
.../processor/iteration/PrefixDotProduct.java | 110 ++
.../processor/iteration/TerminalNode.java | 38 +
.../processor/iteration/package.html | 4 +
.../serialization/DeserializationException.java | 32 +
.../serialization/SerializationException.java | 32 +
.../workflowmodel/utils/AnnotationTools.java | 170 +++
.../utils/NamedWorkflowEntityComparator.java | 38 +
.../workflowmodel/utils/PortComparator.java | 36 +
.../taverna/workflowmodel/utils/Tools.java | 794 +++++++++++
.../services/net.sf.taverna.t2.visit.VisitKind | 1 -
...averna.t2.workflowmodel.health.HealthChecker | 2 -
.../services/org.apache.taverna.visit.VisitKind | 1 +
...e.taverna.workflowmodel.health.HealthChecker | 2 +
.../spring/workflowmodel-api-context-osgi.xml | 26 +-
.../spring/workflowmodel-api-context.xml | 26 +-
.../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 ---
.../taverna/monitor/TestMonitorManager.java | 172 +++
.../workflowmodel/health/DummyVisitKind.java | 42 +
.../health/FloatHealthChecker.java | 43 +
.../health/FloatHealthChecker2.java | 43 +
.../workflowmodel/health/HealthReportTest.java | 87 ++
.../health/StringHealthChecker.java | 43 +
.../iteration/TestIterationStrategyNodes.java | 211 +++
...averna.t2.workflowmodel.health.HealthChecker | 3 -
...e.taverna.workflowmodel.health.HealthChecker | 3 +
.../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 -
.../layers/CoreDispatchLayerFactory.java | 102 ++
.../processor/dispatch/layers/ErrorBounce.java | 323 +++++
.../processor/dispatch/layers/Failover.java | 110 ++
.../dispatch/layers/IntermediateProvenance.java | 507 +++++++
.../processor/dispatch/layers/Invoke.java | 368 ++++++
.../processor/dispatch/layers/Loop.java | 423 ++++++
.../dispatch/layers/LoopConfiguration.java | 94 ++
.../processor/dispatch/layers/Parallelize.java | 462 +++++++
.../dispatch/layers/ParallelizeConfig.java | 49 +
.../processor/dispatch/layers/Retry.java | 179 +++
.../processor/dispatch/layers/RetryConfig.java | 96 ++
.../processor/dispatch/layers/Stop.java | 179 +++
.../processor/dispatch/layers/package.html | 4 +
...rkflowmodel-core-extensions-context-osgi.xml | 2 +-
.../workflowmodel-core-extensions-context.xml | 2 +-
.../processor/dispatch/layers/TestRetry.java | 110 --
.../processor/dispatch/layers/TestRetry.java | 129 ++
.../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 -
.../impl/AnnotationAssertionImpl.java | 134 ++
.../annotation/impl/AnnotationChainImpl.java | 49 +
.../taverna/annotation/impl/DisputeEvent.java | 73 +
.../annotation/impl/DisputeEventDetails.java | 27 +
.../taverna/annotation/impl/PersonImpl.java | 31 +
.../taverna/annotation/impl/URISource.java | 45 +
.../facade/impl/WorkflowInstanceFacadeImpl.java | 630 +++++++++
.../invocation/impl/InvocationContextImpl.java | 71 +
.../taverna/monitor/impl/MonitorTreeModel.java | 422 ++++++
.../impl/AbstractActivityEdit.java | 68 +
.../impl/AbstractAnnotationEdit.java | 69 +
.../impl/AbstractBinaryProcessorEdit.java | 94 ++
.../workflowmodel/impl/AbstractCrystalizer.java | 193 +++
.../impl/AbstractDataflowEdit.java | 67 +
.../impl/AbstractDataflowInputPortEdit.java | 67 +
.../impl/AbstractDataflowOutputPortEdit.java | 69 +
.../impl/AbstractDatalinkEdit.java | 66 +
.../impl/AbstractEventHandlingInputPort.java | 52 +
.../impl/AbstractFilteringInputPort.java | 177 +++
.../workflowmodel/impl/AbstractMergeEdit.java | 51 +
.../impl/AbstractProcessorEdit.java | 67 +
.../impl/BasicEventForwardingOutputPort.java | 92 ++
.../workflowmodel/impl/ConditionImpl.java | 60 +
.../workflowmodel/impl/ConfigureEdit.java | 77 ++
.../taverna/workflowmodel/impl/Crystalizer.java | 65 +
.../workflowmodel/impl/DataflowImpl.java | 796 +++++++++++
.../impl/DataflowInputPortImpl.java | 92 ++
.../impl/DataflowOutputPortImpl.java | 111 ++
.../impl/DataflowValidationReportImpl.java | 93 ++
.../workflowmodel/impl/DatalinkImpl.java | 67 +
.../taverna/workflowmodel/impl/EditSupport.java | 65 +
