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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:36:59 UTC
[28/28] incubator-taverna-common-activities git commit: Temporarily
empty repository
Temporarily empty repository
.. as Software Grant is not formally on file
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/2e8f451e
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/2e8f451e
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/2e8f451e
Branch: refs/heads/empty
Commit: 2e8f451eab758d80d338bd478a00ce371ce13af1
Parents: ec504ab
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 17 20:36:14 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 17 20:36:14 2015 +0000
----------------------------------------------------------------------
.gitignore | 5 -
.travis.yml | 1 -
pom.xml | 40 -
taverna-beanshell-activity/pom.xml | 90 -
.../activities/beanshell/BeanshellActivity.java | 251 -
.../BeanshellActivityConfigurationBean.java | 86 -
.../beanshell/BeanshellActivityFactory.java | 79 -
.../BeanshellActivityHealthChecker.java | 111 -
.../t2/activities/beanshell/package.html | 3 -
...averna.t2.workflowmodel.health.HealthChecker | 1 -
.../spring/beanshell-activity-context-osgi.xml | 15 -
.../spring/beanshell-activity-context.xml | 12 -
.../src/main/resources/schema.json | 21 -
.../beanshell/BeanshellActivityFactoryTest.java | 64 -
.../BeanshellActivityHealthCheckerTest.java | 173 -
.../beanshell/BeanshellActivityTest.java | 86 -
taverna-external-tool-activity/pom.xml | 91 -
.../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 | 114 -
.../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 -
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.../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 | 301 -
.../ExternalToolActivityConfigurationBean.java | 194 -
.../ExternalToolActivityFactory.java | 100 -
.../ExternalToolActivityHealthChecker.java | 195 -
.../ExternalToolActivityMimeTypeChecker.java | 174 -
.../ExternalToolRunDeletionListener.java | 38 -
.../externaltool/InvocationCreator.java | 25 -
.../externaltool/RetrieveLoginFromTaverna.java | 57 -
.../ExternalToolLocalInvocationMechanism.java | 131 -
.../local/LocalInvocationCreator.java | 49 -
.../local/LocalInvocationPersister.java | 45 -
.../local/LocalMechanismCreator.java | 48 -
.../externaltool/manager/InvocationGroup.java | 141 -
.../manager/InvocationGroupAddedEvent.java | 18 -
.../manager/InvocationGroupChangedEvent.java | 18 -
.../manager/InvocationGroupManager.java | 102 -
.../manager/InvocationGroupRemovedEvent.java | 24 -
.../manager/InvocationManagerEvent.java | 5 -
.../manager/InvocationMechanism.java | 60 -
.../manager/InvocationMechanismAddedEvent.java | 18 -
.../InvocationMechanismChangedEvent.java | 18 -
.../InvocationMechanismRemovedEvent.java | 24 -
.../manager/InvocationPersister.java | 20 -
.../externaltool/manager/MechanismCreator.java | 49 -
.../impl/InvocationGroupManagerImpl.java | 446 -
.../t2/activities/externaltool/package.html | 3 -
.../repository/ExternalToolRepositoryUtil.java | 12 -
.../ssh/ExternalToolSshInvocationMechanism.java | 96 -
.../externaltool/ssh/SshInvocationCreator.java | 119 -
.../ssh/SshInvocationPersister.java | 56 -
.../externaltool/ssh/SshMechanismCreator.java | 84 -
...t2.activities.externaltool.InvocationCreator | 2 -
...ies.externaltool.manager.InvocationPersister | 2 -
...vities.externaltool.manager.MechanismCreator | 2 -
...sf.taverna.t2.reference.ExternalReferenceSPI | 2 -
...na.t2.reference.ValueToReferenceConverterSPI | 3 -
...taverna.t2.workflowmodel.RunDeletionListener | 1 -
...averna.t2.workflowmodel.health.HealthChecker | 2 -
.../external-tool-activity-context-osgi.xml | 42 -
.../spring/external-tool-activity-context.xml | 50 -
.../invocation/ssh/SshReference.hbm.xml | 23 -
taverna-interaction-activity/pom.xml | 158 -
.../t2/activities/interaction/FeedReader.java | 87 -
.../interaction/InteractionActivity.java | 156 -
.../interaction/InteractionActivityFactory.java | 135 -
.../InteractionActivityHealthChecker.java | 39 -
.../InteractionActivityRunnable.java | 329 -
.../interaction/InteractionActivityType.java | 15 -
.../InteractionCallbackRequestor.java | 193 -
.../interaction/InteractionRecorder.java | 163 -
.../interaction/InteractionRequestor.java | 38 -
.../InteractionRunDeletionListener.java | 31 -
.../activities/interaction/InteractionType.java | 14 -
.../interaction/InteractionUtils.java | 127 -
.../interaction/ResponseFeedListener.java | 159 -
.../activities/interaction/atom/AtomUtils.java | 83 -
.../feed/ShowRequestFeedListener.java | 65 -
.../jetty/HackedFilesystemAdapter.java | 263 -
.../interaction/jetty/InteractionJetty.java | 203 -
.../preference/InteractionPreference.java | 268 -
.../velocity/InteractionVelocity.java | 130 -
.../interaction/velocity/NotifyChecker.java | 26 -
.../interaction/velocity/NotifyDirective.java | 58 -
.../interaction/velocity/ProduceChecker.java | 35 -
.../interaction/velocity/ProduceDirective.java | 58 -
.../interaction/velocity/RequireChecker.java | 35 -
.../interaction/velocity/RequireDirective.java | 58 -
.../src/main/resources/Authorize.vm | 73 -
...taverna.t2.activities.interaction.FeedReader | 2 -
...taverna.t2.workflowmodel.RunDeletionListener | 1 -
...averna.t2.workflowmodel.health.HealthChecker | 1 -
.../interaction-activity-context-osgi.xml | 21 -
.../spring/interaction-activity-context.xml | 61 -
.../src/main/resources/MasterPassword.vm | 47 -
.../src/main/resources/TrustedCertificate.vm | 57 -
.../src/main/resources/TruststorePassword.vm | 48 -
.../src/main/resources/UsernamePassword.vm | 57 -
.../resources/abdera/adapter/feed.properties | 5 -
.../src/main/resources/ask.vm | 51 -
.../src/main/resources/choose.vm | 74 -
.../src/main/resources/index | 15 -
.../src/main/resources/interaction.css | 5 -
.../src/main/resources/interaction.vm | 168 -
.../src/main/resources/json2.js | 487 -
.../src/main/resources/notify.vm | 39 -
.../src/main/resources/pmrpc.js | 686 -
.../src/main/resources/schema.json | 31 -
.../src/main/resources/select.vm | 61 -
.../src/main/resources/tell.vm | 54 -
.../src/main/resources/warn.vm | 54 -
taverna-rest-activity/pom.xml | 96 -
.../taverna/t2/activities/rest/HTTPRequest.java | 105 -
.../t2/activities/rest/HTTPRequestHandler.java | 586 -
