Merge branch 'master' into docker
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/commit/1806041c Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/1806041c Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/1806041c Branch: refs/heads/docker Commit: 1806041cad04d0b5f5812f09e2755559f75b71f9 Parents: df96dce 9d7ec5d Author: Stian Soiland-Reyes <st...@apache.org> Authored: Thu Jun 30 14:52:56 2016 +0100 Committer: Stian Soiland-Reyes <st...@apache.org> Committed: Thu Jun 30 14:52:56 2016 +0100 ---------------------------------------------------------------------- .travis.yml | 15 + LICENSE | 10 + README.md | 120 +- pom.xml | 33 +- taverna-beanshell-activity/pom.xml | 5 +- .../src/main/resources/schema.json | 3 + taverna-external-tool-activity/pom.xml | 7 +- .../inb/knowarc/gui/AskUserForPwPopup.java | 77 - .../inb/knowarc/gui/PleaseWaitDialog.java | 75 - .../knowarc/usecases/RuntimeEnvironment.java | 253 - .../usecases/RuntimeEnvironmentConstraint.java | 162 - .../inb/knowarc/usecases/ScriptInput.java | 136 - .../inb/knowarc/usecases/ScriptInputStatic.java | 75 - .../inb/knowarc/usecases/ScriptInputUser.java | 101 - .../inb/knowarc/usecases/ScriptOutput.java | 90 - .../knowarc/usecases/UseCaseDescription.java | 899 - .../knowarc/usecases/UseCaseEnumeration.java | 113 - .../usecases/invocation/AskUserForPw.java | 34 - .../invocation/InvocationException.java | 25 - .../usecases/invocation/UseCaseInvocation.java | 324 - .../local/LocalUseCaseInvocation.java | 563 - .../ssh/SshAutoLoginTrustEveryone.java | 72 - .../usecases/invocation/ssh/SshNode.java | 159 - .../usecases/invocation/ssh/SshNodeFactory.java | 56 - .../usecases/invocation/ssh/SshPool.java | 148 - .../usecases/invocation/ssh/SshReference.java | 208 - .../knowarc/usecases/invocation/ssh/SshUrl.java | 153 - .../invocation/ssh/SshUrlToSshReference.java | 43 - .../invocation/ssh/SshUseCaseInvocation.java | 563 - .../externaltool/ExternalToolActivity.java | 21 +- .../ExternalToolActivityConfigurationBean.java | 8 +- .../ExternalToolActivityMimeTypeChecker.java | 5 +- .../externaltool/InvocationCreator.java | 7 +- .../externaltool/RetrieveLoginFromTaverna.java | 2 +- .../externaltool/desc/RuntimeEnvironment.java | 250 + .../desc/RuntimeEnvironmentConstraint.java | 160 + .../externaltool/desc/ScriptInput.java | 134 + .../externaltool/desc/ScriptInputStatic.java | 73 + .../externaltool/desc/ScriptInputUser.java | 99 + .../externaltool/desc/ScriptOutput.java | 88 + .../externaltool/desc/ToolDescription.java | 897 + .../desc/ToolDescriptionParser.java | 111 + .../externaltool/invocation/AskUserForPw.java | 32 + .../invocation/InvocationException.java | 36 + .../externaltool/invocation/ToolInvocation.java | 321 + .../ExternalToolLocalInvocationMechanism.java | 4 +- .../local/LocalInvocationCreator.java | 14 +- .../local/LocalInvocationPersister.java | 8 +- .../local/LocalMechanismCreator.java | 4 +- .../externaltool/local/LocalToolInvocation.java | 560 + .../activities/externaltool/package.html | 17 + .../ssh/ExternalToolSshInvocationMechanism.java | 7 +- .../ssh/SshAutoLoginTrustEveryone.java | 69 + .../externaltool/ssh/SshInvocationCreator.java | 19 +- .../ssh/SshInvocationPersister.java | 10 +- .../externaltool/ssh/SshMechanismCreator.java | 6 +- .../activities/externaltool/ssh/SshNode.java | 157 + .../externaltool/ssh/SshNodeFactory.java | 66 + .../activities/externaltool/ssh/SshPool.java | 157 + .../externaltool/ssh/SshReference.java | 222 + .../externaltool/ssh/SshToolInvocation.java | 560 + .../activities/externaltool/ssh/SshUrl.java | 163 + .../externaltool/ssh/SshUrlToSshReference.java | 54 + ...pache.taverna.reference.ExternalReferenceSPI | 2 +- ...verna.reference.ValueToReferenceConverterSPI | 2 +- .../spring/external-tool-activity-context.xml | 4 +- .../invocation/ssh/SshReference.hbm.xml | 41 - .../externaltool/ssh/SshReference.hbm.xml | 41 + taverna-interaction-activity/pom.xml | 9 +- .../src/main/resources/Authorize.vm | 17 + .../src/main/resources/MasterPassword.vm | 17 + .../src/main/resources/TrustedCertificate.vm | 17 + .../src/main/resources/TruststorePassword.vm | 17 + .../src/main/resources/UsernamePassword.vm | 17 + .../resources/abdera/adapter/feed.properties | 14 + .../src/main/resources/ask.vm | 17 + .../src/main/resources/choose.vm | 17 + .../src/main/resources/index | 14 + .../src/main/resources/interaction.css | 16 + .../src/main/resources/interaction.vm | 17 + .../src/main/resources/notify.vm | 17 + .../src/main/resources/schema.json | 5 +- .../src/main/resources/select.vm | 17 + .../src/main/resources/tell.vm | 17 + .../src/main/resources/warn.vm | 17 + taverna-rest-activity/pom.xml | 189 +- .../src/main/resources/schema.json | 3 + .../rest/ApacheHttpClientUsageTest.java.bak | 215 - .../rest/ExampleActivityTest.java.bak | 153 - taverna-spreadsheet-import-activity/pom.xml | 5 +- .../taverna/activities/spreadsheet/package.html | 17 + .../src/main/resources/schema.json | 3 + taverna-wsdl-activity/pom.xml | 14 +- .../apache/taverna/activities/wsdl/package.html | 17 + .../src/main/resources/schema.json | 3 + .../src/main/resources/xml-splitter.schema.json | 2 + .../activities/wsdl/WSRFActivityTest.java | 16 +- ...XMLSplitterConfigurationBeanBuilderTest.java | 18 + .../src/test/resources/log4j.properties | 15 + .../wsrf/counterService/CounterService_.wsdl | 9 - .../wsdl/wsrf/counterService/WS-Addressing.xsd | 121 - .../wsdl/wsrf/counterService/WS-BaseFaults.xsd | 47 - .../wsdl/wsrf/counterService/WS-BaseN.wsdl | 298 - .../wsdl/wsrf/counterService/WS-BaseN.xsd | 50 - .../counterService/WS-ResourceLifetime.wsdl | 117 - .../wsrf/counterService/WS-ResourceLifetime.xsd | 26 - .../counterService/WS-ResourceProperties.wsdl | 240 - .../counterService/WS-ResourceProperties.xsd | 42 - .../wsrf/counterService/counter_bindings.wsdl | 157 - .../wsrf/counterService/counter_flattened.wsdl | 111 - .../activities/wsdl/wsrf/counterService/xml.xsd | 105 - taverna-wsdl-generic/pom.xml | 90 +- .../org/apache/taverna/wsdl/parser/package.html | 17 + .../org/apache/taverna/wsdl/soap/package.html | 17 + .../src/main/resources/META-INF/LICENSE | 235 + .../taverna/wsdl/parser/WSDLParserTest.java | 8 +- .../taverna/wsdl/parser/WSRFParserTest.java | 7 +- .../wsdl/soap/LiteralBodyBuilderTest.java | 10 +- .../wsdl/testutils/LocationConstants.java | 2 +- .../taverna/wsdl/testutils/WSDLTestHelper.java | 89 +- .../wsdl/xmlsplitter/XMLInputSplitterTest.java | 8 +- .../wsdl/xmlsplitter/XMLOutputSplitterTest.java | 4 +- .../getComplexWithInternalListResponse.xml | 20 - .../src/test/resources/jws-splitter-input.xml | 95 - .../src/test/resources/log4j.properties | 15 + .../TAV-744/InstrumentServiceContextTypes.xsd | 12 - .../parser/TAV-744/InstrumentServiceTypes.xsd | 12 - .../wsdl/parser/TAV-744/InstrumentService_.wsdl | 129 - .../parser/TAV-744/InstrumentService__.wsdl | 9 - .../TAV-744/InstrumentService_bindings.wsdl | 97 - .../wsdl/parser/TAV-744/ServiceSecurity.wsdl | 72 - .../wsdl/parser/TAV-744/WS-Addressing.xsd | 121 - .../wsdl/parser/TAV-744/WS-BaseFaults.wsdl | 22 - .../wsdl/parser/TAV-744/WS-BaseFaults.xsd | 47 - .../taverna/wsdl/parser/TAV-744/WS-BaseN.wsdl | 298 - .../taverna/wsdl/parser/TAV-744/WS-BaseN.xsd | 50 - .../parser/TAV-744/WS-ResourceLifetime.wsdl | 117 - .../wsdl/parser/TAV-744/WS-ResourceLifetime.xsd | 26 - .../parser/TAV-744/WS-ResourceProperties.wsdl | 240 - .../parser/TAV-744/WS-ResourceProperties.xsd | 42 - .../taverna/wsdl/parser/TAV-744/security.xsd | 78 - .../apache/taverna/wsdl/parser/TAV-744/xml.xsd | 105 - .../wsrf/counterService/CounterService_.wsdl | 9 - .../wsrf/counterService/WS-Addressing.xsd | 121 - .../wsrf/counterService/WS-BaseFaults.xsd | 47 - .../parser/wsrf/counterService/WS-BaseN.wsdl | 298 - .../parser/wsrf/counterService/WS-BaseN.xsd | 50 - .../counterService/WS-ResourceLifetime.wsdl | 117 - .../wsrf/counterService/WS-ResourceLifetime.xsd | 26 - .../counterService/WS-ResourceProperties.wsdl | 240 - .../counterService/WS-ResourceProperties.xsd | 42 - .../wsrf/counterService/counter_bindings.wsdl | 157 - .../wsrf/counterService/counter_flattened.wsdl | 111 - .../wsdl/parser/wsrf/counterService/xml.xsd | 105 - .../testwsdls/CurrencyExchangeService.wsdl | 37 - .../src/test/resources/testwsdls/GoViz.wsdl | 202 - .../testwsdls/MyService-rpc-literal.wsdl | 392 - .../src/test/resources/testwsdls/SBWReader.wsdl | 602 - .../testwsdls/TestServices-rpcencoded.wsdl | 396 - .../testwsdls/TestServices-unwrapped.wsdl | 434 - .../src/test/resources/testwsdls/VSOi.wsdl | 305 - .../src/test/resources/testwsdls/bind.wsdl | 354 - .../test/resources/testwsdls/eutils/efetch.xsd | 118 - .../resources/testwsdls/eutils/efetch_bio.xsd | 18079 ----------------- .../resources/testwsdls/eutils/efetch_nlmc.xsd | 1021 - .../resources/testwsdls/eutils/efetch_pmc.xsd | 5910 ------ .../testwsdls/eutils/efetch_pubmed.xsd | 359 - .../resources/testwsdls/eutils/efetch_taxon.xsd | 150 - .../test/resources/testwsdls/eutils/egquery.xsd | 60 - .../test/resources/testwsdls/eutils/einfo.xsd | 95 - .../test/resources/testwsdls/eutils/elink.xsd | 188 - .../test/resources/testwsdls/eutils/esearch.xsd | 165 - .../test/resources/testwsdls/eutils/espell.xsd | 60 - .../resources/testwsdls/eutils/esummary.xsd | 85 - .../test/resources/testwsdls/eutils/eutils.wsdl | 333 - .../resources/testwsdls/eutils/eutils_lite.wsdl | 289 - .../test/resources/testwsdls/jws-online.wsdl | 1001 - .../test/resources/testwsdls/jws_online.wsdl | 1001 - .../src/test/resources/testwsdls/ma.wsdl | 1901 -- .../testwsdls/menagerie-complex-rpc.wsdl | 208 - .../src/test/resources/testwsdls/prodoric.wsdl | 360 - .../src/test/resources/testwsdls/whatizit.wsdl | 233 - taverna-xpath-activity/pom.xml | 95 +- .../src/main/resources/schema.json | 3 + 184 files changed, 5397 insertions(+), 43664 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1806041c/pom.xml ----------------------------------------------------------------------