.../taverna/workflowmodel/impl/EditsImpl.java | 1250 +++++++++++++++++
.../taverna/workflowmodel/impl/MergeImpl.java | 233 ++++
.../workflowmodel/impl/MergeInputPortImpl.java | 44 +
.../workflowmodel/impl/MergeOutputPortImpl.java | 39 +
.../impl/ProcessorCrystalizerImpl.java | 102 ++
.../workflowmodel/impl/ProcessorImpl.java | 425 ++++++
.../impl/ProcessorInputPortImpl.java | 71 +
.../impl/ProcessorOutputPortImpl.java | 58 +
.../taverna/workflowmodel/impl/package.html | 3 +
.../activity/impl/ActivityInputPortImpl.java | 87 ++
.../activity/impl/ActivityOutputPortImpl.java | 74 ++
.../processor/activity/impl/package.html | 3 +
.../impl/AbstractDispatchLayerEdit.java | 97 ++
.../dispatch/impl/DispatchStackImpl.java | 316 +++++
.../processor/dispatch/impl/package.html | 8 +
.../iteration/impl/IterationStrategyImpl.java | 344 +++++
.../impl/IterationStrategyStackImpl.java | 153 +++
.../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 -
....apache.taverna.annotation.AnnotationBeanSPI | 10 +
...pache.taverna.annotation.AnnotationSourceSPI | 1 +
...ache.taverna.annotation.CurationEventBeanSPI | 1 +
.../org.apache.taverna.workflowmodel.Edits | 1 +
...e.taverna.workflowmodel.health.HealthChecker | 1 +
.../spring/workflowmodel-impl-context-osgi.xml | 6 +-
.../spring/workflowmodel-impl-context.xml | 6 +-
.../src/main/resources/provenanceContext.xml | 4 +-
.../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 ---
.../taverna/annotation/TestAnnotations.java | 191 +++
.../monitor/impl/MonitorTreeModelTest.java | 55 +
.../impl/AbstractDatalinkEditTest.java | 186 +++
.../impl/AddProcessorEditTest.java | 89 ++
.../ChangeDataflowInputPortDepthEditTest.java | 76 ++
...eDataflowInputPortGranularDepthEditTest.java | 72 +
.../impl/ConfigureActivityEditTest.java | 89 ++
.../impl/ConnectDatalinkEditTest.java | 87 ++
.../impl/ConnectMergedDatalinkEditTest.java | 128 ++
.../impl/CreateDataflowInputPortEditTest.java | 86 ++
.../impl/CreateDataflowOutputPortEditTest.java | 80 ++
.../workflowmodel/impl/DataflowImplTest.java | 42 +
.../impl/DefaultDispatchStackEditTest.java | 78 ++
.../workflowmodel/impl/DummyActivity.java | 39 +
.../workflowmodel/impl/DummyDataflow.java | 142 ++
.../impl/DummyDataflowInputPort.java | 38 +
.../impl/DummyDataflowOutputPort.java | 36 +
.../workflowmodel/impl/DummyProcessor.java | 149 +++
.../impl/DummyValidationReport.java | 65 +
.../workflowmodel/impl/EditsImplTests.java | 60 +
.../taverna/workflowmodel/impl/EventKeeper.java | 36 +
.../MapProcessorPortsToActivityEditTest.java | 132 ++
.../impl/ProcessorHealthReportTest.java | 139 ++
.../impl/RemoveProcessorInputPortEditTest.java | 68 +
.../impl/RemoveProcessorOutputPortEditTest.java | 70 +
...pdateDataflowInternalIdentifierEditTest.java | 38 +
.../processor/AsynchEchoActivity.java | 60 +
.../processor/DiagnosticEventHandler.java | 66 +
.../workflowmodel/processor/EchoConfig.java | 51 +
.../NaiveProcessorConstructionTest.java | 46 +
.../taverna/workflowmodel/processor/Tools.java | 89 ++
.../processor/dispatch/DiagnosticLayer.java | 74 ++
.../DiagnosticIterationStrategyNode.java | 130 ++
.../impl/IterationTypeCheckerTest.java | 216 +++
.../resources/serialized-fragments/activity.xml | 2 +-
.../serialized-fragments/dispatchLayer.xml | 6 +-
.../serialized-fragments/dispatchStack.xml | 18 +-
1160 files changed, 53441 insertions(+), 52894 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml b/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml
index 32ad4f1..2485411 100644
--- a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml
+++ b/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml
@@ -6,21 +6,21 @@
http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi.xsd">
- <service ref="${classPrefix}ServiceIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
+ <service ref="${classPrefix}ServiceIcon" interface="org.apache.taverna.workbench.activityicons.ActivityIconSPI" />