.../t2/activities/rest/HTTPRequestHeader.java | 66 -
.../t2/activities/rest/RESTActivity.java | 345 -
.../rest/RESTActivityConfigurationBean.java | 306 -
.../rest/RESTActivityCredentialsProvider.java | 178 -
.../t2/activities/rest/RESTActivityFactory.java | 165 -
.../rest/RESTActivityHealthCheck.java | 32 -
.../rest/RESTActivityHealthChecker.java | 58 -
.../t2/activities/rest/URISignatureHandler.java | 412 -
...t2.workbench.report.explainer.VisitExplainer | 1 -
...averna.t2.workflowmodel.health.HealthChecker | 1 -
.../spring/rest-activity-context-osgi.xml | 16 -
.../META-INF/spring/rest-activity-context.xml | 13 -
.../src/main/resources/schema.json | 75 -
.../rest/ApacheHttpClientUsageTest.java.bak | 215 -
.../rest/ExampleActivityTest.java.bak | 153 -
.../rest/URISignatureHandlerTest.java | 594 -
taverna-spreadsheet-import-activity/pom.xml | 121 -
.../spreadsheet/CSVSpreadsheetReader.java | 79 -
.../spreadsheet/ExcelSpreadsheetReader.java | 324 -
.../spreadsheet/ODFSpreadsheetReader.java | 193 -
.../t2/activities/spreadsheet/Range.java | 298 -
.../spreadsheet/SpreadsheetEmptyCellPolicy.java | 39 -
.../spreadsheet/SpreadsheetImportActivity.java | 358 -
.../SpreadsheetImportActivityFactory.java | 95 -
.../SpreadsheetImportConfiguration.java | 416 -
.../SpreadsheetImportHealthChecker.java | 61 -
.../spreadsheet/SpreadsheetOutputFormat.java | 37 -
.../spreadsheet/SpreadsheetReadException.java | 69 -
.../spreadsheet/SpreadsheetReader.java | 52 -
.../spreadsheet/SpreadsheetRowProcessor.java | 42 -
.../spreadsheet/SpreadsheetUtils.java | 128 -
.../t2/activities/spreadsheet/package.html | 3 -
...averna.t2.workflowmodel.health.HealthChecker | 1 -
.../spreadsheetimport-activity-context-osgi.xml | 15 -
.../spreadsheetimport-activity-context.xml | 12 -
.../src/main/resources/schema.json | 126 -
.../spreadsheet/CSVSpreadsheetReaderTest.java | 259 -
.../spreadsheet/ExcelSpreadsheetReaderTest.java | 299 -
.../spreadsheet/ODFSpreadsheetReaderTest.java | 293 -
.../t2/activities/spreadsheet/RangeTest.java | 195 -
.../SpreadsheetImportActivityFactoryTest.java | 75 -
.../SpreadsheetImportActivityTest.java | 186 -
.../SpreadsheetImportConfigurationTest.java | 265 -
.../SpreadsheetImportHealthCheckerTest.java | 91 -
.../SpreadsheetReadExceptionTest.java | 38 -
.../spreadsheet/SpreadsheetUtilsTest.java | 98 -
.../src/test/resources/test-spreadsheet.csv | 1 -
.../src/test/resources/test-spreadsheet.ods | Bin 16319 -> 0 bytes
.../src/test/resources/test-spreadsheet.xls | Bin 8192 -> 0 bytes
.../src/test/resources/test-spreadsheet.xlsx | Bin 7300 -> 0 bytes
taverna-wsdl-activity/pom.xml | 118 -
.../wsdl/InputPortTypeDescriptorActivity.java | 57 -
.../wsdl/OutputPortTypeDescriptorActivity.java | 57 -
.../t2/activities/wsdl/T2WSDLSOAPInvoker.java | 282 -
.../t2/activities/wsdl/WSDLActivity.java | 328 -
.../wsdl/WSDLActivityConfigurationBean.java | 82 -
.../wsdl/WSDLActivityDescriptorChecker.java | 147 -
.../t2/activities/wsdl/WSDLActivityFactory.java | 141 -
.../wsdl/WSDLActivityHealthChecker.java | 170 -
.../wsdl/WSDLOperationConfigurationBean.java | 57 -
.../sf/taverna/t2/activities/wsdl/package.html | 3 -
.../activities/wsdl/security/SSLUtilities.java | 151 -
.../wsdl/security/SecurityProfiles.java | 130 -
.../TavernaAxisCustomSSLSocketFactory.java | 40 -
.../security/ThreadLocalSSLSocketFactory.java | 186 -
.../activities/wsdl/wss4j/T2WSDoAllSender.java | 231 -
.../wsdl/xmlsplitter/AddXMLSplitterEdit.java | 290 -
.../xmlsplitter/XMLInputSplitterActivity.java | 186 -
.../XMLInputSplitterActivityFactory.java | 96 -
.../XMLInputSplitterHealthChecker.java | 65 -
.../xmlsplitter/XMLOutputSplitterActivity.java | 207 -
.../XMLOutputSplitterActivityFactory.java | 96 -
.../XMLOutputSplitterHealthChecker.java | 65 -
.../XMLSplitterConfigurationBean.java | 42 -
.../XMLSplitterConfigurationBeanBuilder.java | 205 -
...averna.t2.workflowmodel.health.HealthChecker | 4 -
.../spring/wsdl-activity-context-osgi.xml | 20 -
.../META-INF/spring/wsdl-activity-context.xml | 21 -
.../src/main/resources/schema.json | 39 -
.../src/main/resources/xml-splitter.schema.json | 80 -
.../wsdl/WSDLActivityFactoryTest.java | 64 -
.../t2/activities/wsdl/WSDLActivityTest.java | 148 -
.../t2/activities/wsdl/WSRFActivityTest.java | 226 -
.../wsdl/security/HTTPSConnectionsTest.java | 50 -
.../security/SecureServicesInvokerTest.java | 116 -
.../xmlsplitter/AddXMLSplitterEditTest.java | 136 -
.../XMLInputSplitterActivityTest.java | 88 -
.../XMLOutputSplitterActivityTest.java | 53 -
...XMLSplitterConfigurationBeanBuilderTest.java | 86 -
.../src/test/resources/log4j.properties | 8 -
.../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 | 92 -
.../wsdl/parser/ArrayTypeDescriptor.java | 57 -
.../wsdl/parser/AttributeTypeDescriptor.java | 30 -
.../taverna/wsdl/parser/BaseTypeDescriptor.java | 32 -
.../wsdl/parser/ComplexTypeDescriptor.java | 72 -
.../sf/taverna/wsdl/parser/TypeDescriptor.java | 297 -
.../wsdl/parser/UnknownOperationException.java | 37 -
.../net/sf/taverna/wsdl/parser/WSDLParser.java | 936 -
.../net/sf/taverna/wsdl/parser/package.html | 5 -
.../taverna/wsdl/soap/AbstractBodyBuilder.java | 362 -
.../net/sf/taverna/wsdl/soap/BodyBuilder.java | 49 -
.../taverna/wsdl/soap/BodyBuilderFactory.java | 53 -
.../wsdl/soap/CyclicReferenceException.java | 49 -
.../taverna/wsdl/soap/EncodedBodyBuilder.java | 160 -
.../taverna/wsdl/soap/LiteralBodyBuilder.java | 237 -
.../sf/taverna/wsdl/soap/ObjectConverter.java | 159 -
.../soap/SOAPResponseEncodedMultiRefParser.java | 197 -
.../wsdl/soap/SOAPResponseEncodedParser.java | 191 -
.../wsdl/soap/SOAPResponseLiteralParser.java | 97 -
.../taverna/wsdl/soap/SOAPResponseParser.java | 61 -
.../wsdl/soap/SOAPResponseParserFactory.java | 108 -
.../SOAPResponsePrimitiveLiteralParser.java | 72 -
.../wsdl/soap/SOAPResponsePrimitiveParser.java | 100 -
.../sf/taverna/wsdl/soap/WSDLSOAPInvoker.java | 323 -
.../java/net/sf/taverna/wsdl/soap/package.html | 5 -
.../wsdl/xmlsplitter/XMLInputSplitter.java | 290 -
.../wsdl/xmlsplitter/XMLOutputSplitter.java | 212 -
.../XMLSplitterExecutionException.java | 34 -
.../XMLSplitterSerialisationHelper.java | 359 -
.../taverna/wsdl/parser/TypeDescriptorTest.java | 240 -
.../sf/taverna/wsdl/parser/WSDLParserTest.java | 295 -
.../sf/taverna/wsdl/parser/WSRFParserTest.java | 57 -
