taverna-* module names
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/commit/2c71f9a9 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/tree/2c71f9a9 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/diff/2c71f9a9 Branch: refs/heads/master Commit: 2c71f9a95c7fe6c525cacedeac76646262059dfe Parents: 529e59d Author: Stian Soiland-Reyes <[email protected]> Authored: Mon Feb 23 15:33:34 2015 +0000 Committer: Stian Soiland-Reyes <[email protected]> Committed: Mon Feb 23 15:33:34 2015 +0000 ---------------------------------------------------------------------- pom.xml | 20 +- server-client/pom.xml | 130 -- .../uk/org/taverna/server/client/Connected.java | 20 - .../uk/org/taverna/server/client/DirEntry.java | 39 - .../uk/org/taverna/server/client/Directory.java | 94 -- .../java/uk/org/taverna/server/client/File.java | 95 -- .../uk/org/taverna/server/client/Property.java | 18 - .../java/uk/org/taverna/server/client/Run.java | 215 --- .../uk/org/taverna/server/client/Status.java | 36 - .../taverna/server/client/TavernaServer.java | 128 -- .../client/TavernaServerConnectionFactory.java | 23 - .../org/taverna/server/client/package-info.java | 5 - server-client/src/main/wadl/tavserv.wadl | 591 ------- server-distribution/pom.xml | 145 -- server-distribution/src/assemble/dist.xml | 82 - server-execution-delegate/pom.xml | 41 - .../execution_delegate/ExecutionDelegate.java | 172 -- .../execution_delegate/RemoteExecution.java | 188 --- .../src/test/java/SerializationTest.java | 54 - server-port-description/.gitignore | 1 - server-port-description/pom.xml | 45 - .../server/port_description/AbsentValue.java | 13 - .../server/port_description/AbstractPort.java | 26 - .../AbstractPortDescription.java | 29 - .../server/port_description/AbstractValue.java | 32 - .../server/port_description/ErrorValue.java | 25 - .../port_description/InputDescription.java | 51 - .../server/port_description/LeafValue.java | 19 - .../server/port_description/ListValue.java | 32 - .../server/port_description/Namespaces.java | 12 - .../port_description/OutputDescription.java | 52 - .../server/port_description/package-info.java | 19 - .../port_description/utils/IntAdapter.java | 32 - .../server/port_description/JaxbSanityTest.java | 98 -- server-rmidaemon/pom.xml | 61 - .../org/taverna/server/rmidaemon/Registry.java | 72 - .../taverna/server/rmidaemon/package-info.java | 5 - server-runinterface/.gitignore | 1 - server-runinterface/pom.xml | 30 - .../src/main/java/META-INF/MANIFEST.MF | 3 - .../remote/IllegalStateTransitionException.java | 36 - .../remote/ImplementationException.java | 26 - .../localworker/remote/RemoteDirectory.java | 62 - .../remote/RemoteDirectoryEntry.java | 62 - .../server/localworker/remote/RemoteFile.java | 98 -- .../server/localworker/remote/RemoteInput.java | 92 -- .../localworker/remote/RemoteListener.java | 77 - .../localworker/remote/RemoteRunFactory.java | 84 - .../remote/RemoteSecurityContext.java | 34 - .../localworker/remote/RemoteSingleRun.java | 254 --- .../server/localworker/remote/RemoteStatus.java | 40 - .../remote/StillWorkingOnItException.java | 20 - .../server/localworker/remote/package-info.java | 9 - .../localworker/server/UsageRecordReceiver.java | 29 - .../server/localworker/server/package-info.java | 9 - server-unix-forker/pom.xml | 61 - .../org/taverna/server/unixforker/Forker.java | 208 --- server-usagerecord/.gitignore | 1 - server-usagerecord/pom.xml | 79 - .../main/java/org/ogf/usage/JobUsageRecord.java | 304 ---- server-usagerecord/src/main/xsd/ur.xsd | 425 ----- server-usagerecord/src/main/xsd/xmlds.xsd | 318 ---- server-usagerecord/src/test/java/TestUR.java | 120 -- server-webapp/.gitignore | 1 - server-webapp/.springBeans | 59 - server-webapp/pom.xml | 889 ---------- .../resources/datanucleus_log4j.properties | 4 - .../master/ContentsDescriptorBuilder.java | 292 ---- .../taverna/server/master/DirectoryREST.java | 375 ----- .../server/master/FileConcatenation.java | 68 - .../org/taverna/server/master/InputREST.java | 252 --- .../taverna/server/master/InteractionFeed.java | 107 -- .../server/master/ListenerPropertyREST.java | 78 - .../taverna/server/master/ListenersREST.java | 93 -- .../taverna/server/master/ManagementState.java | 215 --- .../java/org/taverna/server/master/RunREST.java | 499 ------ .../taverna/server/master/RunSecurityREST.java | 303 ---- .../server/master/SingleListenerREST.java | 97 -- .../taverna/server/master/TavernaServer.java | 1425 ---------------- .../server/master/TavernaServerSupport.java | 957 ----------- .../org/taverna/server/master/admin/Admin.java | 1100 ------------- .../taverna/server/master/admin/AdminBean.java | 794 --------- .../server/master/admin/package-info.java | 33 - .../taverna/server/master/api/ContentTypes.java | 50 - .../server/master/api/DirectoryBean.java | 16 - .../org/taverna/server/master/api/FeedBean.java | 13 - .../taverna/server/master/api/InputBean.java | 21 - .../server/master/api/ListenerPropertyBean.java | 15 - .../server/master/api/ListenersBean.java | 13 - .../server/master/api/ManagementModel.java | 61 - .../server/master/api/OneListenerBean.java | 14 - .../org/taverna/server/master/api/RunBean.java | 17 - .../taverna/server/master/api/SecurityBean.java | 14 - .../taverna/server/master/api/SupportAware.java | 21 - .../server/master/api/TavernaServerBean.java | 101 -- .../taverna/server/master/api/package-info.java | 6 - .../server/master/common/Capability.java | 22 - .../server/master/common/Credential.java | 149 -- .../server/master/common/DirEntryReference.java | 93 -- .../server/master/common/InputDescription.java | 110 -- .../server/master/common/Namespaces.java | 39 - .../server/master/common/Permission.java | 43 - .../server/master/common/ProfileList.java | 42 - .../org/taverna/server/master/common/Roles.java | 25 - .../server/master/common/RunReference.java | 67 - .../taverna/server/master/common/Status.java | 44 - .../org/taverna/server/master/common/Trust.java | 79 - .../org/taverna/server/master/common/Uri.java | 432 ----- .../server/master/common/VersionedElement.java | 65 - .../taverna/server/master/common/Workflow.java | 367 ----- .../server/master/common/package-info.java | 29 - .../server/master/common/version/Version.java | 43 - .../taverna/server/master/defaults/Default.java | 99 -- .../server/master/defaults/package-info.java | 5 - .../exceptions/BadInputPortNameException.java | 21 - .../exceptions/BadPropertyValueException.java | 26 - .../exceptions/BadStateChangeException.java | 35 - .../exceptions/FilesystemAccessException.java | 38 - .../exceptions/GeneralFailureException.java | 28 - .../exceptions/InvalidCredentialException.java | 36 - .../master/exceptions/NoCreateException.java | 32 - .../exceptions/NoCredentialException.java | 18 - .../master/exceptions/NoDestroyException.java | 24 - .../exceptions/NoDirectoryEntryException.java | 24 - .../master/exceptions/NoListenerException.java | 33 - .../master/exceptions/NoUpdateException.java | 33 - .../master/exceptions/NotOwnerException.java | 23 - .../master/exceptions/OverloadedException.java | 35 - .../master/exceptions/UnknownRunException.java | 27 - .../server/master/exceptions/package-info.java | 29 - .../taverna/server/master/facade/Facade.java | 73 - .../server/master/facade/package-info.java | 10 - .../factories/ConfigurableRunFactory.java | 133 -- .../master/factories/ListenerFactory.java | 46 - .../server/master/factories/RunFactory.java | 40 - .../server/master/factories/package-info.java | 10 - .../identity/AuthorityDerivedIDMapper.java | 50 - .../master/identity/CompositeIDMapper.java | 65 - .../master/identity/ConstantIDMapper.java | 32 - .../server/master/identity/NameIDMapper.java | 50 - .../identity/StrippedDownAuthProvider.java | 278 ---- .../taverna/server/master/identity/User.java | 153 -- .../server/master/identity/UserStore.java | 389 ----- .../server/master/identity/UserStoreAPI.java | 91 - .../identity/WorkflowInternalAuthProvider.java | 304 ---- .../server/master/identity/package-info.java | 10 - .../interaction/InteractionFeedSupport.java | 316 ---- .../server/master/interaction/package-info.java | 10 - .../server/master/interfaces/Directory.java | 82 - .../master/interfaces/DirectoryEntry.java | 47 - .../taverna/server/master/interfaces/File.java | 69 - .../taverna/server/master/interfaces/Input.java | 92 -- .../server/master/interfaces/Listener.java | 64 - .../master/interfaces/LocalIdentityMapper.java | 29 - .../master/interfaces/MessageDispatcher.java | 45 - .../server/master/interfaces/Policy.java | 120 -- .../server/master/interfaces/RunStore.java | 82 - .../interfaces/SecurityContextFactory.java | 32 - .../server/master/interfaces/TavernaRun.java | 219 --- .../interfaces/TavernaSecurityContext.java | 213 --- .../master/interfaces/UriBuilderFactory.java | 43 - .../server/master/interfaces/package-info.java | 10 - .../localworker/AbstractRemoteRunFactory.java | 440 ----- .../master/localworker/ForkRunFactory.java | 323 ---- .../localworker/IdAwareForkRunFactory.java | 516 ------ .../master/localworker/LocalWorkerFactory.java | 31 - .../master/localworker/LocalWorkerState.java | 454 ----- .../master/localworker/PersistedState.java | 257 --- .../server/master/localworker/StreamLogger.java | 62 - .../server/master/localworker/package-info.java | 10 - .../master/notification/EmailDispatcher.java | 113 -- .../master/notification/JabberDispatcher.java | 140 -- .../master/notification/NotificationEngine.java | 145 -- .../notification/RateLimitedDispatcher.java | 89 - .../master/notification/SMSDispatcher.java | 158 -- .../master/notification/TwitterDispatcher.java | 132 -- .../master/notification/atom/AtomFeed.java | 134 -- .../server/master/notification/atom/Event.java | 110 -- .../master/notification/atom/EventDAO.java | 206 --- .../master/notification/atom/package-info.java | 29 - .../master/notification/package-info.java | 10 - .../org/taverna/server/master/package-info.java | 11 - .../server/master/rest/ContentTypes.java | 28 - .../server/master/rest/DirectoryContents.java | 61 - .../taverna/server/master/rest/FileSegment.java | 78 - .../server/master/rest/InteractionFeedREST.java | 126 -- .../server/master/rest/ListenerDefinition.java | 32 - .../master/rest/MakeOrUpdateDirEntry.java | 56 - .../master/rest/TavernaServerDirectoryREST.java | 240 --- .../master/rest/TavernaServerInputREST.java | 355 ---- .../master/rest/TavernaServerListenersREST.java | 428 ----- .../server/master/rest/TavernaServerREST.java | 604 ------- .../master/rest/TavernaServerRunREST.java | 797 --------- .../master/rest/TavernaServerSecurityREST.java | 775 --------- .../rest/handler/AccessDeniedHandler.java | 21 - .../rest/handler/BadInputPortNameHandler.java | 23 - .../rest/handler/BadPropertyValueHandler.java | 23 - .../rest/handler/BadStateChangeHandler.java | 23 - .../master/rest/handler/EntryHandler.java | 131 -- .../server/master/rest/handler/FeedHandler.java | 66 - .../rest/handler/FileConcatenationHandler.java | 61 - .../master/rest/handler/FileMessageHandler.java | 80 - .../master/rest/handler/FileSegmentHandler.java | 74 - .../rest/handler/FilesystemAccessHandler.java | 23 - .../rest/handler/GeneralFailureHandler.java | 21 - .../server/master/rest/handler/HandlerCore.java | 71 - .../rest/handler/IllegalArgumentHandler.java | 21 - .../handler/ImplementationProblemHandler.java | 21 - .../rest/handler/InputStreamMessageHandler.java | 107 -- .../rest/handler/InvalidCredentialHandler.java | 23 - .../rest/handler/JAXBExceptionHandler.java | 22 - .../rest/handler/NegotiationFailedHandler.java | 25 - .../master/rest/handler/NoCreateHandler.java | 23 - .../rest/handler/NoCredentialHandler.java | 21 - .../master/rest/handler/NoDestroyHandler.java | 23 - .../rest/handler/NoDirectoryEntryHandler.java | 23 - .../master/rest/handler/NoListenerHandler.java | 23 - .../master/rest/handler/NoUpdateHandler.java | 23 - .../master/rest/handler/NotOwnerHandler.java | 21 - .../master/rest/handler/OverloadedHandler.java | 22 - .../master/rest/handler/PermissionHandler.java | 74 - .../rest/handler/Scufl2DocumentHandler.java | 87 - .../rest/handler/T2FlowDocumentHandler.java | 118 -- .../master/rest/handler/URIListHandler.java | 121 -- .../master/rest/handler/UnknownRunHandler.java | 23 - .../master/rest/handler/ZipStreamHandler.java | 54 - .../master/rest/handler/package-info.java | 31 - .../server/master/rest/package-info.java | 31 - .../taverna/server/master/soap/DirEntry.java | 100 -- .../server/master/soap/FileContents.java | 171 -- .../server/master/soap/PermissionList.java | 50 - .../server/master/soap/TavernaServerSOAP.java | 1553 ------------------ .../server/master/soap/WrappedWorkflow.java | 156 -- .../server/master/soap/ZippedDirectory.java | 89 - .../server/master/soap/package-info.java | 31 - .../server/master/usage/UsageRecord.java | 118 -- .../master/usage/UsageRecordRecorder.java | 163 -- .../server/master/usage/package-info.java | 9 - .../server/master/utils/CallTimeLogger.java | 87 - .../server/master/utils/CallTimingFilter.java | 65 - .../server/master/utils/CapabilityLister.java | 44 - .../master/utils/CertificateChainFetcher.java | 199 --- .../server/master/utils/Contextualizer.java | 66 - .../taverna/server/master/utils/DerbyUtils.java | 68 - .../server/master/utils/FilenameUtils.java | 268 --- .../utils/FlushThreadLocalCacheInterceptor.java | 18 - .../server/master/utils/InvocationCounter.java | 48 - .../taverna/server/master/utils/JCECheck.java | 60 - .../taverna/server/master/utils/JDOSupport.java | 270 --- .../master/utils/LoggingDerbyAdapter.java | 138 -- .../server/master/utils/OneShotThread.java | 10 - .../taverna/server/master/utils/RestUtils.java | 32 - .../master/utils/RuntimeExceptionWrapper.java | 37 - .../server/master/utils/UsernamePrincipal.java | 69 - .../utils/WSDLHeadOptionsInterceptor.java | 65 - .../master/utils/WebappAwareDataSource.java | 134 -- .../taverna/server/master/utils/X500Utils.java | 107 -- .../server/master/utils/package-info.java | 10 - .../master/worker/CompletionNotifier.java | 45 - .../server/master/worker/FactoryBean.java | 26 - .../server/master/worker/PasswordIssuer.java | 57 - .../server/master/worker/PolicyImpl.java | 158 -- .../server/master/worker/PolicyLimits.java | 43 - .../server/master/worker/RemoteRunDelegate.java | 967 ----------- .../server/master/worker/RunConnection.java | 239 --- .../server/master/worker/RunDBSupport.java | 83 - .../server/master/worker/RunDatabase.java | 311 ---- .../server/master/worker/RunDatabaseDAO.java | 306 ---- .../master/worker/RunFactoryConfiguration.java | 395 ----- .../master/worker/SecurityContextDelegate.java | 649 -------- .../worker/SecurityContextDelegateImpl.java | 298 ---- .../master/worker/SecurityContextFactory.java | 154 -- .../SimpleFormattedCompletionNotifier.java | 64 - .../worker/VelocityCompletionNotifier.java | 105 -- .../server/master/worker/WorkerModel.java | 203 --- .../server/master/worker/package-info.java | 10 - .../main/replacementscripts/executeworkflow.bat | 25 - .../main/replacementscripts/executeworkflow.sh | 72 - server-webapp/src/main/resources/admin.html | 240 --- .../src/main/resources/capabilities.properties | 38 - .../src/main/resources/log4j.properties | 39 - .../src/main/resources/security.policy | 3 - .../src/main/resources/static/admin.js | 549 ------- .../main/resources/static/jquery-1.8.0.min.js | 2 - .../static/jquery-ui-1.8.23.custom.css | 563 ------- .../static/jquery-ui-1.8.23.custom.min.js | 125 -- .../src/main/resources/static/t2cogs.png | Bin 135202 -> 0 bytes .../ui-bg_diagonals-small_25_c5ddfc_40x40.png | Bin 194 -> 0 bytes .../ui-bg_diagonals-thick_20_e69700_40x40.png | Bin 257 -> 0 bytes .../ui-bg_diagonals-thick_22_1484e6_40x40.png | Bin 384 -> 0 bytes .../ui-bg_diagonals-thick_26_2293f7_40x40.png | Bin 259 -> 0 bytes .../static/ui-bg_flat_0_e69700_40x100.png | Bin 181 -> 0 bytes .../static/ui-bg_flat_0_e6b900_40x100.png | Bin 212 -> 0 bytes .../ui-bg_highlight-soft_100_f9f9f9_1x100.png | Bin 88 -> 0 bytes .../ui-bg_inset-hard_100_eeeeee_1x100.png | Bin 91 -> 0 bytes .../static/ui-icons_0a82eb_256x240.png | Bin 4369 -> 0 bytes .../static/ui-icons_0b54d5_256x240.png | Bin 4369 -> 0 bytes .../static/ui-icons_5fa5e3_256x240.png | Bin 5355 -> 0 bytes .../static/ui-icons_fcdd4a_256x240.png | Bin 4369 -> 0 bytes .../static/ui-icons_ffffff_256x240.png | Bin 4369 -> 0 bytes .../src/main/resources/version.properties | 5 - server-webapp/src/main/resources/welcome.html | 122 -- .../src/main/webapp/META-INF/MANIFEST.MF | 3 - .../webapp/META-INF/cxf/org.apache.cxf.Logger | 1 - .../src/main/webapp/META-INF/persistence.xml | 14 - server-webapp/src/main/webapp/WEB-INF/beans.xml | 518 ------ .../src/main/webapp/WEB-INF/insecure.xml | 32 - ...orker.VelocityCompletionNotifier_email.vtmpl | 15 - ....worker.VelocityCompletionNotifier_sms.vtmpl | 1 - ...ker.VelocityCompletionNotifier_twitter.vtmpl | 1 - .../src/main/webapp/WEB-INF/partsecure.xml | 36 - .../src/main/webapp/WEB-INF/providers.xml | 96 -- .../src/main/webapp/WEB-INF/secure.xml | 35 - .../webapp/WEB-INF/security/users.properties | 48 - .../webapp/WEB-INF/tavernaserver.properties | 77 - .../src/main/webapp/WEB-INF/web-nosec.xml | 79 - .../src/main/webapp/WEB-INF/web-partsec.xml | 79 - .../src/main/webapp/WEB-INF/web-sec.xml | 79 - .../src/main/webapp/WEB-INF/webappBeans.xml | 213 --- server-webapp/src/misc/xsd/persistence_1_0.xsd | 305 ---- .../taverna/server/master/JaxbSanityTest.java | 357 ---- .../server/master/TavernaServerImplTest.java | 246 --- .../master/WorkflowSerializationTest.java | 68 - .../taverna/server/master/mocks/ExampleRun.java | 452 ----- .../taverna/server/master/mocks/MockPolicy.java | 59 - .../master/mocks/SimpleListenerFactory.java | 64 - .../mocks/SimpleNonpersistentRunStore.java | 151 -- .../server/master/mocks/SimpleServerPolicy.java | 110 -- server-webapp/src/test/resources/example.xml | 55 - .../src/test/resources/log4j.properties | 4 - server-worker/pom.xml | 125 -- .../src/main/java/META-INF/MANIFEST.MF | 3 - .../server/localworker/api/Constants.java | 141 -- .../server/localworker/api/RunAccounting.java | 22 - .../taverna/server/localworker/api/Worker.java | 135 -- .../server/localworker/api/WorkerFactory.java | 18 - .../localworker/impl/DirectoryDelegate.java | 161 -- .../server/localworker/impl/FileDelegate.java | 142 -- .../server/localworker/impl/LocalWorker.java | 769 --------- .../localworker/impl/TavernaRunManager.java | 243 --- .../server/localworker/impl/WorkerCore.java | 918 ----------- .../impl/utils/FilenameVerifier.java | 156 -- .../localworker/impl/utils/TimingOutTask.java | 40 - .../src/main/resources/security.policy | 11 - .../localworker/impl/LocalWorkerTest.java | 551 ------- taverna-server-client/pom.xml | 130 ++ .../uk/org/taverna/server/client/Connected.java | 20 + .../uk/org/taverna/server/client/DirEntry.java | 39 + .../uk/org/taverna/server/client/Directory.java | 94 ++ .../java/uk/org/taverna/server/client/File.java | 95 ++ .../uk/org/taverna/server/client/Property.java | 18 + .../java/uk/org/taverna/server/client/Run.java | 215 +++ .../uk/org/taverna/server/client/Status.java | 36 + .../taverna/server/client/TavernaServer.java | 128 ++ .../client/TavernaServerConnectionFactory.java | 23 + .../org/taverna/server/client/package-info.java | 5 + .../src/main/wadl/tavserv.wadl | 591 +++++++ taverna-server-distribution/pom.xml | 145 ++ .../src/assemble/dist.xml | 82 + taverna-server-execution-delegate/pom.xml | 41 + .../execution_delegate/ExecutionDelegate.java | 172 ++ .../execution_delegate/RemoteExecution.java | 188 +++ .../src/test/java/SerializationTest.java | 54 + taverna-server-port-description/.gitignore | 1 + taverna-server-port-description/pom.xml | 45 + .../server/port_description/AbsentValue.java | 13 + .../server/port_description/AbstractPort.java | 26 + .../AbstractPortDescription.java | 29 + .../server/port_description/AbstractValue.java | 32 + .../server/port_description/ErrorValue.java | 25 + .../port_description/InputDescription.java | 51 + .../server/port_description/LeafValue.java | 19 + .../server/port_description/ListValue.java | 32 + .../server/port_description/Namespaces.java | 12 + .../port_description/OutputDescription.java | 52 + .../server/port_description/package-info.java | 19 + .../port_description/utils/IntAdapter.java | 32 + .../server/port_description/JaxbSanityTest.java | 98 ++ taverna-server-rmidaemon/pom.xml | 61 + .../org/taverna/server/rmidaemon/Registry.java | 72 + .../taverna/server/rmidaemon/package-info.java | 5 + taverna-server-runinterface/.gitignore | 1 + taverna-server-runinterface/pom.xml | 30 + .../src/main/java/META-INF/MANIFEST.MF | 3 + .../remote/IllegalStateTransitionException.java | 36 + .../remote/ImplementationException.java | 26 + .../localworker/remote/RemoteDirectory.java | 62 + .../remote/RemoteDirectoryEntry.java | 62 + .../server/localworker/remote/RemoteFile.java | 98 ++ .../server/localworker/remote/RemoteInput.java | 92 ++ .../localworker/remote/RemoteListener.java | 77 + .../localworker/remote/RemoteRunFactory.java | 84 + .../remote/RemoteSecurityContext.java | 34 + .../localworker/remote/RemoteSingleRun.java | 254 +++ .../server/localworker/remote/RemoteStatus.java | 40 + .../remote/StillWorkingOnItException.java | 20 + .../server/localworker/remote/package-info.java | 9 + .../localworker/server/UsageRecordReceiver.java | 29 + .../server/localworker/server/package-info.java | 9 + taverna-server-unix-forker/pom.xml | 61 + .../org/taverna/server/unixforker/Forker.java | 208 +++ taverna-server-usagerecord/.gitignore | 1 + taverna-server-usagerecord/pom.xml | 79 + .../main/java/org/ogf/usage/JobUsageRecord.java | 304 ++++ taverna-server-usagerecord/src/main/xsd/ur.xsd | 425 +++++ .../src/main/xsd/xmlds.xsd | 318 ++++ .../src/test/java/TestUR.java | 120 ++ taverna-server-webapp/.gitignore | 1 + taverna-server-webapp/pom.xml | 889 ++++++++++ .../resources/datanucleus_log4j.properties | 4 + .../master/ContentsDescriptorBuilder.java | 292 ++++ .../taverna/server/master/DirectoryREST.java | 375 +++++ .../server/master/FileConcatenation.java | 68 + .../org/taverna/server/master/InputREST.java | 252 +++ .../taverna/server/master/InteractionFeed.java | 107 ++ .../server/master/ListenerPropertyREST.java | 78 + .../taverna/server/master/ListenersREST.java | 93 ++ .../taverna/server/master/ManagementState.java | 215 +++ .../java/org/taverna/server/master/RunREST.java | 499 ++++++ .../taverna/server/master/RunSecurityREST.java | 303 ++++ .../server/master/SingleListenerREST.java | 97 ++ .../taverna/server/master/TavernaServer.java | 1425 ++++++++++++++++ .../server/master/TavernaServerSupport.java | 957 +++++++++++ .../org/taverna/server/master/admin/Admin.java | 1100 +++++++++++++ .../taverna/server/master/admin/AdminBean.java | 794 +++++++++ .../server/master/admin/package-info.java | 33 + .../taverna/server/master/api/ContentTypes.java | 50 + .../server/master/api/DirectoryBean.java | 16 + .../org/taverna/server/master/api/FeedBean.java | 13 + .../taverna/server/master/api/InputBean.java | 21 + .../server/master/api/ListenerPropertyBean.java | 15 + .../server/master/api/ListenersBean.java | 13 + .../server/master/api/ManagementModel.java | 61 + .../server/master/api/OneListenerBean.java | 14 + .../org/taverna/server/master/api/RunBean.java | 17 + .../taverna/server/master/api/SecurityBean.java | 14 + .../taverna/server/master/api/SupportAware.java | 21 + .../server/master/api/TavernaServerBean.java | 101 ++ .../taverna/server/master/api/package-info.java | 6 + .../server/master/common/Capability.java | 22 + .../server/master/common/Credential.java | 149 ++ .../server/master/common/DirEntryReference.java | 93 ++ .../server/master/common/InputDescription.java | 110 ++ .../server/master/common/Namespaces.java | 39 + .../server/master/common/Permission.java | 43 + .../server/master/common/ProfileList.java | 42 + .../org/taverna/server/master/common/Roles.java | 25 + .../server/master/common/RunReference.java | 67 + .../taverna/server/master/common/Status.java | 44 + .../org/taverna/server/master/common/Trust.java | 79 + .../org/taverna/server/master/common/Uri.java | 432 +++++ .../server/master/common/VersionedElement.java | 65 + .../taverna/server/master/common/Workflow.java | 367 +++++ .../server/master/common/package-info.java | 29 + .../server/master/common/version/Version.java | 43 + .../taverna/server/master/defaults/Default.java | 99 ++ .../server/master/defaults/package-info.java | 5 + .../exceptions/BadInputPortNameException.java | 21 + .../exceptions/BadPropertyValueException.java | 26 + .../exceptions/BadStateChangeException.java | 35 + .../exceptions/FilesystemAccessException.java | 38 + .../exceptions/GeneralFailureException.java | 28 + .../exceptions/InvalidCredentialException.java | 36 + .../master/exceptions/NoCreateException.java | 32 + .../exceptions/NoCredentialException.java | 18 + .../master/exceptions/NoDestroyException.java | 24 + .../exceptions/NoDirectoryEntryException.java | 24 + .../master/exceptions/NoListenerException.java | 33 + .../master/exceptions/NoUpdateException.java | 33 + .../master/exceptions/NotOwnerException.java | 23 + .../master/exceptions/OverloadedException.java | 35 + .../master/exceptions/UnknownRunException.java | 