- <service ref="${classPrefix}ServiceProvider" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
+ <service ref="${classPrefix}ServiceProvider" interface="org.apache.taverna.servicedescriptions.ServiceDescriptionProvider" />
<service ref="${classPrefix}ConfigureMenuAction" auto-export="interfaces" />
- <service ref="${classPrefix}ActivityContextViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+ <service ref="${classPrefix}ActivityContextViewFactory" interface="org.apache.taverna.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
- <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
- <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
- <reference id="menuManager" interface="net.sf.taverna.t2.ui.menu.MenuManager" />
- <reference id="selectionManager" interface="net.sf.taverna.t2.workbench.selection.SelectionManager" />
- <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
- <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
- <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" />
- <reference id="serviceRegistry" interface="uk.org.taverna.commons.services.ServiceRegistry" />
+ <reference id="editManager" interface="org.apache.taverna.workbench.edits.EditManager" />
+ <reference id="fileManager" interface="org.apache.taverna.workbench.file.FileManager" />
+ <reference id="menuManager" interface="org.apache.taverna.ui.menu.MenuManager" />
+ <reference id="selectionManager" interface="org.apache.taverna.workbench.selection.SelectionManager" />
+ <reference id="activityIconManager" interface="org.apache.taverna.workbench.activityicons.ActivityIconManager" />
+ <reference id="colourManager" interface="org.apache.taverna.workbench.configuration.colour.ColourManager" />
+ <reference id="serviceDescriptionRegistry" interface="org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry" />
+ <reference id="serviceRegistry" interface="org.apache.taverna.commons.services.ServiceRegistry" />
</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity/src/main/resources/META-INF/spring/context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity/src/main/resources/META-INF/spring/context-osgi.xml b/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity/src/main/resources/META-INF/spring/context-osgi.xml
index e8d6e12..2a22552 100644
--- a/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity/src/main/resources/META-INF/spring/context-osgi.xml
+++ b/taverna-activity-archetype/src/main/resources/archetype-resources/__rootArtifactId__-activity/src/main/resources/META-INF/spring/context-osgi.xml
@@ -7,11 +7,11 @@
http://www.springframework.org/schema/osgi/spring-osgi.xsd">
<!-- Services to be registered with the OSGi service register -->
- <service ref="${classPrefix}ActivityHealthChecker" interface="net.sf.taverna.t2.workflowmodel.health.HealthChecker" />
+ <service ref="${classPrefix}ActivityHealthChecker" interface="org.apache.taverna.workflowmodel.health.HealthChecker" />
- <service ref="${classPrefix}ActivityFactory" interface="net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory" />
+ <service ref="${classPrefix}ActivityFactory" interface="org.apache.taverna.workflowmodel.processor.activity.ActivityFactory" />
<!-- References to services required from the OSGi service register -->
- <reference id="edits" interface="net.sf.taverna.t2.workflowmodel.Edits" />
+ <reference id="edits" interface="org.apache.taverna.workflowmodel.Edits" />
</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-activity-test-utils/src/main/java/net/sf/taverna/t2/activities/testutils/ActivityInvoker.java
----------------------------------------------------------------------
diff --git a/taverna-activity-test-utils/src/main/java/net/sf/taverna/t2/activities/testutils/ActivityInvoker.java b/taverna-activity-test-utils/src/main/java/net/sf/taverna/t2/activities/testutils/ActivityInvoker.java