.../wsdl/soap/EncodedBodyBuilderTest.java | 108 -
.../wsdl/soap/LiteralBodyBuilderTest.java | 170 -
.../wsdl/soap/SOAPResponseEncodedTest.java | 97 -
.../wsdl/soap/SOAPResponseLiteralTest.java | 174 -
.../wsdl/soap/SOAPResponseMultiRefTest.java | 246 -
.../soap/SOAPResponseParserFactoryTest.java | 64 -
.../wsdl/testutils/LocationConstants.java | 32 -
.../taverna/wsdl/testutils/WSDLTestHelper.java | 51 -
.../wsdl/xmlsplitter/XMLInputSplitterTest.java | 95 -
.../wsdl/xmlsplitter/XMLOutputSplitterTest.java | 79 -
.../XMLSplitterSerialisationHelperTest.java | 137 -
.../getComplexWithInternalListResponse.xml | 1 -
.../src/test/resources/jws-splitter-input.xml | 76 -
.../src/test/resources/log4j.properties | 8 -
.../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 -
.../sf/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 -
.../sf/taverna/wsdl/parser/TAV-744/security.xsd | 78 -
.../net/sf/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 | 49 -
.../t2/activities/xpath/XPathActivity.java | 211 -
.../xpath/XPathActivityConfigurationBean.java | 145 -
.../activities/xpath/XPathActivityFactory.java | 92 -
.../xpath/XPathActivityHealthCheck.java | 38 -
.../xpath/XPathActivityHealthChecker.java | 139 -
.../taverna/t2/activities/xpath/XPathUtils.java | 80 -
...t2.workbench.report.explainer.VisitExplainer | 1 -
...averna.t2.workflowmodel.health.HealthChecker | 1 -
.../spring/xpath-activity-context-osgi.xml | 15 -
.../META-INF/spring/xpath-activity-context.xml | 12 -
.../src/main/resources/schema.json | 45 -
349 files changed, 71434 deletions(-)
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/.gitignore
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-.classpath
-.project
-.settings/
-target/
-.svn
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/.travis.yml
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-language: java
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/pom.xml
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diff --git a/pom.xml b/pom.xml
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-<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.commonactivities</groupId>
- <artifactId>taverna-common-activities</artifactId>
- <version>2.1.0-incubating-SNAPSHOT</version>
- <packaging>pom</packaging>
- <name>Apache Taverna Common Activities</name>
- <properties>
- <taverna.language.version>0.15.0-incubating-SNAPSHOT</taverna.language.version>
- <taverna.osgi.version>0.2.0-incubating-SNAPSHOT</taverna.osgi.version>
- <taverna.engine.version>3.1.0-incubating-SNAPSHOT</taverna.engine.version>
- </properties>
- <modules>
- <module>taverna-beanshell-activity</module>
- <module>taverna-external-tool-activity</module>
- <module>taverna-interaction-activity</module>
- <module>taverna-rest-activity</module>
- <module>taverna-spreadsheet-import-activity</module>
- <module>taverna-wsdl-activity</module>
- <module>taverna-wsdl-generic</module>
- <module>taverna-xpath-activity</module>
- </modules>
- <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-common-activities/blob/2e8f451e/taverna-beanshell-activity/pom.xml
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diff --git a/taverna-beanshell-activity/pom.xml b/taverna-beanshell-activity/pom.xml
deleted file mode 100644
index 1654296..0000000
--- a/taverna-beanshell-activity/pom.xml
+++ /dev/null
@@ -1,90 +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>org.apache.taverna.commonactivities</groupId>
- <artifactId>taverna-common-activities</artifactId>
- <version>2.1.0-incubating-SNAPSHOT</version>
- </parent>
- <artifactId>taverna-beanshell-activity</artifactId>
- <packaging>bundle</packaging>
- <name>Apache Taverna Beanshell Activity</name>
-
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <extensions>true</extensions>
- <configuration>
- <instructions>
- <Embed-Dependency>artifactId=bsh</Embed-Dependency>
- </instructions>
- </configuration>
- </plugin>
- </plugins>
- </build>
-
-
- <dependencies>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-reference-api</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-workflowmodel-api</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.osgi</groupId>
- <artifactId>taverna-app-configuration-api</artifactId>
- <version>${taverna.osgi.version}</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
- <version>${jackson.version}</version>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-activity-test-utils</artifactId>
- <version>${taverna.engine.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-workflowmodel-impl</artifactId>
- <version>${taverna.engine.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.apache-extras.beanshell</groupId>
- <artifactId>bsh</artifactId>
- <version>${bsh.version}</version>
- </dependency>
- </dependencies>
-
-<!-- See https://code.google.com/a/apache-extras.org/p/beanshell/issues/detail?id=6
- TODO: Remove below <repository> once in Maven Central -->
-
- <repositories>
- <repository>
- <id>bintray.beanshell</id>
- <name>bintray</name>
- <url>http://dl.bintray.com/beanshell/Beanshell</url>
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- </repository>
- </repositories>
-
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivity.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivity.java b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivity.java
deleted file mode 100644
index 134d3fe..0000000
--- a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivity.java
+++ /dev/null
@@ -1,251 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.beanshell;
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.regex.Pattern;
-
-import net.sf.taverna.t2.activities.dependencyactivity.AbstractAsynchronousDependencyActivity;
-import net.sf.taverna.t2.reference.ErrorDocumentService;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.ReferenceServiceException;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.workflowmodel.OutputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback;
-
-import org.apache.log4j.Logger;
-
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import bsh.EvalError;
-import bsh.Interpreter;
-import bsh.TargetError;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-/**
- * An Activity providing Beanshell functionality.