27 + .../server/master/exceptions/package-info.java | 29 + .../taverna/server/master/facade/Facade.java | 73 + .../server/master/facade/package-info.java | 10 + .../factories/ConfigurableRunFactory.java | 133 ++ .../master/factories/ListenerFactory.java | 46 + .../server/master/factories/RunFactory.java | 40 + .../server/master/factories/package-info.java | 10 + .../identity/AuthorityDerivedIDMapper.java | 50 + .../master/identity/CompositeIDMapper.java | 65 + .../master/identity/ConstantIDMapper.java | 32 + .../server/master/identity/NameIDMapper.java | 50 + .../identity/StrippedDownAuthProvider.java | 278 ++++ .../taverna/server/master/identity/User.java | 153 ++ .../server/master/identity/UserStore.java | 389 +++++ .../server/master/identity/UserStoreAPI.java | 91 + .../identity/WorkflowInternalAuthProvider.java | 304 ++++ .../server/master/identity/package-info.java | 10 + .../interaction/InteractionFeedSupport.java | 316 ++++ .../server/master/interaction/package-info.java | 10 + .../server/master/interfaces/Directory.java | 82 + .../master/interfaces/DirectoryEntry.java | 47 + .../taverna/server/master/interfaces/File.java | 69 + .../taverna/server/master/interfaces/Input.java | 92 ++ .../server/master/interfaces/Listener.java | 64 + .../master/interfaces/LocalIdentityMapper.java | 29 + .../master/interfaces/MessageDispatcher.java | 45 + .../server/master/interfaces/Policy.java | 120 ++ .../server/master/interfaces/RunStore.java | 82 + .../interfaces/SecurityContextFactory.java | 32 + .../server/master/interfaces/TavernaRun.java | 219 +++ .../interfaces/TavernaSecurityContext.java | 213 +++ .../master/interfaces/UriBuilderFactory.java | 43 + .../server/master/interfaces/package-info.java | 10 + .../localworker/AbstractRemoteRunFactory.java | 440 +++++ .../master/localworker/ForkRunFactory.java | 323 ++++ .../localworker/IdAwareForkRunFactory.java | 516 ++++++ .../master/localworker/LocalWorkerFactory.java | 31 + .../master/localworker/LocalWorkerState.java | 454 +++++ .../master/localworker/PersistedState.java | 257 +++ .../server/master/localworker/StreamLogger.java | 62 + .../server/master/localworker/package-info.java | 10 + .../master/notification/EmailDispatcher.java | 113 ++ .../master/notification/JabberDispatcher.java | 140 ++ .../master/notification/NotificationEngine.java | 145 ++ .../notification/RateLimitedDispatcher.java | 89 + .../master/notification/SMSDispatcher.java | 158 ++ .../master/notification/TwitterDispatcher.java | 132 ++ .../master/notification/atom/AtomFeed.java | 134 ++ .../server/master/notification/atom/Event.java | 110 ++ .../master/notification/atom/EventDAO.java | 206 +++ .../master/notification/atom/package-info.java | 29 + .../master/notification/package-info.java | 10 + .../org/taverna/server/master/package-info.java | 11 + .../server/master/rest/ContentTypes.java | 28 + .../server/master/rest/DirectoryContents.java | 61 + .../taverna/server/master/rest/FileSegment.java | 78 + .../server/master/rest/InteractionFeedREST.java | 126 ++ .../server/master/rest/ListenerDefinition.java | 32 + .../master/rest/MakeOrUpdateDirEntry.java | 56 + .../master/rest/TavernaServerDirectoryREST.java | 240 +++ .../master/rest/TavernaServerInputREST.java | 355 ++++ .../master/rest/TavernaServerListenersREST.java | 428 +++++ .../server/master/rest/TavernaServerREST.java | 604 +++++++ .../master/rest/TavernaServerRunREST.java | 797 +++++++++ .../master/rest/TavernaServerSecurityREST.java | 775 +++++++++ .../rest/handler/AccessDeniedHandler.java | 21 + .../rest/handler/BadInputPortNameHandler.java | 23 + .../rest/handler/BadPropertyValueHandler.java | 23 + .../rest/handler/BadStateChangeHandler.java | 23 + .../master/rest/handler/EntryHandler.java | 131 ++ .../server/master/rest/handler/FeedHandler.java | 66 + .../rest/handler/FileConcatenationHandler.java | 61 + .../master/rest/handler/FileMessageHandler.java | 80 + .../master/rest/handler/FileSegmentHandler.java | 74 + .../rest/handler/FilesystemAccessHandler.java | 23 + .../rest/handler/GeneralFailureHandler.java | 21 + .../server/master/rest/handler/HandlerCore.java | 71 + .../rest/handler/IllegalArgumentHandler.java | 21 + .../handler/ImplementationProblemHandler.java | 21 + .../rest/handler/InputStreamMessageHandler.java | 107 ++ .../rest/handler/InvalidCredentialHandler.java | 23 + .../rest/handler/JAXBExceptionHandler.java | 22 + .../rest/handler/NegotiationFailedHandler.java | 25 + .../master/rest/handler/NoCreateHandler.java | 23 + .../rest/handler/NoCredentialHandler.java | 21 + .../master/rest/handler/NoDestroyHandler.java | 23 + .../rest/handler/NoDirectoryEntryHandler.java | 23 + .../master/rest/handler/NoListenerHandler.java | 23 + .../master/rest/handler/NoUpdateHandler.java | 23 + .../master/rest/handler/NotOwnerHandler.java | 21 + .../master/rest/handler/OverloadedHandler.java | 22 + .../master/rest/handler/PermissionHandler.java | 74 + .../rest/handler/Scufl2DocumentHandler.java | 87 + .../rest/handler/T2FlowDocumentHandler.java | 118 ++ .../master/rest/handler/URIListHandler.java | 121 ++ .../master/rest/handler/UnknownRunHandler.java | 23 + .../master/rest/handler/ZipStreamHandler.java | 54 + .../master/rest/handler/package-info.java | 31 + .../server/master/rest/package-info.java | 31 + .../taverna/server/master/soap/DirEntry.java | 100 ++ .../server/master/soap/FileContents.java | 171 ++ .../server/master/soap/PermissionList.java | 50 + .../server/master/soap/TavernaServerSOAP.java | 1553 ++++++++++++++++++ .../server/master/soap/WrappedWorkflow.java | 156 ++ .../server/master/soap/ZippedDirectory.java | 89 + .../server/master/soap/package-info.java | 31 + .../server/master/usage/UsageRecord.java | 118 ++ .../master/usage/UsageRecordRecorder.java | 163 ++ .../server/master/usage/package-info.java | 9 + .../server/master/utils/CallTimeLogger.java | 87 + .../server/master/utils/CallTimingFilter.java | 65 + .../server/master/utils/CapabilityLister.java | 44 + .../master/utils/CertificateChainFetcher.java | 199 +++ .../server/master/utils/Contextualizer.java | 66 + .../taverna/server/master/utils/DerbyUtils.java | 68 + .../server/master/utils/FilenameUtils.java | 268 +++ .../utils/FlushThreadLocalCacheInterceptor.java | 18 + .../server/master/utils/InvocationCounter.java | 48 + .../taverna/server/master/utils/JCECheck.java | 60 + .../taverna/server/master/utils/JDOSupport.java | 270 +++ .../master/utils/LoggingDerbyAdapter.java | 138 ++ .../server/master/utils/OneShotThread.java | 10 + .../taverna/server/master/utils/RestUtils.java | 32 + .../master/utils/RuntimeExceptionWrapper.java | 37 + .../server/master/utils/UsernamePrincipal.java | 69 + .../utils/WSDLHeadOptionsInterceptor.java | 65 + .../master/utils/WebappAwareDataSource.java | 134 ++ .../taverna/server/master/utils/X500Utils.java | 107 ++ .../server/master/utils/package-info.java | 10 + .../master/worker/CompletionNotifier.java | 45 + .../server/master/worker/FactoryBean.java | 26 + .../server/master/worker/PasswordIssuer.java | 57 + .../server/master/worker/PolicyImpl.java | 158 ++ .../server/master/worker/PolicyLimits.java | 43 + .../server/master/worker/RemoteRunDelegate.java | 967 +++++++++++ .../server/master/worker/RunConnection.java | 239 +++ .../server/master/worker/RunDBSupport.java | 83 + .../server/master/worker/RunDatabase.java | 311 ++++ .../server/master/worker/RunDatabaseDAO.java | 306 ++++ .../master/worker/RunFactoryConfiguration.java | 395 +++++ .../master/worker/SecurityContextDelegate.java | 649 ++++++++ .../worker/SecurityContextDelegateImpl.java | 298 ++++ .../master/worker/SecurityContextFactory.java | 154 ++ .../SimpleFormattedCompletionNotifier.java | 64 + .../worker/VelocityCompletionNotifier.java | 105 ++ .../server/master/worker/WorkerModel.java | 203 +++ .../server/master/worker/package-info.java | 10 + .../main/replacementscripts/executeworkflow.bat | 25 + .../main/replacementscripts/executeworkflow.sh | 72 + .../src/main/resources/admin.html | 240 +++ .../src/main/resources/capabilities.properties | 38 + .../src/main/resources/log4j.properties | 39 + .../src/main/resources/security.policy | 3 + .../src/main/resources/static/admin.js | 549 +++++++ .../main/resources/static/jquery-1.8.0.min.js | 2 + .../static/jquery-ui-1.8.23.custom.css | 563 +++++++ .../static/jquery-ui-1.8.23.custom.min.js | 125 ++ .../src/main/resources/static/t2cogs.png | Bin 0 -> 135202 bytes .../ui-bg_diagonals-small_25_c5ddfc_40x40.png | Bin 0 -> 194 bytes .../ui-bg_diagonals-thick_20_e69700_40x40.png | Bin 0 -> 257 bytes .../ui-bg_diagonals-thick_22_1484e6_40x40.png | Bin 0 -> 384 bytes .../ui-bg_diagonals-thick_26_2293f7_40x40.png | Bin 0 -> 259 bytes .../static/ui-bg_flat_0_e69700_40x100.png | Bin 0 -> 181 bytes .../static/ui-bg_flat_0_e6b900_40x100.png | Bin 0 -> 212 bytes .../ui-bg_highlight-soft_100_f9f9f9_1x100.png | Bin 0 -> 88 bytes .../ui-bg_inset-hard_100_eeeeee_1x100.png | Bin 0 -> 91 bytes .../static/ui-icons_0a82eb_256x240.png | Bin 0 -> 4369 bytes .../static/ui-icons_0b54d5_256x240.png | Bin 0 -> 4369 bytes .../static/ui-icons_5fa5e3_256x240.png | Bin 0 -> 5355 bytes .../static/ui-icons_fcdd4a_256x240.png | Bin 0 -> 4369 bytes .../static/ui-icons_ffffff_256x240.png | Bin 0 -> 4369 bytes .../src/main/resources/version.properties | 5 + .../src/main/resources/welcome.html | 122 ++ .../src/main/webapp/META-INF/MANIFEST.MF | 3 + .../webapp/META-INF/cxf/org.apache.cxf.Logger | 1 + .../src/main/webapp/META-INF/persistence.xml | 14 + .../src/main/webapp/WEB-INF/beans.xml | 518 ++++++ .../src/main/webapp/WEB-INF/insecure.xml | 32 + ...orker.VelocityCompletionNotifier_email.vtmpl | 15 + ....worker.VelocityCompletionNotifier_sms.vtmpl | 1 + ...ker.VelocityCompletionNotifier_twitter.vtmpl | 1 + .../src/main/webapp/WEB-INF/partsecure.xml | 36 + .../src/main/webapp/WEB-INF/providers.xml | 96 ++ .../src/main/webapp/WEB-INF/secure.xml | 35 + .../webapp/WEB-INF/security/users.properties | 48 + .../webapp/WEB-INF/tavernaserver.properties | 77 + .../src/main/webapp/WEB-INF/web-nosec.xml | 79 + .../src/main/webapp/WEB-INF/web-partsec.xml | 79 + .../src/main/webapp/WEB-INF/web-sec.xml | 79 + .../src/main/webapp/WEB-INF/webappBeans.xml | 213 +++ .../src/misc/xsd/persistence_1_0.xsd | 305 ++++ .../taverna/server/master/JaxbSanityTest.java | 357 ++++ .../server/master/TavernaServerImplTest.java | 246 +++ .../master/WorkflowSerializationTest.java | 68 + .../taverna/server/master/mocks/ExampleRun.java | 452 +++++ .../taverna/server/master/mocks/MockPolicy.java | 59 + .../master/mocks/SimpleListenerFactory.java | 64 + .../mocks/SimpleNonpersistentRunStore.java | 151 ++ .../server/master/mocks/SimpleServerPolicy.java | 110 ++ .../src/test/resources/example.xml | 55 + .../src/test/resources/log4j.properties | 4 + taverna-server-worker/pom.xml | 125 ++ .../src/main/java/META-INF/MANIFEST.MF | 3 + .../server/localworker/api/Constants.java | 141 ++ .../server/localworker/api/RunAccounting.java | 22 + .../taverna/server/localworker/api/Worker.java | 135 ++ .../server/localworker/api/WorkerFactory.java | 18 + .../localworker/impl/DirectoryDelegate.java | 161 ++ .../server/localworker/impl/FileDelegate.java | 142 ++ .../server/localworker/impl/LocalWorker.java | 769 +++++++++ .../localworker/impl/TavernaRunManager.java | 243 +++ .../server/localworker/impl/WorkerCore.java | 918 +++++++++++ .../impl/utils/FilenameVerifier.java | 156 ++ .../localworker/impl/utils/TimingOutTask.java | 40 + .../src/main/resources/security.policy | 11 + .../localworker/impl/LocalWorkerTest.java | 551 +++++++ 688 files changed, 43826 insertions(+), 43885 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/pom.xml ---------------------------------------------------------------------- diff --git a/pom.xml b/pom.xml index 4240e5d..850b30b 100644 --- a/pom.xml +++ b/pom.xml @@ -412,16 +412,16 @@ executing.</description> </profiles> <modules> - <module>server-webapp</module> - <module>server-runinterface</module> - <module>server-worker</module> - <module>server-unix-forker</module> - <module>server-usagerecord</module> - <module>server-port-description</module> - <module>server-execution-delegate</module> - <module>server-rmidaemon</module> - <module>server-client</module> - <module>server-distribution</module> + <module>taverna-server-webapp</module> + <module>taverna-server-runinterface</module> + <module>taverna-server-worker</module> + <module>taverna-server-unix-forker</module> + <module>taverna-server-usagerecord</module> + <module>taverna-server-port-description</module> + <module>taverna-server-execution-delegate</module> + <module>taverna-server-rmidaemon</module> + <module>taverna-server-client</module> + <module>taverna-server-distribution</module> </modules> <scm> http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-client/pom.xml ---------------------------------------------------------------------- diff --git a/server-client/pom.xml b/server-client/pom.xml deleted file mode 100644 index d16b07a..0000000 --- a/server-client/pom.xml +++ /dev/null @@ -1,130 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!-- -Licensed to the Apache Software Foundation (ASF) under one or more -contributor license agreements. See the NOTICE file distributed with -this work for additional information regarding copyright ownership. -The ASF licenses this file to You under the Apache License, Version 2.0 -(the "License"); you may not use this file except in compliance with -the License. You may obtain a copy of the License at - -http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. ---> -<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.server</groupId> - <artifactId>taverna-server</artifactId> - <version>3.1.0-incubating-SNAPSHOT</version> - </parent> - <artifactId>taverna-server-client</artifactId> - <packaging>bundle</packaging> - <name>Apache Taverna Server Client OSGi Module</name> - - <dependencies> - <dependency> - <groupId>org.jvnet.ws.wadl</groupId> - <artifactId>wadl-core</artifactId> - <version>1.1.6</version> - </dependency> - <dependency> - <groupId>com.sun.jersey</groupId> - <artifactId>jersey-client</artifactId> - <version>1.8</version> - </dependency> - <dependency> - <groupId>commons-io</groupId> - <artifactId>commons-io</artifactId> - <version>2.4</version> - </dependency> - <dependency> - <groupId>org.apache.tika</groupId> - <artifactId>tika-core</artifactId> - <version>1.5</version> - </dependency> - <dependency> - <groupId>${project.parent.groupId}</groupId> - <artifactId>taverna-server-usagerecord</artifactId> - <version>${project.parent.version}</version> - </dependency> - </dependencies> - - <build> - <plugins> - <plugin> - <groupId>org.apache.felix</groupId> - <artifactId>maven-bundle-plugin</artifactId> - <extensions>true</extensions> - <configuration> - <instructions> - <Export-Package>uk.org.taverna.server.client</Export-Package> - <Private-Package>uk.org.taverna.server.client.*</Private-Package> - </instructions> - </configuration> - </plugin> - <plugin> - <groupId>org.jvnet.ws.wadl</groupId> - <artifactId>wadl-client-plugin</artifactId> - <version>1.1.6</version> - <executions> - <execution> - <goals> - <goal>generate</goal> - </goals> - </execution> - </executions> - <configuration> - <packageName>org.taverna.server.client.wadl</packageName> - <includes>*.wadl</includes> - <customClassNames> - <property> - <name>http://example.com/taverna/rest</name> - <value>TavernaServer</value> - </property> - </customClassNames> - </configuration> - </plugin> - </plugins> - <pluginManagement> - <plugins> - <!--This plugin's configuration is used to store Eclipse m2e settings - only. It has no influence on the Maven build itself. --> - <plugin> - <groupId>org.eclipse.m2e</groupId> - <artifactId>lifecycle-mapping</artifactId> - <version>1.0.0</version> - <configuration> - <lifecycleMappingMetadata> - <pluginExecutions> - <pluginExecution> - <pluginExecutionFilter> - <groupId> - org.jvnet.ws.wadl - </groupId> - <artifactId> - wadl-client-plugin - </artifactId> - <versionRange> - [1.1.6,) - </versionRange> - <goals> - <goal>generate</goal> - </goals> - </pluginExecutionFilter> - <action> - <execute /> - </action> - </pluginExecution> - </pluginExecutions> - </lifecycleMappingMetadata> - </configuration> - </plugin> - </plugins> - </pluginManagement> - </build> -</project> http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-client/src/main/java/uk/org/taverna/server/client/Connected.java ---------------------------------------------------------------------- diff --git a/server-client/src/main/java/uk/org/taverna/server/client/Connected.java b/server-client/src/main/java/uk/org/taverna/server/client/Connected.java deleted file mode 100644 index 263034c..0000000 --- a/server-client/src/main/java/uk/org/taverna/server/client/Connected.java +++ /dev/null @@ -1,20 +0,0 @@ -package