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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/23 11:23:14 UTC

[51/51] [partial] incubator-taverna-workbench git commit: Revert "temporarily empty repository"

Revert "temporarily empty repository"

This reverts commit dc466d6d0d588fefbec8f009ac57cfa520679050.


Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/commit/8c4b365e
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/tree/8c4b365e
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/diff/8c4b365e

Branch: refs/heads/master
Commit: 8c4b365ef376575a2eab290376c18d2610707b72
Parents: dc466d6
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Mon Feb 23 10:21:47 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Mon Feb 23 10:21:47 2015 +0000

----------------------------------------------------------------------
 pom.xml                                         |   91 +
 taverna-dataflow-activity-ui/pom.xml            |  121 +
 .../actions/EditNestedDataflowAction.java       |   49 +
 .../menu/EditNestedDataflowMenuAction.java      |   28 +
 .../DataflowActivityIcon.java                   |   57 +
 .../DataflowTemplateService.java                |   54 +
 .../views/DataflowActivityContextualView.java   |  140 +
 .../views/DataflowActivityViewFactory.java      |   93 +
 .../file/importworkflow/DataflowMerger.java     |  124 +
 .../file/importworkflow/MergeException.java     |   22 +
 .../actions/AddNestedWorkflowAction.java        |   59 +
 .../actions/ImportWorkflowAction.java           |   59 +
 .../actions/MergeWorkflowAction.java            |   58 +
 .../actions/OpenSourceWorkflowAction.java       |  139 +
 .../actions/ReplaceNestedWorkflowAction.java    |   84 +
 .../gui/ImportWorkflowWizard.java               | 1272 +++++++
 .../menu/AddNestedWorkflowMenuAction.java       |  104 +
 .../menu/ImportWorkflowMenuAction.java          |   98 +
 .../menu/MergeWorkflowMenuAction.java           |   65 +
 .../menu/ReplaceNestedWorkflowMenuAction.java   |   76 +
 ...rvicedescriptions.ServiceDescriptionProvider |    1 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |    9 +
 ...a.t2.workbench.activityicons.ActivityIconSPI |    1 +
 ...t2.workbench.file.DataflowPersistenceHandler |    1 +
 ...ntextualviews.activity.ContextualViewFactory |    1 +
 .../dataflow-activity-ui-context-osgi.xml       |   33 +
 .../spring/dataflow-activity-ui-context.xml     |   64 +
 .../src/main/resources/dataflow.png             |  Bin 0 -> 814 bytes
 .../file/importworkflow/AbstractTestHelper.java |  266 ++
 .../file/importworkflow/TestPortMerge.java      |   38 +
 .../file/importworkflow/TestRename.java         |   58 +
 .../file/importworkflow/TestSimpleMerge.java    |   98 +
 .../file/importworkflow/TestTestHelper.java     |   24 +
 .../gui/ImportWizardLauncher.java               |   24 +
 .../src/test/resources/abc.t2flow               |  116 +
 .../src/test/resources/p.t2flow                 |   36 +
 .../src/test/resources/q.t2flow                 |   36 +
 taverna-disabled-activity-ui/pom.xml            |   94 +
 .../DisabledActivityConfigurationAction.java    |  118 +
 .../menu/ConfigureDisabledMenuAction.java       |   52 +
 .../views/DisabledActivityViewFactory.java      |   80 +
 .../disabled/views/DisabledConfigView.java      |  141 +
 .../disabled/views/DisabledContextualView.java  |  128 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |    1 +
 ...ntextualviews.activity.ContextualViewFactory |    1 +
 .../disabled-activity-ui-context-osgi.xml       |   20 +
 .../spring/disabled-activity-ui-context.xml     |   23 +
 taverna-stringconstant-activity-ui/pom.xml      |   97 +
 ...ringConstantActivityConfigurationAction.java |   71 +
 .../menu/AddStringConstantTemplateAction.java   |  112 +
 .../AddStringConstantTemplateMenuAction.java    |  124 +
 .../menu/ConfigureStringConstantMenuAction.java |   64 +
 .../StringConstantActivityIcon.java             |   58 +
 .../StringConstantTemplateService.java          |   84 +
 .../StringConstantActivityContextualView.java   |   93 +
 .../StringConstantActivityViewFactory.java      |   87 +
 .../views/StringConstantConfigView.java         |  243 ++
 ...rvicedescriptions.ServiceDescriptionProvider |    1 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |    3 +