- *
- * @author David Withers
- * @author Stuart Owen
- * @author Alex Nenadic
- */
-public class BeanshellActivity extends AbstractAsynchronousDependencyActivity {
-
- public static final String URI = "http://ns.taverna.org.uk/2010/activity/beanshell";
-
- protected BeanshellActivityConfigurationBean configurationBean;
-
- private static Logger logger = Logger.getLogger(BeanshellActivity.class);
-
- private Interpreter interpreter;
-
- private static String CLEAR_COMMAND = "clear();";
-
- private JsonNode json;
-
- public BeanshellActivity(ApplicationConfiguration applicationConfiguration) {
- super(applicationConfiguration);
- createInterpreter();
- }
-
- @Override
- public JsonNode getConfiguration() {
- return json;
- }
-
- @Override
- public void configure(JsonNode json) {
- this.json = json;
- checkGranularDepths();
- }
-
- /**
- * Creates the interpreter required to run the beanshell script, and assigns
- * the correct classloader setting according to the
- */
- private void createInterpreter() {
- interpreter = new Interpreter();
- }
-
- /**
- * As the Beanshell activity currently only can output values at the
- * specified depth, the granular depths should always be equal to the actual
- * depth.
- * <p>
- * Workflow definitions created with Taverna 2.0b1 would not honour this and
- * always set the granular depth to 0.
- * <p>
- * This method modifies the granular depths to be equal to the depths.
- */
- protected void checkGranularDepths() {
- for (OutputPort outputPort : getOutputPorts()) {
- if (outputPort.getGranularDepth() != outputPort.getDepth()) {
- logger.warn("Replacing granular depth of port "
- + outputPort.getName());
- // outputPort.setGranularDepth(outputPort.getDepth());
- }
- }
- }
-
- public ActivityInputPort getInputPort(String name) {
- for (ActivityInputPort port : getInputPorts()) {
- if (port.getName().equals(name)) {
- return port;
- }
- }
- return null;
- }
-
- private void clearInterpreter() {
- try {
- interpreter.eval(CLEAR_COMMAND);
- } catch (EvalError e) {
- logger.error("Could not clear the interpreter", e);
- }
- }
-
- @Override
- public void executeAsynch(final Map<String, T2Reference> data,
- final AsynchronousActivityCallback callback) {
- callback.requestRun(new Runnable() {
-
- public void run() {
-
- // Workflow run identifier (needed when classloader sharing is
- // set to 'workflow').
- String procID = callback.getParentProcessIdentifier();
- String workflowRunID;
- if (procID.contains(":")) {
- workflowRunID = procID.substring(0, procID.indexOf(':'));
- } else {
- workflowRunID = procID; // for tests, will be an empty
- // string
- }
-
- synchronized (interpreter) {
-
- // Configure the classloader for executing the Beanshell
- if (classLoader == null) {
- try {
- classLoader = findClassLoader(json, workflowRunID);
- interpreter.setClassLoader(classLoader);
- } catch (RuntimeException rex) {
- String message = "Unable to obtain the classloader for Beanshell service";
- callback.fail(message, rex);
- return;
- }
- }
-
- ReferenceService referenceService = callback.getContext()
- .getReferenceService();
-
- Map<String, T2Reference> outputData = new HashMap<String, T2Reference>();
-
- clearInterpreter();
- try {
- // set inputs
- for (String inputName : data.keySet()) {
- ActivityInputPort inputPort = getInputPort(inputName);
- Object input = referenceService.renderIdentifier(
- data.get(inputName),
- inputPort.getTranslatedElementClass(),
- callback.getContext());
- inputName = sanatisePortName(inputName);
- interpreter.set(inputName, input);
- }
- // run
- interpreter.eval(json.get("script").asText());
- // get outputs
- for (OutputPort outputPort : getOutputPorts()) {
- String name = outputPort.getName();
- Object value = interpreter.get(name);
- if (value == null) {
- ErrorDocumentService errorDocService = referenceService
- .getErrorDocumentService();
- value = errorDocService.registerError(
- "No value produced for output variable "
- + name, outputPort.getDepth(),
- callback.getContext());
- }
- outputData.put(name, referenceService.register(
- value, outputPort.getDepth(), true,
- callback.getContext()));
- }
- callback.receiveResult(outputData, new int[0]);
- } catch (EvalError e) {
- logger.error(e);
- try {
- int lineNumber = e.getErrorLineNumber();
-
- callback.fail("Line " + lineNumber + ": "
- + determineMessage(e));
- } catch (NullPointerException e2) {
- callback.fail(determineMessage(e));
- }
- } catch (ReferenceServiceException e) {
- callback.fail(
- "Error accessing beanshell input/output data for "
- + this, e);
- }
- clearInterpreter();
- }
- }
-
- /**
- * Removes any invalid characters from the port name. For example,
- * xml-text would become xmltext.
- *
- * @param name
- * @return
- */
- private String sanatisePortName(String name) {
- String result = name;
- if (Pattern.matches("\\w++", name) == false) {
- result = "";
- for (char c : name.toCharArray()) {
- if (Character.isLetterOrDigit(c) || c == '_') {
- result += c;
- }
- }
- }
- return result;
- }
- });
-
- }
-
- private static String determineMessage(Throwable e) {
- if (e instanceof TargetError) {
- Throwable t = ((TargetError) e).getTarget();
- if (t != null) {
- return t.getClass().getCanonicalName() + ": "
- + determineMessage(t);
- }
- }
- Throwable cause = e.getCause();
- if (cause != null) {
- return determineMessage(cause);
- }
- return e.getMessage();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityConfigurationBean.java b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityConfigurationBean.java
deleted file mode 100644
index 8a5f06f..0000000
--- a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityConfigurationBean.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.beanshell;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.dependencyactivity.DependencyActivityConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * A configuration bean specific to a Beanshell activity; provides details
- * about the Beanshell script and its local and artifact dependencies.
- *
- * @author Stuart Owen
- * @author David Withers
- * @author Alex Nenadic
- */
-@ConfigurationBean(uri = BeanshellActivity.URI + "#Config")
-public class BeanshellActivityConfigurationBean extends DependencyActivityConfigurationBean {
-
- private String script;
-
- public BeanshellActivityConfigurationBean() {
- super();
- this.script = "";
- }
-
- /**
- * @return the Beanshell script
- */
- public String getScript() {
- return script;
- }
-
- /**
- * @param script the Beanshell script
- */
- @ConfigurationProperty(name = "script", label = "Beanshell Script", description = "The beanshell script to be executed")
- public void setScript(String script) {
- this.script = script;
- }
-
- ///////////// From old code //////////
- @Deprecated
- private List<String> dependencies = new ArrayList<String>();
-
- /**
- * Returns the dependencies.
- *
- * @return the dependencies
- */
- public List<String> getDependencies() {
- return dependencies;
- }
-
- /**
- * Sets the dependencies.
- *
- * @param dependencies the new dependencies
- */
- public void setDependencies(List<String> dependencies) {
- this.dependencies = dependencies;
- }
- ///////////// From old code //////////
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityFactory.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityFactory.java b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityFactory.java
deleted file mode 100644
index c1b0e5d..0000000
--- a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityFactory.java
+++ /dev/null
@@ -1,79 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.beanshell;
-
-import java.io.IOException;
-import java.net.URI;
-import java.util.HashSet;
-import java.util.Set;
-
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-/**
- * An {@link ActivityFactory} for creating <code>BeanshellActivity</code>.