uk.org.taverna.server.client; - -import uk.org.taverna.server.client.TavernaServer.ClientException; -import uk.org.taverna.server.client.TavernaServer.ServerException; - -import com.sun.jersey.api.client.ClientResponse; - -abstract class Connected { - void checkError(ClientResponse response) throws ClientException, - ServerException { - ClientResponse.Status s = response.getClientResponseStatus(); - if (s.getStatusCode() == 401) - throw new TavernaServer.AuthorizationException("not authorized", - null); - if (s.getStatusCode() >= 500) - throw new TavernaServer.ServerException(s.getReasonPhrase(), null); - if (s.getStatusCode() >= 400) - throw new TavernaServer.ClientException(s.getReasonPhrase(), null); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-client/src/main/java/uk/org/taverna/server/client/DirEntry.java ---------------------------------------------------------------------- diff --git a/server-client/src/main/java/uk/org/taverna/server/client/DirEntry.java b/server-client/src/main/java/uk/org/taverna/server/client/DirEntry.java deleted file mode 100644 index 267707d..0000000 --- a/server-client/src/main/java/uk/org/taverna/server/client/DirEntry.java +++ /dev/null @@ -1,39 +0,0 @@ -package uk.org.taverna.server.client; - -import org.taverna.server.client.wadl.TavernaServer.Root.RunsRunName.Wd.Path2; - -import uk.org.taverna.server.client.TavernaServer.ClientException; -import uk.org.taverna.server.client.TavernaServer.ServerException; - -import com.sun.jersey.api.client.ClientResponse; - -public abstract class DirEntry extends Connected { - final Path2 handle; - final String path; - final Run run; - - protected DirEntry(Run run, String path) { - this.run = run; - this.path = path.replaceFirst("/+$", ""); - this.handle = run.run.wd().path2(this.path); - } - - public void delete() throws ClientException, ServerException { - checkError(handle.deleteAsXml(ClientResponse.class)); - } - - String path(ClientResponse response) throws ClientException, ServerException { - checkError(response); - String[] bits = response.getLocation().getPath().split("/"); - return concat(bits[bits.length - 1]); - } - - String localName() { - String[] bits = path.split("/"); - return bits[bits.length - 1]; - } - - String concat(String name) { - return path + "/" + name.split("/", 2)[0]; - } -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-client/src/main/java/uk/org/taverna/server/client/Directory.java ---------------------------------------------------------------------- diff --git a/server-client/src/main/java/uk/org/taverna/server/client/Directory.java b/server-client/src/main/java/uk/org/taverna/server/client/Directory.java deleted file mode 100644 index 38dc394..0000000 --- a/server-client/src/main/java/uk/org/taverna/server/client/Directory.java +++ /dev/null @@ -1,94 +0,0 @@ -package uk.org.taverna.server.client; - -import static java.io.File.createTempFile; -import static javax.ws.rs.client.Entity.entity; -import static javax.ws.rs.core.MediaType.APPLICATION_OCTET_STREAM_TYPE; - -import java.io.FileOutputStream; -import java.io.IOException; -import java.io.OutputStream; -import java.net.URI; -import java.util.ArrayList; -import java.util.List; -import java.util.zip.ZipFile; - -import org.taverna.server.client.wadl.TavernaServer.Root.RunsRunName.Wd; - -import uk.org.taverna.server.client.TavernaServer.ClientException; -import uk.org.taverna.server.client.TavernaServer.ServerException; -import uk.org.taverna.server.client.generic.DirectoryEntry; -import uk.org.taverna.server.client.generic.DirectoryReference; -import uk.org.taverna.server.client.generic.FileReference; -import uk.org.taverna.server.client.rest.DirectoryContents; -import uk.org.taverna.server.client.rest.MakeDirectory; -import uk.org.taverna.server.client.rest.UploadFile; - -import com.sun.jersey.api.client.ClientResponse; - -public class Directory extends DirEntry { - private final Wd wd; - - Directory(Run run) { - super(run, ""); - this.wd = run.run.wd(); - } - - Directory(Run run, String path) { - super(run, path); - this.wd = run.run.wd(); - } - - public List<DirEntry> list() { - List<DirEntry> result = new ArrayList<>(); - for (DirectoryEntry de : wd.path3(path) - .getAsXml(DirectoryContents.class).getDirOrFile()) - if (de instanceof DirectoryReference) - result.add(new Directory(run, de.getValue())); - else if (de instanceof FileReference) - result.add(new File(run, de.getValue())); - return result; - } - - public File createFile(String name, byte[] content) throws ClientException, - ServerException { - UploadFile uf = new UploadFile(); - uf.setName(name); - uf.setValue(content); - return new File(run, path(wd.path(path).putAsXml(uf, - ClientResponse.class))); - } - - public File createFile(String name, java.io.File content) - throws ClientException, ServerException { - return new File(run, path(wd.path(concat(name)).putOctetStreamAsXml( - entity(content, APPLICATION_OCTET_STREAM_TYPE), - ClientResponse.class))); - } - - public File createFile(String name, URI source) throws ClientException, - ServerException { - return new File(run, path(wd.path(concat(name)).postTextUriListAsXml( - source.toString(), ClientResponse.class))); - } - - public Directory createDirectory(String name) throws ClientException, - ServerException { - MakeDirectory mkdir = new MakeDirectory(); - mkdir.setName(name); - return new Directory(run, path(wd.path(path).putAsXml(mkdir, - ClientResponse.class))); - } - - public byte[] getZippedContents() { - return wd.path3(path).getAsZip(byte[].class); - } - - public ZipFile getZip() throws IOException { - byte[] contents = getZippedContents(); - java.io.File tmp = createTempFile(localName(), ".zip"); - try (OutputStream os = new FileOutputStream(tmp)) { - os.write(contents); - } - return new ZipFile(tmp); - } -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-client/src/main/java/uk/org/taverna/server/client/File.java ---------------------------------------------------------------------- diff --git a/server-client/src/main/java/uk/org/taverna/server/client/File.java b/server-client/src/main/java/uk/org/taverna/server/client/File.java deleted file mode 100644 index 0287afb..0000000 --- a/server-client/src/main/java/uk/org/taverna/server/client/File.java +++ /dev/null @@ -1,95 +0,0 @@ -package uk.org.taverna.server.client; - -import static java.io.File.createTempFile; -import static javax.ws.rs.client.Entity.entity; -import static javax.ws.rs.core.MediaType.APPLICATION_OCTET_STREAM_TYPE; -import static org.apache.commons.io.IOUtils.copy; -import static org.apache.tika.mime.MimeTypes.getDefaultMimeTypes; - -import java.io.FileOutputStream; -import java.io.IOException; -import java.io.InputStream; -import java.io.OutputStream; -import java.nio.charset.Charset; - -import org.apache.tika.mime.MimeTypeException; -import org.taverna.server.client.wadl.TavernaServer.Root.RunsRunName.Wd; - -import uk.org.taverna.server.client.TavernaServer.ClientException; -import uk.org.taverna.server.client.TavernaServer.ServerException; - -import com.sun.jersey.api.client.ClientHandlerException; -import com.sun.jersey.api.client.ClientResponse; -import com.sun.jersey.api.client.UniformInterfaceException; - -public class File extends DirEntry { - private final Wd wd; - - File(Run run, String path) { - super(run, path); - wd = run.run.wd(); - } - - public InputStream getAsStream() { - return wd.path3(path).getAsOctetStream(InputStream.class); - } - - public byte[] get() { - return wd.path3(path).getAsOctetStream(byte[].class); - } - - public String get(Charset encoding) { - return new String(wd.path3(path).getAsOctetStream(byte[].class), - encoding); - } - - public java.io.File getAsFile() throws ClientHandlerException, - UniformInterfaceException, IOException, MimeTypeException, - ClientException, ServerException { - ClientResponse cr = wd.path3(path).getAsOctetStream( - ClientResponse.class); - checkError(cr); - String[] bits = localName().split("[.]"); - String ext = getDefaultMimeTypes().forName( - cr.getHeaders().getFirst("Content-Type")).getExtension(); - if (ext == null) - ext = bits[bits.length - 1]; - java.io.File tmp = createTempFile(bits[0], ext); - try (OutputStream os = new FileOutputStream(tmp); - InputStream is = cr.getEntity(InputStream.class)) { - copy(is, os); - } - return tmp; - } - - public void setContents(byte[] newContents) throws ClientException, - ServerException { - checkError(wd.path(path).putOctetStreamAsXml(newContents, - ClientResponse.class)); - } - - public void setContents(String newContents) throws ClientException, - ServerException { - checkError(wd.path(path).putOctetStreamAsXml(newContents, - ClientResponse.class)); - } - - public void setContents(String newContents, Charset encoding) - throws ClientException, ServerException { - checkError(wd.path(path).putOctetStreamAsXml( - newContents.getBytes(encoding), ClientResponse.class)); - } - - public void setContents(InputStream newContents) throws ClientException, - ServerException { - checkError(wd.path(path).putOctetStreamAsXml(newContents, - ClientResponse.class)); - } - - public void setContents(java.io.File newContents) throws IOException, - ClientException, ServerException { - checkError(wd.path(path).putOctetStreamAsXml( - entity(newContents, APPLICATION_OCTET_STREAM_TYPE), - ClientResponse.class)); - } -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-client/src/main/java/uk/org/taverna/server/client/Property.java ---------------------------------------------------------------------- diff --git a/server-client/src/main/java/uk/org/taverna/server/client/Property.java b/server-client/src/main/java/uk/org/taverna/server/client/Property.java deleted file mode 100644 index 0e6542f..0000000 --- a/server-client/src/main/java/uk/org/taverna/server/client/Property.java +++ /dev/null @@ -1,18 +0,0 @@ -package uk.org.taverna.server.client; - -public enum Property { - STDOUT("stdout"), STDERR("stderr"), EXIT_CODE("exitcode"), READY_TO_NOTIFY( - "readyToNotify"), EMAIL("notificationAddress"), USAGE( - "usageRecord"); - - private String s; - - private Property(String s) { - this.s = s; - } - - @Override - public String toString() { - return s; - } -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-client/src/main/java/uk/org/taverna/server/client/Run.java ---------------------------------------------------------------------- diff --git a/server-client/src/main/java/uk/org/taverna/server/client/Run.java b/server-client/src/main/java/uk/org/taverna/server/client/Run.java deleted file mode 100644 index 5c6875e..0000000 --- a/server-client/src/main/java/uk/org/taverna/server/client/Run.java +++ /dev/null @@ -1,215 +0,0 @@ -package uk.org.taverna.server.client; - -import static org.joda.time.format.ISODateTimeFormat.dateTime; -import static org.joda.time.format.ISODateTimeFormat.dateTimeParser; - -import java.io.FileInputStream; -import java.io.IOException; -import java.io.InputStream; -import java.net.URI; -import java.util.Date; -import java.util.List; - -import javax.xml.bind.JAXBException; - -import org.apache.commons.io.IOUtils; -import org.joda.time.DateTime; -import org.ogf.usage.JobUsageRecord; -import org.taverna.server.client.wadl.TavernaServer.Root.RunsRunName; -import org.w3c.dom.Element; - -import uk.org.taverna.server.client.TavernaServer.ClientException; -import uk.org.taverna.server.client.TavernaServer.ServerException; -import uk.org.taverna.server.client.generic.KeyPairCredential; -import uk.org.taverna.server.client.generic.PasswordCredential; -import uk.org.taverna.server.client.generic.port.InputPort; -import uk.org.taverna.server.client.generic.port.OutputPort; -import uk.org.taverna.server.client.rest.InputDescription; -import uk.org.taverna.server.client.rest.InputDescription.Value; - -import com.sun.jersey.api.client.ClientResponse; - -public class Run extends Connected { - RunsRunName run; - - Run(TavernaServer server, String value) { - run = server.root.runsRunName(value); - } - - public String getName() { - return run.name().getAsTextPlain(ClientResponse.class) - .getEntity(String.class); - } - - public void setName(String name) { - run.name().putTextPlain(name, String.class); - } - - public Date getExpiry() { - return dateTimeParser().parseDateTime( - run.expiry().getAsTextPlain(String.class)).toDate(); - } - - public void setExpiry(Date expiryTimestamp) { - run.expiry().putTextPlain( - dateTime().print(new DateTime(expiryTimestamp)), String.class); - } - - public Date getCreate() { - String timestamp = run.createTime().getAsTextPlain(String.class); - if (timestamp == null || timestamp.trim().isEmpty()) - return null; - return dateTimeParser().parseDateTime(timestamp).toDate(); - } - - public Date getStart() { - String timestamp = run.startTime().getAsTextPlain(String.class); - if (timestamp == null || timestamp.trim().isEmpty()) - return null; - return dateTimeParser().parseDateTime(timestamp).toDate(); - } - - public Date getFinish() { - String timestamp = run.finishTime().getAsTextPlain(String.class); - if (timestamp == null || timestamp.trim().isEmpty()) - return null; - return dateTimeParser().parseDateTime(timestamp).toDate(); - } - - public Status getStatus() { - return Status.valueOf(run.status().getAsTextPlain(String.class)); - } - - public void setStatus(Status status) { - run.status().putTextPlain(status, String.class); - } - - public void start() { - setStatus(Status.Operating); - } - - public void kill() { - setStatus(Status.Finished); - } - - public boolean isRunning() { - return getStatus() == Status.Operating; - } - - public String getStandardOutput() { - return run.stdout().getAsTextPlain(String.class); - } - - public String getStandardError() { - return run.stderr().getAsTextPlain(String.class); - } - - public String getLog() { - return run.log().getAsTextPlain(String.class); - } - - public Integer getExitCode() { - String code = run.listeners().name("io") - .propertiesPropertyName("exitCode") - .getAsTextPlain(String.class); - if (code == null || code.trim().isEmpty()) - return null; - return Integer.parseInt(code); - } - - public String getProperty(Property prop) { - return run.listeners().name("io") - .propertiesPropertyName(prop.toString()) - .getAsTextPlain(String.class); - } - - public void setGenerateRunBundle(boolean generateRunBundle) { - run.generateProvenance().putTextPlain(generateRunBundle, String.class); - } - - public byte[] getRunBundle() { - return run.runBundle().getAsVndWf4everRobundleZip(byte[].class); - } - - public List<InputPort> getInputs() { - return run.input().expected().getAsInputDescriptionXml().getInput(); - } - - public List<OutputPort> getOutputs() { - return run.output().getAsOutputDescriptionXml().getOutput(); - } - - public void setInput(String name, String value) { - Value v = new Value(); - v.setValue(value); - InputDescription idesc = new InputDescription(); - idesc.setValue(v); - run.input().inputName(name).putXmlAsInputDescription(idesc); - } - - public void setInput(String name, String value, char listSeparator) { - Value v = new Value(); - v.setValue(value); - InputDescription idesc = new InputDescription(); - idesc.setValue(v); - idesc.setListDelimiter(new String(new char[] { listSeparator })); - run.input().inputName(name).putXmlAsInputDescription(idesc); - } - - public byte[] getWorkflow() { - return run.workflow().getAsVndTavernaT2flowXml(byte[].class); - } - - // TODO Consider better ways to do this - public Element getInteractionFeed() { - return run.interaction().getAsAtomXml(Element.class); - } - - public Element getInteractionEntry(String id) { - return run.interaction().id(id).getAsAtomXml(Element.class); - } - - public JobUsageRecord getUsageRecord() throws JAXBException { - return JobUsageRecord.unmarshal(run.usage().getAsXml(Element.class)); - } - - public Directory getWorkingDirectory() { - return new Directory(this); - } - - public String getOwner() { - return run.security().owner().getAsTextPlain(String.class); - } - - // TODO permissions - - public void grantPasswordCredential(URI contextService, String username, - String password) throws ClientException, ServerException { - PasswordCredential pc = new PasswordCredential(); - pc.setServiceURI(contextService.toString()); - pc.setUsername(username); - pc.setPassword(password); - checkError(run.security().credentials() - .postXmlAsOctetStream(pc, ClientResponse.class)); - } - - public void grantKeyCredential(URI contextService, java.io.File source, - String unlockPassword, String aliasEntry) throws IOException, - ClientException, ServerException { - KeyPairCredential kpc = new KeyPairCredential(); - kpc.setServiceURI(contextService.toString()); - try (InputStream in = new FileInputStream(source)) { - byte[] buffer = new byte[(int) source.length()]; - IOUtils.read(in, buffer); - kpc.setCredentialBytes(buffer); - } - if (source.getName().endsWith(".p12")) - kpc.setFileType("PKCS12"); - else - kpc.setFileType("JKS"); - kpc.setCredentialName(aliasEntry); - kpc.setUnlockPassword(unlockPassword); - checkError(run.security().credentials() - .postXmlAsOctetStream(kpc, ClientResponse.class)); - } -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-client/src/main/java/uk/org/taverna/server/client/Status.java ---------------------------------------------------------------------- diff --git a/server-client/src/main/java/uk/org/taverna/server/client/Status.java b/server-client/src/main/java/uk/org/taverna/server/client/Status.java deleted file mode 100644 index 9c375ad..0000000 --- a/server-client/src/main/java/uk/org/taverna/server/client/Status.java +++ /dev/null @@ -1,36 +0,0 @@ -package uk.org.taverna.server.client; - -/** - * States of a workflow run. They are {@link #Initialized Initialized}, - * {@link #Operating Operating}, {@link #Stopped Stopped}, and - * {@link #Finished Finished}. Conceptually, there is also a - * <tt>Destroyed</tt> state, but the workflow run does not exist (and hence - * can't have its state queried or set) in that case. - * - * @author Donal Fellows - */ -public enum Status { - /** - * The workflow run has been created, but is not yet running. The run - * will need to be manually moved to {@link #Operating Operating} when - * ready. - */ - Initialized, - /** - * The workflow run is going, reading input, generating output, etc. - * Will eventually either move automatically to {@link #Finished - * Finished} or can be moved manually to {@link #Stopped Stopped} (where - * supported). - */ - Operating, - /** - * The workflow run is paused, and will need to be moved back to - * {@link #Operating Operating} manually. - */ - Stopped, - /** - * The workflow run has ceased; data files will continue to exist until - * the run is destroyed (which may be manual or automatic). - */ - Finished -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-client/src/main/java/uk/org/taverna/server/client/TavernaServer.java ---------------------------------------------------------------------- diff --git a/server-client/src/main/java/uk/org/taverna/server/client/TavernaServer.java b/server-client/src/main/java/uk/org/taverna/server/client/TavernaServer.java deleted file mode 100644 index 7c0dcdd..0000000 --- a/server-client/src/main/java/uk/org/taverna/server/client/TavernaServer.java +++ /dev/null @@ -1,128 +0,0 @@ -package uk.org.taverna.server.client; - -import static java.nio.file.Files.readAllBytes; -import static org.taverna.server.client.wadl.TavernaServer.createClient; -import static org.taverna.server.client.wadl.TavernaServer.root; - -import java.io.File; -import java.io.IOException; -import java.net.URI; -import java.util.ArrayList; -import java.util.List; - -import org.taverna.server.client.wadl.TavernaServer.Root; - -import uk.org.taverna.server.client.generic.Capability; -import uk.org.taverna.server.client.generic.TavernaRun; -import uk.org.taverna.server.client.generic.VersionedElement; - -import com.sun.jersey.api.client.Client; -import com.sun.jersey.api.client.ClientResponse; -import com.sun.jersey.api.client.filter.HTTPBasicAuthFilter; - -public class TavernaServer extends Connected { - final Root root; - private final URI location; - private final boolean authenticated; - - TavernaServer(URI serviceRoot) { - root = root(createClient(), location = serviceRoot); - authenticated = false; - } - - TavernaServer(URI serviceRoot, String username, String password) { - Client client = createClient(); - client.addFilter(new HTTPBasicAuthFilter(username, password)); - authenticated = true; - root = root(client, location = serviceRoot); - } - - TavernaServer(TavernaServer service, String username, String password) { - Client client = createClient(); - client.addFilter(new HTTPBasicAuthFilter(username, password)); - authenticated = true; - root = root(client, location = service.location); - getServerVersionInfo(); - } - - public TavernaServer upgradeToAuth(String username, String password) { - if (authenticated) - throw new IllegalStateException("may only upgrade an unauthenticated connection"); - return new TavernaServer(this, username, password); - } - - public List<Capability> getCapabilities() { - return root.policy().capabilities().getAsCapabilitiesXml() - .getCapability(); - } - - public int getRunLimit() { - return root.policy().runLimit().getAsTextPlain(Integer.class); - } - - public int getOperatingLimit() { - return root.policy().operatingLimit().getAsTextPlain(Integer.class); - } - - public List<String> getPermittedWorkflows() { - return root.policy().permittedWorkflows().getAsPermittedWorkflowsXml() - .getWorkflow(); - } - - public List<Run> getExistingRuns() { - List<Run> runs = new ArrayList<>(); - for (TavernaRun run : root.runs().getAsRunListXml().getRun()) - runs.add(new Run(this, run.getValue())); - return runs; - } - - public VersionedElement getServerVersionInfo() { - return root.getAsServerDescriptionXml(); - } - - private Run response2run(ClientResponse response) throws ClientException, ServerException { - checkError(response); - if (response.getClientResponseStatus().getStatusCode() == 201) { - String[] path = response.getLocation().getPath().split("/"); - return new Run(this, path[path.length - 1]); - } - return null; - } - - public Run createWorkflowRun(byte[] t2flowBytes) throws ClientException, ServerException { - return response2run(root.runs().postVndTavernaT2flowXmlAsOctetStream( - t2flowBytes, ClientResponse.class)); - } - - public Run createWorkflowRun(File t2flowFile) throws IOException, ClientException, ServerException { - return createWorkflowRun(readAllBytes(t2flowFile.toPath())); - } - - public Run createWorkflowRun(URI t2flowUri) throws ClientException, ServerException { - return response2run(root.runs().postTextUriListAsOctetStream( - t2flowUri.toString(), ClientResponse.class)); - } - - - public static class ClientException extends Exception { - private static final long serialVersionUID = 1L; - - ClientException(String msg, Throwable cause) { - super(msg, cause); - } - } - public static class AuthorizationException extends ClientException { - private static final long serialVersionUID = 1L; - - AuthorizationException(String msg, Throwable cause) { - super(msg, cause); - } - } - static class ServerException extends Exception { - private static final long serialVersionUID = 1L; - - ServerException(String msg, Throwable cause) { - super(msg, cause); - } - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-client/src/main/java/uk/org/taverna/server/client/TavernaServerConnectionFactory.java ---------------------------------------------------------------------- diff --git a/server-client/src/main/java/uk/org/taverna/server/client/TavernaServerConnectionFactory.java b/server-client/src/main/java/uk/org/taverna/server/client/TavernaServerConnectionFactory.java deleted file mode 100644 index b00b075..0000000 --- a/server-client/src/main/java/uk/org/taverna/server/client/TavernaServerConnectionFactory.java +++ /dev/null @@ -1,23 +0,0 @@ -package uk.org.taverna.server.client; - -import java.net.URI; -import java.util.HashMap; -import java.util.Map; - -public class TavernaServerConnectionFactory { - private Map<URI, TavernaServer> cache = new HashMap<>(); - - public synchronized TavernaServer connectNoAuth(URI uri) { - TavernaServer conn = cache.get(uri); - if (conn == null) - cache.put(uri, conn = new TavernaServer(uri)); - return conn; - } - - public TavernaServer connectAuth(URI uri, String username, String password) { - TavernaServer conn = new TavernaServer(uri, username, password); - // Force a check of the credentials by getting the server version - conn.getServerVersionInfo(); - return conn; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/server-client/src/main/java/uk/org/taverna/server/client/package-info.java ---------------------------------------------------------------------- diff --git a/server-client/src/main/java/uk/org/taverna/server/client/package-info.java b/server-client/src/main/java/uk/org/taverna/server/client/package-info.java deleted file mode 100644 index 59e809d..0000000 --- a/server-client/src/main/java/uk/org/taverna/server/client/package-info.java +++ /dev/null @@ -1,5 +0,0 @@ -/** - * Implementation of a basic client for Taverna Server. - * @author Donal Fellows - */ -package uk.org.taverna.server.client; \ No newline at end of file