 ...a.t2.workbench.activityicons.ActivityIconSPI |    1 +
 ...ntextualviews.activity.ContextualViewFactory |    1 +
 .../stringconstant-activity-ui-context-osgi.xml |   25 +
 .../stringconstant-activity-ui-context.xml      |   49 +
 .../src/main/resources/stringconstant.png       |  Bin 0 -> 733 bytes
 .../views/TestStringConstantContextualView.java |   53 +
 taverna-unrecognized-activity-ui/pom.xml        |   48 +
 .../views/UnrecognizedActivityViewFactory.java  |   48 +
 .../views/UnrecognizedContextualView.java       |   56 +
 ...ntextualviews.activity.ContextualViewFactory |    1 +
 .../unrecognized-activity-ui-context-osgi.xml   |   13 +
 .../spring/unrecognized-activity-ui-context.xml |   10 +
 taverna-workbench-activity-icons-api/pom.xml    |   20 +
 .../activityicons/ActivityIconManager.java      |   41 +
 .../activityicons/ActivityIconSPI.java          |   57 +
 .../activityicons/DefaultActivityIcon.java      |   54 +
 .../impl/ActivityIconManagerImpl.java           |   85 +
 ...a.t2.workbench.activityicons.ActivityIconSPI |    1 +
 .../spring/activity-icons-api-context-osgi.xml  |   15 +
 .../spring/activity-icons-api-context.xml       |   13 +
 .../main/resources/default-activity-icon.png    |  Bin 0 -> 577 bytes
 taverna-workbench-activity-palette-api/pom.xml  |   61 +
 .../AbstractConfigurableServiceProvider.java    |   53 +
 .../AbstractTemplateService.java                |   85 +
 .../ConfigurableServiceProvider.java            |   10 +
 .../CustomizedConfigurePanelProvider.java       |   36 +
 .../servicedescriptions/IdentifiedObject.java   |   30 +
 .../servicedescriptions/ServiceDescription.java |   80 +
 .../ServiceDescriptionProvider.java             |   61 +
 .../ServiceDescriptionRegistry.java             |   50 +
 .../ServiceDescriptionsConfiguration.java       |   36 +
 .../events/AbstractProviderEvent.java           |   16 +
 .../events/AbstractProviderNotification.java    |   18 +
 .../events/AddedProviderEvent.java              |   10 +
 .../PartialServiceDescriptionsNotification.java |   22 +
 .../events/ProviderErrorNotification.java       |   19 +
 .../events/ProviderStatusNotification.java      |   12 +
 .../events/ProviderUpdatingNotification.java    |   11 +
 .../events/ProviderWarningNotification.java     |   12 +
 .../events/RemovedProviderEvent.java            |   10 +
 .../events/ServiceDescriptionProvidedEvent.java |   20 +
 .../events/ServiceDescriptionRegistryEvent.java |    4 +
 taverna-workbench-activity-palette-impl/pom.xml |   80 +
 .../impl/ServiceDescriptionConstants.java       |   10 +
 .../impl/ServiceDescriptionDeserializer.java    |  167 +
 .../impl/ServiceDescriptionRegistryImpl.java    |  652 ++++
 .../impl/ServiceDescriptionSerializer.java      |  102 +
 .../impl/ServiceDescriptionXMLConstants.java    |   15 +
 .../ServiceDescriptionsConfigurationImpl.java   |   92 +
 .../ActivityPaletteConfiguration.java           |   81 +
 .../ActivityPaletteConfigurationPanel.java      |  284 ++
 .../ActivityPaletteConfigurationUIFactory.java  |   52 +
 ...rkbench.configuration.ConfigurationUIFactory |    1 +
 .../activity-palette-impl-context-osgi.xml      |   17 +
 .../spring/activity-palette-impl-context.xml    |   23 +
 .../ActivityPaletteConfigurationTest.java       |   97 +
 ...averna.t2.partition.PartitionAlgorithmSetSPI |    1 +
 ...sf.taverna.t2.partition.PropertyExtractorSPI |    3 +
 .../net.sf.taverna.t2.partition.QueryFactory    |    2 +
 taverna-workbench-activity-palette-ui/pom.xml   |   73 +
 .../servicepanel/PathElementFilterTreeNode.java |   34 +
 .../ui/servicepanel/RootFilterTreeNode.java     |   34 +
 .../ui/servicepanel/ServiceFilter.java          |  158 +
 .../ui/servicepanel/ServiceFilterTreeNode.java  |   40 +
 .../workbench/ui/servicepanel/ServicePanel.java |  411 ++
 .../ServicePanelComponentFactory.java           |   82 +
 .../servicepanel/ServiceTreeCellRenderer.java   |   77 +
 .../servicepanel/ServiceTreeClickListener.java  |  252 ++
 .../ui/servicepanel/ServiceTreePanel.java       |  176 +
 .../actions/AddServiceProviderAction.java       |  256 ++
 .../ExportServiceDescriptionsAction.java        |  155 +
 ...ImportServiceDescriptionsFromFileAction.java |  158 +