- *
- * @author David Withers
- */
-public class BeanshellActivityFactory implements ActivityFactory {
-
- private ApplicationConfiguration applicationConfiguration;
-
- @Override
- public BeanshellActivity createActivity() {
- return new BeanshellActivity(applicationConfiguration);
- }
-
- @Override
- public URI getActivityType() {
- return URI.create(BeanshellActivity.URI);
- }
-
- @Override
- public JsonNode getActivityConfigurationSchema() {
- ObjectMapper objectMapper = new ObjectMapper();
- try {
- return objectMapper.readTree(getClass().getResource("/schema.json"));
- } catch (IOException e) {
- return objectMapper.createObjectNode();
- }
- }
-
- public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
- this.applicationConfiguration = applicationConfiguration;
- }
-
- @Override
- public Set<ActivityInputPort> getInputPorts(JsonNode configuration) {
- return new HashSet<>();
- }
-
- @Override
- public Set<ActivityOutputPort> getOutputPorts(JsonNode configuration) {
- return new HashSet<>();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityHealthChecker.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityHealthChecker.java b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityHealthChecker.java
deleted file mode 100644
index 9913d77..0000000
--- a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityHealthChecker.java
+++ /dev/null
@@ -1,111 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.beanshell;
-
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.LinkedHashSet;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.dependencyactivity.AbstractAsynchronousDependencyActivity.FileExtFilter;
-import net.sf.taverna.t2.visit.VisitReport;
-import net.sf.taverna.t2.visit.VisitReport.Status;
-import net.sf.taverna.t2.workflowmodel.Processor;
-import net.sf.taverna.t2.workflowmodel.health.HealthCheck;
-import net.sf.taverna.t2.workflowmodel.health.HealthChecker;
-import bsh.ParseException;
-import bsh.Parser;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-public class BeanshellActivityHealthChecker implements HealthChecker<BeanshellActivity> {
-
- public boolean canVisit(Object subject) {
- return (subject!=null && subject instanceof BeanshellActivity);
- }
-
- public VisitReport visit(BeanshellActivity activity, List<Object> ancestors) {
- Object subject = (Processor) VisitReport.findAncestor(ancestors, Processor.class);
- if (subject == null) {
- // Fall back to using the activity itself as the subject of the reports
- subject = activity;
- }
- List<VisitReport> reports = new ArrayList<VisitReport>();
-
- String script = activity.getConfiguration().get("script").textValue();
- if (! script.trim().endsWith(";")) {
- /** Missing ; on last line is not allowed by Parser,
- * but is allowed by Interpreter.eval() used at runtime
- */
- script = script + ";";
- }
- Parser parser = new Parser(new StringReader(script));
- try {
- while (!parser.Line());
- reports.add(new VisitReport(HealthCheck.getInstance(), subject, "Script OK", HealthCheck.NO_PROBLEM, Status.OK));
- } catch (ParseException e) {
- VisitReport report = new VisitReport(HealthCheck.getInstance(), subject ,e.getMessage(), HealthCheck.INVALID_SCRIPT, Status.SEVERE);
- report.setProperty("exception", e);
- reports.add(report);
- }
-
- // Check if we can find all the Beanshell's dependencies
- if (activity.getConfiguration().has("localDependency")) {
- LinkedHashSet<String> localDependencies = new LinkedHashSet<>();
- for (JsonNode localDependency : activity.getConfiguration().get("localDependency")) {
- localDependencies.add(localDependency.textValue());
- }
-
- String[] jarArray = activity.libDir.list(new FileExtFilter(".jar"));
- if (jarArray != null) {
- List<String> jarFiles = Arrays.asList(jarArray); // URLs of all jars found in the lib directory
- for (String jar : localDependencies) {
- if (jarFiles.contains(jar)){
- localDependencies.remove(jar);
- }
- }
- }
- if (localDependencies.isEmpty()){ // all dependencies found
- reports.add(new VisitReport(HealthCheck.getInstance(), subject, "Beanshell dependencies found", HealthCheck.NO_PROBLEM, Status.OK));
- }
- else{
- VisitReport vr = new VisitReport(HealthCheck.getInstance(), subject, "Beanshell dependencies missing", HealthCheck.MISSING_DEPENDENCY, Status.SEVERE);
- vr.setProperty("dependencies", localDependencies);
- vr.setProperty("directory", activity.libDir);
- reports.add(vr);
- }
-
- }
- Status status = VisitReport.getWorstStatus(reports);
- VisitReport report = new VisitReport(HealthCheck.getInstance(), subject, "Beanshell report", HealthCheck.NO_PROBLEM,
- status, reports);
-
- return report;
-
- }
-
- public boolean isTimeConsuming() {
- return false;
- }
-
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/package.html
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/package.html b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/package.html
deleted file mode 100644
index 8b6e7a5..0000000
--- a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/package.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<body>
-Contains the activity classes required to include String constants within a DataFlow.
-</body>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-beanshell-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker b/taverna-beanshell-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
deleted file mode 100644
index 3fbf5a8..0000000
--- a/taverna-beanshell-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.beanshell.BeanshellActivityHealthChecker
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-beanshell-activity/src/main/resources/META-INF/spring/beanshell-activity-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/resources/META-INF/spring/beanshell-activity-context-osgi.xml b/taverna-beanshell-activity/src/main/resources/META-INF/spring/beanshell-activity-context-osgi.xml
deleted file mode 100644
index b98c9e4..0000000
--- a/taverna-beanshell-activity/src/main/resources/META-INF/spring/beanshell-activity-context-osgi.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <service ref="beanshellActivityHealthChecker" interface="net.sf.taverna.t2.workflowmodel.health.HealthChecker" />
-
- <service ref="beanshellActivityFactory" interface="net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory" />
-
- <reference id="applicationConfiguration" interface="uk.org.taverna.configuration.app.ApplicationConfiguration" />
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-beanshell-activity/src/main/resources/META-INF/spring/beanshell-activity-context.xml
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/resources/META-INF/spring/beanshell-activity-context.xml b/taverna-beanshell-activity/src/main/resources/META-INF/spring/beanshell-activity-context.xml
deleted file mode 100644
index c6cc552..0000000
--- a/taverna-beanshell-activity/src/main/resources/META-INF/spring/beanshell-activity-context.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="beanshellActivityHealthChecker" class="net.sf.taverna.t2.activities.beanshell.BeanshellActivityHealthChecker" />
-
- <bean id="beanshellActivityFactory" class="net.sf.taverna.t2.activities.beanshell.BeanshellActivityFactory">
- <property name="applicationConfiguration" ref="applicationConfiguration" />
- </bean>
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-beanshell-activity/src/main/resources/schema.json
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/resources/schema.json b/taverna-beanshell-activity/src/main/resources/schema.json
deleted file mode 100644
index fcf07b2..0000000
--- a/taverna-beanshell-activity/src/main/resources/schema.json
+++ /dev/null
@@ -1,21 +0,0 @@
-{
- "$schema": "http://json-schema.org/draft-03/schema#",
- "id": "http://ns.taverna.org.uk/2010/activity/beanshell.schema.json",
- "title": "Beanshell activity configuration",
- "type": "object",
- "extends" : "http://ns.taverna.org.uk/2010/activity/dependency.schema.json",
- "properties": {
- "@context": {
- "description": "JSON-LD context for interpreting the configuration as RDF",
- "required": true,
- "enum": ["http://ns.taverna.org.uk/2010/activity/beanshell.context.json"]
- },
- "script": {
- "title": "Beanshell Script",
- "description": "The beanshell script to be executed",
- "type": "string",
- "required": true,
- "default": ""
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-beanshell-activity/src/test/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityFactoryTest.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/test/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityFactoryTest.java b/taverna-beanshell-activity/src/test/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityFactoryTest.java
deleted file mode 100644
index 32290ac..0000000
--- a/taverna-beanshell-activity/src/test/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityFactoryTest.java
+++ /dev/null
@@ -1,64 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.beanshell;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.net.URI;
-
-import org.junit.Before;
-import org.junit.Test;
-
-/**
- *
- * @author David Withers
- */
-public class BeanshellActivityFactoryTest {
-
- private BeanshellActivityFactory factory;
-
- /**
- * @throws java.lang.Exception
- */
- @Before
- public void setUp() throws Exception {
- factory = new BeanshellActivityFactory();
- }
-
- /**
- * Test method for {@link net.sf.taverna.t2.activities.beanshell.BeanshellActivityFactory#createActivity()}.