deleted file mode 100644
index 934e31a..0000000
--- a/taverna-activity-test-utils/src/main/java/net/sf/taverna/t2/activities/testutils/ActivityInvoker.java
+++ /dev/null
@@ -1,250 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.testutils;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.ServiceLoader;
-
-import net.sf.taverna.t2.reference.ExternalReferenceBuilderSPI;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.ExternalReferenceTranslatorSPI;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.StreamToValueConverterSPI;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.reference.ValueToReferenceConverterSPI;
-import net.sf.taverna.t2.reference.impl.ErrorDocumentServiceImpl;
-import net.sf.taverna.t2.reference.impl.InMemoryErrorDocumentDao;
-import net.sf.taverna.t2.reference.impl.InMemoryListDao;
-import net.sf.taverna.t2.reference.impl.InMemoryReferenceSetDao;
-import net.sf.taverna.t2.reference.impl.ListServiceImpl;
-import net.sf.taverna.t2.reference.impl.ReferenceServiceImpl;
-import net.sf.taverna.t2.reference.impl.ReferenceSetAugmentorImpl;
-import net.sf.taverna.t2.reference.impl.ReferenceSetServiceImpl;
-import net.sf.taverna.t2.reference.impl.SimpleT2ReferenceGenerator;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivity;
-
-/**
- * Helper class to facilitate in executing Activities in isolation.
- *
- * @author Stuart Owen
- * @author Alex Nenadic
- * @author Stian Soiland-Reyes
- * @author David Withers
- */
-public class ActivityInvoker {
-
- /**
- * Timeout in seconds
- */
- public static long TIMEOUT = 30;
-
-
- /**
- * Invokes an {@link AsynchronousActivity} with a given set of input Objects
- * and returns a Map<String,Object> of requested output values.
- *
- * @param activity
- * the activity to be tested
- * @param inputs
- * a Map<String,Object> of input Objects
- * @param requestedOutputs
- * a List<String> of outputs to be examined
- *
- * @return a Map<String,Object> of the outputs requested by requestedOutput
- * or <code>null</code> if a failure occurs
- * @throws InterruptedException
- * @throws Throwable
- */
-/* public static Map<String, Object> invokeAsyncActivity(
- AbstractAsynchronousActivity<?> activity,
- Map<String, Object> inputs, Map<String, Class<?>> requestedOutputs)
- throws Exception {
- Map<String, Object> results = new HashMap<String, Object>();
-
- ApplicationContext context = new RavenAwareClassPathXmlApplicationContext(
- "inMemoryActivityTestsContext.xml");
- ReferenceService referenceService = (ReferenceService) context.getBean("t2reference.service.referenceService");
-
- DummyCallback callback = new DummyCallback(referenceService);
- Map<String, T2Reference> inputEntities = new HashMap<String, T2Reference>();
- for (String inputName : inputs.keySet()) {
- Object val = inputs.get(inputName);
- if (val instanceof List) {
- inputEntities.put(inputName, referenceService.register(val, 1, true, callback.getContext()));
- } else {
- inputEntities.put(inputName, referenceService.register(val, 0, true, callback.getContext()));
- }
- }
-
- activity.executeAsynch(inputEntities, callback);
- callback.thread.join();
-
- if (callback.failed) {
- results = null;
- } else {
- for (Map.Entry<String, Class<?>> output : requestedOutputs.entrySet()) {
- T2Reference id = callback.data.get(output.getKey());
- if (id != null) {
- Object result;
- result = referenceService.renderIdentifier(id, output.getValue(), callback.getContext());
- results.put(output.getKey(), result);
- }
- }
- }
- return results;
- }
- */
-
- // Changed this method to render the T2Reference to an object only if the type of the object in
- // requestedOutputs is not an instance of ExternalReferenceSPI. Otherwise, the calling test method
- // should get activity ReferenceSet and render the object itself. This was needed for API consumer activity
- // testing - see ApiConsumerActivityTest.
