You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:43:55 UTC

[51/51] [partial] incubator-taverna-engine git commit: temporarily empty repository

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 <st...@apache.org>
Authored: Tue Feb 17 20:42:45 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
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
-
-[![Build Status](https://travis-ci.org/taverna-incubator/incubator-taverna-engine.svg)](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;
-	}
-
-}