- */
- @Test
- public void testCreateActivity() {
- BeanshellActivity createActivity = factory.createActivity();
- assertNotNull(createActivity);
- }
-
- /**
- * Test method for {@link net.sf.taverna.t2.activities.beanshell.BeanshellActivityFactory#getActivityType()}.
- */
- @Test
- public void testGetActivityURI() {
- assertEquals(URI.create(BeanshellActivity.URI), factory.getActivityType());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-beanshell-activity/src/test/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityHealthCheckerTest.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/test/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityHealthCheckerTest.java b/taverna-beanshell-activity/src/test/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityHealthCheckerTest.java
deleted file mode 100644
index 0b4b5ff..0000000
--- a/taverna-beanshell-activity/src/test/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityHealthCheckerTest.java
+++ /dev/null
@@ -1,173 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.beanshell;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Map;
-
-import net.sf.taverna.t2.activities.testutils.ActivityInvoker;
-import net.sf.taverna.t2.visit.VisitReport;
-import net.sf.taverna.t2.visit.VisitReport.Status;
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.impl.EditsImpl;
-
-import org.junit.Before;
-import org.junit.Test;
-
-import com.fasterxml.jackson.databind.node.JsonNodeFactory;
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
-/**
- * BeanshellActivityHealthChecker tests
- *
- * @author Stian Soiland-Reyes
- *
- */
-public class BeanshellActivityHealthCheckerTest {
-
- private Edits edits = new EditsImpl();
-
- private ObjectNode configuration;
-
- @Before
- public void setup() throws Exception {
- configuration = JsonNodeFactory.instance.objectNode();
- configuration.put("classLoaderSharing", "workflow");
- }
-
- @Test
- public void oneLinerNoSemicolon() throws Exception {
- BeanshellActivity activity = new BeanshellActivity(null);
- configuration.put("script", "a = 5+3");
- // Notice lack of ;
- activity.configure(configuration);
-
- Map<String,Object> inputs = new HashMap<String, Object>();
- Map<String, Class<?>> expectedOutputs = new HashMap<String, Class<?>>();
- ActivityInvoker.invokeAsyncActivity(activity, inputs, expectedOutputs);
-
- BeanshellActivityHealthChecker healthChecker = new BeanshellActivityHealthChecker();
- assertTrue(healthChecker.canVisit(activity));
- ArrayList<Object> ancestors = new ArrayList<Object>();
-
- ancestors.add(edits.createProcessor("beanie"));
- VisitReport visit = healthChecker.visit(activity, ancestors);
- assertEquals(Status.OK, visit.getStatus());
- }
-
- @Test
- public void oneLiner() throws Exception {
- BeanshellActivity activity = new BeanshellActivity(null);
- configuration.put("script", "System.out.println(\"Hello\");");
- activity.configure(configuration);
-
- Map<String,Object> inputs = new HashMap<String, Object>();
- Map<String, Class<?>> expectedOutputs = new HashMap<String, Class<?>>();
- ActivityInvoker.invokeAsyncActivity(activity, inputs, expectedOutputs);
-
- BeanshellActivityHealthChecker healthChecker = new BeanshellActivityHealthChecker();
- assertTrue(healthChecker.canVisit(activity));
- ArrayList<Object> ancestors = new ArrayList<Object>();
-
- ancestors.add(edits.createProcessor("beanie"));
- VisitReport visit = healthChecker.visit(activity, ancestors);
- assertEquals(Status.OK, visit.getStatus());
- }
-
- @Test
- public void threeLines() throws Exception {
- BeanshellActivity activity = new BeanshellActivity(null);
- configuration.put("script", "if (2>1) {\n" +
- " new Integer(4);\n" +
- "}");
- activity.configure(configuration);
-
- Map<String,Object> inputs = new HashMap<String, Object>();
- Map<String, Class<?>> expectedOutputs = new HashMap<String, Class<?>>();
- ActivityInvoker.invokeAsyncActivity(activity, inputs, expectedOutputs);
-
- BeanshellActivityHealthChecker healthChecker = new BeanshellActivityHealthChecker();
- assertTrue(healthChecker.canVisit(activity));
- ArrayList<Object> ancestors = new ArrayList<Object>();
-
- ancestors.add(edits.createProcessor("beanie"));
- VisitReport visit = healthChecker.visit(activity, ancestors);
- assertEquals(Status.OK, visit.getStatus());
-
-
-
- }
-
- @Test
- public void invalidScript() throws Exception {
- BeanshellActivity activity = new BeanshellActivity(null);
- configuration.put("script", "invalid script 5 +");
- activity.configure(configuration);
-
- Map<String,Object> inputs = new HashMap<String, Object>();
- Map<String, Class<?>> expectedOutputs = new HashMap<String, Class<?>>();
- try {
- ActivityInvoker.invokeAsyncActivity(activity, inputs, expectedOutputs);
- fail("Script should not be valid");
- } catch (RuntimeException ex) {
- // expected to fail
- }
-
-
- BeanshellActivityHealthChecker healthChecker = new BeanshellActivityHealthChecker();
- assertTrue(healthChecker.canVisit(activity));
- ArrayList<Object> ancestors = new ArrayList<Object>();
-
- ancestors.add(edits.createProcessor("beanie"));
- VisitReport visit = healthChecker.visit(activity, ancestors);
- assertEquals(Status.SEVERE, visit.getStatus());
- }
-
- @Test
- public void strangeWhitespace() throws Exception {
- BeanshellActivity activity = new BeanshellActivity(null);
- configuration.put("script", "b = \"fish\";\n" +
- "a = 2+3\n" +
- "\n" +
- "\n" +
- " +5 ");
- // Notice lots of whitespace, but still valid
- activity.configure(configuration);
-
- Map<String,Object> inputs = new HashMap<String, Object>();
- Map<String, Class<?>> expectedOutputs = new HashMap<String, Class<?>>();
- ActivityInvoker.invokeAsyncActivity(activity, inputs, expectedOutputs);
-
- BeanshellActivityHealthChecker healthChecker = new BeanshellActivityHealthChecker();
- assertTrue(healthChecker.canVisit(activity));
- ArrayList<Object> ancestors = new ArrayList<Object>();
-
- ancestors.add(edits.createProcessor("beanie"));
- VisitReport visit = healthChecker.visit(activity, ancestors);
- System.out.println(visit);
- assertEquals(Status.OK, visit.getStatus());
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-beanshell-activity/src/test/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityTest.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/test/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityTest.java b/taverna-beanshell-activity/src/test/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityTest.java
deleted file mode 100644
index 8d724a5..0000000
--- a/taverna-beanshell-activity/src/test/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityTest.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.beanshell;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import net.sf.taverna.t2.activities.testutils.ActivityInvoker;
-import net.sf.taverna.t2.workflowmodel.AbstractPort;
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.impl.EditsImpl;
-import net.sf.taverna.t2.workflowmodel.processor.activity.impl.ActivityInputPortImpl;
-import net.sf.taverna.t2.workflowmodel.processor.activity.impl.ActivityOutputPortImpl;
-
-import org.junit.Before;
-import org.junit.Test;
-
-import com.fasterxml.jackson.databind.node.JsonNodeFactory;
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
-/**
- * Beanshell Activity Tests
- * @author Stuart Owen
- *
- */
-public class BeanshellActivityTest {
-
- private ObjectNode configuration;
-
- @Before
- public void setup() throws Exception {
- configuration = JsonNodeFactory.instance.objectNode();
- configuration.put("classLoaderSharing", "workflow");
- }
-
- /**
- * Tests a simple script (String output = input + "_returned") to ensure the script is invoked correctly.