- // Also added support for multi-dimensional lists.
- public static Map<String, Object> invokeAsyncActivity(
- AbstractAsynchronousActivity<?> activity,
- Map<String, Object> inputs, Map<String, Class<?>> requestedOutputs) throws InterruptedException
- {
-
- Map<String, Object> results = new HashMap<String, Object>();
-
- ReferenceService referenceService = createReferenceService();
-
- DummyCallback callback = new DummyCallback(referenceService);
- Map<String, T2Reference> inputEntities = new HashMap<String, T2Reference>();
- for (String inputName : inputs.keySet()) {
- Object val = inputs.get(inputName);
- int depth = getDepth(val);
- inputEntities.put(inputName, referenceService.register(val, depth, true, callback.getContext()));
- }
-
- activity.executeAsynch(inputEntities, callback);
- callback.thread.join(TIMEOUT*1000);
-
-
- if (callback.failed) {
- throw callback.failures.get(0);
- } else {
- for (Map.Entry<String, Class<?>> output : requestedOutputs.entrySet()) {
- T2Reference id = callback.data.get(output.getKey());
- if (ExternalReferenceSPI.class.isAssignableFrom(output.getValue())){
- // Do not render the object - just resolve the T2Reference
- Object result;
- result = referenceService.resolveIdentifier(id, null, callback.getContext());
- results.put(output.getKey(), result);
- }
- else{
- // Try to render the object behind the reference
- Object result;
- result = referenceService.renderIdentifier(id, output.getValue(), callback.getContext());
- results.put(output.getKey(), result);
- }
- }
- }
- return results;
- }
-
- private static ReferenceService createReferenceService() {
- SimpleT2ReferenceGenerator referenceGenerator = new SimpleT2ReferenceGenerator();
- ReferenceSetAugmentorImpl referenceSetAugmentor = new ReferenceSetAugmentorImpl();
- referenceSetAugmentor.setBuilders((List<ExternalReferenceBuilderSPI<?>>) getBuilders());
- referenceSetAugmentor.setTranslators(getTranslators());
-
- ReferenceSetServiceImpl referenceSetService = new ReferenceSetServiceImpl();
- referenceSetService.setT2ReferenceGenerator(referenceGenerator);
- referenceSetService.setReferenceSetDao(new InMemoryReferenceSetDao());
- referenceSetService.setReferenceSetAugmentor(referenceSetAugmentor);
-
- ListServiceImpl listService = new ListServiceImpl();
- listService.setT2ReferenceGenerator(referenceGenerator);
- listService.setListDao(new InMemoryListDao());
-
- ErrorDocumentServiceImpl errorDocumentService = new ErrorDocumentServiceImpl();
- errorDocumentService.setT2ReferenceGenerator(referenceGenerator);
- errorDocumentService.setErrorDao(new InMemoryErrorDocumentDao());
-
- ReferenceServiceImpl referenceService = new ReferenceServiceImpl();
- referenceService.setReferenceSetService(referenceSetService);
- referenceService.setListService(listService);
- referenceService.setErrorDocumentService(errorDocumentService);
- referenceService.setConverters(getConverters());
- referenceService.setValueBuilders(getValueBuilders());
-
- return referenceService;
- }
-
- private static <T> List<T> getImplementations(Class<T> api) {
- List<T> implementations = new ArrayList<T>();
- ServiceLoader<T> serviceLoader = ServiceLoader.load(api);
- for (T implementation : serviceLoader) {
- implementations.add(implementation);
- }
- return implementations;
- }
-
- private static List<StreamToValueConverterSPI> getValueBuilders() {
- return getImplementations(StreamToValueConverterSPI.class);
- }
-
- private static List<ValueToReferenceConverterSPI> getConverters() {
- return getImplementations(ValueToReferenceConverterSPI.class);
- }
-
- private static List<ExternalReferenceTranslatorSPI<?, ?>> getTranslators() {
- List<ExternalReferenceTranslatorSPI<?, ?>> implementations = new ArrayList<ExternalReferenceTranslatorSPI<?, ?>>();
- ServiceLoader<ExternalReferenceTranslatorSPI> serviceLoader = ServiceLoader.load(ExternalReferenceTranslatorSPI.class);
- for (ExternalReferenceTranslatorSPI implementation : serviceLoader) {
- implementations.add(implementation);
- }
- return implementations;
- }
-
- private static List<ExternalReferenceBuilderSPI<?>> getBuilders() {
- List<ExternalReferenceBuilderSPI<?>> implementations = new ArrayList<ExternalReferenceBuilderSPI<?>>();
- ServiceLoader<ExternalReferenceBuilderSPI> serviceLoader = ServiceLoader.load(ExternalReferenceBuilderSPI.class);
- for (ExternalReferenceBuilderSPI implementation : serviceLoader) {
- implementations.add(implementation);
- }
- return implementations;
- }
-
- /**
- * If an object is activity list - returns its depth, 0 otherwise (for single objects).