- * @throws Exception
- */
- @Test
- public void simpleScript() throws Exception {
- BeanshellActivity activity = new BeanshellActivity(null);
- Edits edits = new EditsImpl();
- edits.getAddActivityInputPortEdit(activity, new ActivityInputPortImpl("input", 0, false, null, String.class)).doEdit();
- edits.getAddActivityOutputPortEdit(activity, new ActivityOutputPortImpl("output", 0, 0)).doEdit();
-
- configuration.put("script", "String output = input + \"_returned\";");
-
- activity.configure(configuration);
- assertEquals("There should be 1 input port",1,activity.getInputPorts().size());
- assertEquals("There should be 1 output port",1,activity.getOutputPorts().size());
-
- assertEquals("The input should be called input", "input",((AbstractPort)activity.getInputPorts().toArray()[0]).getName());
- assertEquals("The output should be called output", "output",((AbstractPort)activity.getOutputPorts().toArray()[0]).getName());
-
- Map<String,Object> inputs = new HashMap<String, Object>();
- inputs.put("input", "aString");
- Map<String, Class<?>> expectedOutputs = new HashMap<String, Class<?>>();
- expectedOutputs.put("output", String.class);
-
- Map<String,Object> outputs = ActivityInvoker.invokeAsyncActivity(activity, inputs, expectedOutputs);
- assertTrue("there should be an output named output",outputs.containsKey("output"));
- assertEquals("output should have the value aString_returned","aString_returned",outputs.get("output"));
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/pom.xml b/taverna-external-tool-activity/pom.xml
deleted file mode 100644
index 49ddfbd..0000000
--- a/taverna-external-tool-activity/pom.xml
+++ /dev/null
@@ -1,91 +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>org.apache.taverna.commonactivities</groupId>
- <artifactId>taverna-common-activities</artifactId>
- <version>2.1.0-incubating-SNAPSHOT</version>
- </parent>
- <artifactId>taverna-external-tool-activity</artifactId>
- <packaging>bundle</packaging>
- <name>Apache Taverna External Tool Activity</name>
-
- <dependencies>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-reference-api</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-workflowmodel-api</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-credential-manager</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
-
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-reference-types</artifactId>
- <version>${taverna.engine.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.osgi</groupId>
- <artifactId>taverna-app-configuration-api</artifactId>
- <version>${taverna.osgi.version}</version>
- </dependency>
- <dependency>
- <groupId>org.jdom</groupId>
- <artifactId>com.springsource.org.jdom</artifactId>
- <version>${jdom.version}</version>
- </dependency>
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <version>${commons.io.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.commons</groupId>
- <artifactId>com.springsource.org.apache.commons.lang</artifactId>
- <version>${commons.lang.version}</version>
- </dependency>
- <dependency>
- <groupId>org.openengsb.wrapped</groupId>
- <artifactId>com.jcraft.jsch-all</artifactId>
- <version>${jsch.version}</version>
- <exclusions>
- <exclusion>
- <groupId>com.jcraft</groupId>
- <artifactId>jsch</artifactId>
- </exclusion>
- <exclusion>
- <groupId>com.jcraft</groupId>
- <artifactId>jzlib</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
- <!--dependency>
- <groupId>com.jcraft.jsch</groupId>
- <artifactId>com.springsource.com.jcraft.jsch</artifactId>
- <version>${jsch.version}</version>
- </dependency-->
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.engine</groupId>
- <artifactId>taverna-activity-test-utils</artifactId>
- <version>${taverna.engine.version}</version>
- <scope>test</scope>
- </dependency>
- </dependencies>
-
-
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java
deleted file mode 100644
index e2ae7e1..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java
+++ /dev/null
@@ -1,77 +0,0 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
- *
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
- *
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
- */
-
-package de.uni_luebeck.inb.knowarc.gui;
-
-import javax.swing.JOptionPane;
-
-import de.uni_luebeck.inb.knowarc.usecases.invocation.AskUserForPw;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNode;
-
-public final class AskUserForPwPopup implements AskUserForPw {
- private SshNode ret;
- private String pw, pp, kf, us;
-
- public static String ask(String message, String title) {
- return (String) JOptionPane.showInputDialog(null, message, title, JOptionPane.QUESTION_MESSAGE, null, null, "");
- }
-
- public static boolean askYN(String message, String title) {
- return JOptionPane.showConfirmDialog(null, message, title, JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE) == JOptionPane.YES_OPTION;
- }
-
- public String getPassword() {
- getUsername();
- if (pw != null)
- return pw;
- pw = ask("Please enter your password for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost());
- return pw;
- }
-
- public String getPassphrase() {
- getUsername();
- if (pp != null)
- return pp;
- pp = ask("Please enter your passphrase for " + kf + " used for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost());
- return pp;
- }
-
- public String getKeyfile() {
- getUsername();
- if (kf != null)
- return kf;
- kf = ask("Please enter the keyfile for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost());
- return kf;
- }
-
- public String getUsername() {
- if (us != null)
- return us;
- us = ask("Please enter the username for " + ret.getHost(), "Username for " + ret.getHost());
- return us;
- }
-
- public void setSshNode(SshNode sshNode) {
- this.ret = sshNode;
- }
-
- public void authenticationSucceeded() {
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java
deleted file mode 100755
index a6bf707..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java
+++ /dev/null
@@ -1,75 +0,0 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
- *
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
- *
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
- */
-
-package de.uni_luebeck.inb.knowarc.gui;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-
-public class PleaseWaitDialog extends JDialog {
- private static final long serialVersionUID = 1L;
-
- static PleaseWaitDialog instance = new PleaseWaitDialog();
-
- public class WaitMessage{
- public WaitMessage() {
- }
-
- String str;
- public void set(String newstr) {
- synchronized (PleaseWaitDialog.instance) {
- if(this.str != null && this.str.equals(newstr)) return;
- if(this.str != null) messages.remove(this.str);
- this.str = newstr;
- if(this.str != null) messages.add(this.str);
- }
- updateDialog();
- }
- public void done() {
- set(null);
- }
- }
-
- private void updateDialog() {
- synchronized (PleaseWaitDialog.instance) {
- if(messages.size() > 0) this.setVisible(true);
- else this.setVisible(false);
- String t = "";
- for (String cur : messages) {
- t += cur + "<br>";
- }
- l.setText("<html>"+t+"</html>");
- }
- }
-
- List<String> messages = new ArrayList<String>();
-
- JLabel l;
- private PleaseWaitDialog() {
- this.setAlwaysOnTop(true);
- this.setTitle("Please wait");
- l = new JLabel("");
- this.add(l);
- this.setSize(400, 100);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java
deleted file mode 100644
index ea49079..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java
+++ /dev/null
@@ -1,253 +0,0 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
- *
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
- *
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
- */
-
-package de.uni_luebeck.inb.knowarc.usecases;
-
-import java.util.Arrays;
-import java.util.Iterator;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-/**
- * Representation of information about a single runtime environment. It is used
- * to decide if one runtime environment is possibly compatible with another one
- * for the selection of queues to commit to.
- *
- * To experiment/test these functions, run the following java -cp
- * target/taverna-knowarc-processor-0.1.7.jar
- * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1 foo-1 java -cp
- * target/taverna-knowarc-processor-0.1.7.jar
- * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1 bla-2 java -cp
- * target/taverna-knowarc-processor-0.1.7.jar
- * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1.2 bla-1
- *
- * @author Steffen Moeller
- */
-@SuppressWarnings("unchecked")
-public class RuntimeEnvironment implements Comparable {
-
- private static Logger logger = Logger.getLogger(RuntimeEnvironment.class);
-
-
- /**
- * Unique identification of the runtime environment - the full name
- */
- protected String id;
-
- /**
- * Accessor function for the complete identifier of the runtime environment
- */
- public String getID() {
- return id;
- }
-
- protected String name;
-
- /**
- * Accessor function for the RE's name
- */
- public String getName() {
- return name;
- }
-
- protected String version;
-
- /**
- * Accessfor function for the version
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * for those busy fellows who don't have the time to convert the String into
- * a RuntimeEnvironment object.
- *
- * @author Steffen Moeller
- */
- public boolean atLeastAsCapableAs(String s) {
- RuntimeEnvironment tmpRE = new RuntimeEnvironment(s);
- return this.atLeastAsCapableAs(tmpRE);
- }
-
- /**
- * Indicates if a runtime environment has the same name, and if so, if the
- * given RE has the same or a later version.
- *
- * @author Steffen Moeller
- */
- public boolean atLeastAsCapableAs(RuntimeEnvironment re) {
- if (!name.equals(re.name))
- return false;
- int c = compareVersions(getVersion(), re.getVersion());
- if (c >= 0) {
- return true;
- } else {
- return false;
- }
- }
-
- /**
- * Indicates if this runtimeEnvironment is the same version or later as any
- * in that list.
- *
- * @author Steffen Moeller
- */
- public boolean atLeastAsCapableAsAnyOf(Iterable<RuntimeEnvironment> res) {
- boolean compatibleOneFound = false;
- Iterator<RuntimeEnvironment> i = res.iterator();
- while (i.hasNext() && !compatibleOneFound) {
- RuntimeEnvironment r = i.next();
- compatibleOneFound = atLeastAsCapableAs(r);
- }
- return compatibleOneFound;
- }
-
- /**
- * Indicates if any of the runtime environments listed is the same version
- * as this or later.
- *
- * @author Steffen Moeller
- */
- public boolean isInferiorToAtLeastOneIn(Iterable<RuntimeEnvironment> res) {
- boolean compatibleOneFound = false;
- Iterator<RuntimeEnvironment> i = res.iterator();
- while (i.hasNext() && !compatibleOneFound) {
- RuntimeEnvironment r = i.next();
- compatibleOneFound = r.atLeastAsCapableAs(this);
- }
- return compatibleOneFound;
- }
-
- /**
- * Parses a string as commonly presented by the infosystem
- *
- * @author Steffen Moeller
- */
- public RuntimeEnvironment(String raw) {
- id = raw;
- int dashpos = raw.indexOf("-");
- if (-1 == dashpos) {
- version = "";
- name = raw;
- } else {
- name = raw.substring(0, dashpos);
- if (dashpos + 1 <= raw.length()) {
- version = raw.substring(dashpos + 1, raw.length());
- } else {
- version = "";
- }
- }
- }
-
- /**
- * to make it behave like a string at time, as it was originally implemented
- */
- @Override
- public String toString() {
- return id;
- }
-
- /**
- * Implementation of Comparable interface. It comes handy albeit this
- * function says nothing about the compatibility of two runtime environments
- * unless their names are identical and the relation of the constraint was
- * taken into account. It just sorts them in lists.
- */
- public int compareTo(Object o) throws ClassCastException {
- RuntimeEnvironment r = (RuntimeEnvironment) o;
- if (getName().equals(r.getName())) {
- return RuntimeEnvironment.compareVersions(getVersion(), r.getVersion());
- } else {
- return id.compareTo(r.getID());
- }
- }
-
- /**
- * FIXME: For the sake of simplicity, this implementation makes an error in
- * treating . and - in the versions equally. Versions, if numerical, are
- * treated numerically. Otherwise it is lexicographical, which is error
- * prone, though. Should the 'Scanner' class should be tapped into?
- *
- * @author Steffen Moeller
- */
- public static int compareVersions(String a, String b) {
-
- // null pointer exceptions are not risked .. we are nice
- if (null == a)
- a = "";
- if (null == b)
- b = "";
-
- // catching the dumb case first
- if (a.equals(b))
- return 0;
-
- List as = Arrays.asList(a.split("[.-]"));
- List bs = Arrays.asList(b.split("[.-]"));
-
- // both lists have the empty element as members at least
- Iterator aIterator = as.iterator();
- Iterator bIterator = bs.iterator();
-
- while (aIterator.hasNext()) {
- String aa = (String) aIterator.next();
- if (!bIterator.hasNext()) {
- // a is longer while equal so far
- return 1; // a > b
- }
- String bb = (String) bIterator.next();
- if (!aa.equals(bb)) {
- // a and b differ
- try {
- Integer aInt = Integer.parseInt(aa);
- Integer bInt = Integer.parseInt(bb);
- return aInt.compareTo(bInt);
- } catch (Exception e) {
- return aa.compareTo(bb);
- }
- }
- }
- if (bIterator.hasNext()) {
- // b is longer while equal so far
- return -1; // a < b
- }
- return 0; // a == b
- }
-
- /**
- * For testing purposes
- */
- public static void main(String argv[]) {
- if ("compare".equals(argv[0])) {
- RuntimeEnvironment r1 = new RuntimeEnvironment(argv[1]);
- RuntimeEnvironment r2 = new RuntimeEnvironment(argv[2]);
- logger.info("r1.getName(): " + r1.getName());
- logger.info("r1.getVersion(): " + r1.getVersion());
- logger.info("r2.getName(): " + r2.getName());
- logger.info("r2.getVersion(): " + r2.getVersion());
- logger.info("r1.atLeastAsCapableAs(r2): " + String.valueOf(r1.atLeastAsCapableAs(r2)));
- } else {
- logger.info("Don't know how to '" + argv[0] + "'");
- }
- }
-
-}