- * @param obj
- * @return
- */
- private static int getDepth(Object obj){
-
- if (obj instanceof List) {
- // Assumes all sub-lists are of the same depth,
- // so just uses the first sub-list to calculate it.
- Object[] sublists = ((List<?>)obj).toArray();
- int depth = 1;
- depth = getDepth(sublists[0]) + 1;
- return depth;
- } else {
- return 0;
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-activity-test-utils/src/main/java/net/sf/taverna/t2/activities/testutils/DummyCallback.java
----------------------------------------------------------------------
diff --git a/taverna-activity-test-utils/src/main/java/net/sf/taverna/t2/activities/testutils/DummyCallback.java b/taverna-activity-test-utils/src/main/java/net/sf/taverna/t2/activities/testutils/DummyCallback.java
deleted file mode 100644
index 016caef..0000000
--- a/taverna-activity-test-utils/src/main/java/net/sf/taverna/t2/activities/testutils/DummyCallback.java
+++ /dev/null
@@ -1,106 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.testutils;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.invocation.impl.InvocationContextImpl;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback;
-import net.sf.taverna.t2.workflowmodel.processor.dispatch.events.DispatchErrorType;
-
-import org.apache.log4j.Logger;
-
-/**
- * A DummyCallback to aid with testing Activities.
- *
- * @author Stuart Owen
- * @author David Withers
- * @author Stian Soiland-Reyes
- *
- */
-public class DummyCallback implements AsynchronousActivityCallback {
-
- private static Logger logger = Logger
- .getLogger(DummyCallback.class);
-
- public ReferenceService referenceService;
- public InvocationContext invocationContext;
- public Map<String, T2Reference> data;
- public Thread thread;
-
- public boolean failed = false;
-
- public List<RuntimeException> failures = new ArrayList<RuntimeException>();
-
- public DummyCallback(ReferenceService referenceService) {
- this.referenceService = referenceService;
- this.invocationContext = new InvocationContextImpl(referenceService, null);
- }
-
- public void fail(String message, Throwable t) {
- fail(message, t, null);
- }
-
- public void fail(String message) {
- fail(message, null, null);
- }
-
- public void fail(String message, Throwable t, DispatchErrorType arg2) {
- failed = true;
- failures.add(new RuntimeException(arg2+message, t));
- logger.error("", t);
- }
-
- /*public SecurityAgentManager getLocalSecurityManager() {
- // TODO Auto-generated method stub
- return null;
- }*/
-
- public void receiveCompletion(int[] completionIndex) {
- // TODO Auto-generated method stub
-
- }
-
- public void receiveResult(Map<String, T2Reference> data,
- int[] index) {
- this.data = data;
- }
-
- public void requestRun(Runnable runMe) {
- thread = new Thread(runMe);
- thread.start();
- }
-
- public InvocationContext getContext() {
- return invocationContext;
- }
-
- public String getParentProcessIdentifier() {
- // TODO Auto-generated method stub
- return "";
- }
-
-}