 .../ImportServiceDescriptionsFromURLAction.java |  129 +
 .../actions/RefreshProviderRegistryAction.java  |   52 +
 .../actions/RemoveDefaultServicesAction.java    |   51 +
 .../actions/RemoveUserServicesAction.java       |   59 +
 .../actions/RestoreDefaultServicesAction.java   |   50 +
 .../config/ServiceDescriptionConfigPanel.java   |  181 +
 .../ServiceDescriptionConfigUIFactory.java      |   57 +
 .../menu/AddServiceProviderMenu.java            |  113 +
 .../workbench/ui/servicepanel/tree/Filter.java  |   33 +
 .../tree/FilterTreeCellRenderer.java            |   59 +
 .../ui/servicepanel/tree/FilterTreeModel.java   |   92 +
 .../ui/servicepanel/tree/FilterTreeNode.java    |  142 +
 .../tree/FilterTreeSelectionModel.java          |   46 +
 .../ui/servicepanel/tree/MyFilter.java          |   89 +
 .../ui/servicepanel/tree/TreePanel.java         |  371 ++
 ....t2.workbench.ui.zaria.UIComponentFactorySPI |    1 +
 .../spring/activity-palette-ui-context-osgi.xml |   20 +
 .../spring/activity-palette-ui-context.xml      |   22 +
 taverna-workbench-activity-tools/pom.xml        |   30 +
 .../AbstractConfigureActivityMenuAction.java    |   64 +
 taverna-workbench-configuration-api/pom.xml     |   22 +
 .../configuration/colour/ColourManager.java     |   41 +
 .../configuration/mimetype/MimeTypeManager.java |   42 +
 .../workbench/WorkbenchConfiguration.java       |   44 +
 .../workbench/ui/T2ConfigurationFrame.java      |   30 +
 taverna-workbench-configuration-impl/pom.xml    |   61 +
 .../WorkbenchConfigurationImpl.java             |  210 ++
 .../WorkbenchConfigurationPanel.java            |  266 ++
 .../WorkbenchConfigurationUIFactory.java        |   52 +
 .../configuration/colour/ColourManagerImpl.java |  178 +
 .../mimetype/MimeTypeManagerImpl.java           |   82 +
 .../ui/T2ConfigurationFrameImpl.java            |  205 +
 .../ui/WorkbenchConfigurationMenu.java          |   61 +
 .../ui/WorkbenchPreferencesSection.java         |   36 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |    2 +
 ...rkbench.configuration.ConfigurationUIFactory |    1 +
 .../spring/configuration-impl-context-osgi.xml  |   27 +
 .../spring/configuration-impl-context.xml       |   34 +
 .../configuration/ConfigurationManagerTest.java |  109 +
 .../configuration/colour/ColourManagerTest.java |   90 +
 taverna-workbench-contextual-views-api/pom.xml  |   99 +
 .../activity/ActivityConfigurationAction.java   |  167 +
 .../activity/ActivityContextualView.java        |   69 +
 .../HTMLBasedActivityContextualView.java        |   81 +
 .../contextualviews/AddLayerFactorySPI.java     |   43 +
 .../views/contextualviews/ContextualView.java   |  109 +
 .../activity/ActivityConfigurationDialog.java   |  474 +++
 .../activity/ActivityConfigurationPanel.java    |  214 ++
 .../activity/ActivityPortConfiguration.java     |   84 +
 .../activity/ContextualViewFactory.java         |   63 +
 .../activity/ContextualViewFactoryRegistry.java |   43 +
 .../activity/DependencyConfigurationPanel.java  |  293 ++
 .../activity/ListConfigurationComponent.java    |  119 +
 .../contextualviews/activity/ListLayout.java    |   92 +
 .../MultiPageActivityConfigurationPanel.java    |   65 +
 .../activity/ScriptConfigurationComponent.java  |  150 +
 .../activity/ValidatingTextField.java           |   53 +
 .../activity/ValidatingTextGroup.java           |  119 +
 ....t2.workbench.ui.zaria.UIComponentFactorySPI |    2 +
 ...taverna.t2.workbench.ui.zaria.UIComponentSPI |    3 +
 .../contextual-views-api-context-osgi.xml       |    9 +
 .../spring/contextual-views-api-context.xml     |    6 +
 taverna-workbench-contextual-views-impl/pom.xml |   43 +
 .../impl/ContextualViewFactoryRegistryImpl.java |   75 +
 .../annotated/AnnotatedContextualView.java      |  263 ++
 .../AnnotatedContextualViewFactory.java         |   43 +
 .../condition/ConditionContextualView.java      |   74 +
 .../ConditionContextualViewFactory.java         |   51 +
 .../dataflow/DataflowContextualView.java        |  108 +
 .../dataflow/DataflowContextualViewFactory.java |   41 +
 .../DataflowInputPortContextualView.java        |   96 +
 .../DataflowInputPortContextualViewFactory.java |   54 +
 .../DataflowOutputPortContextualView.java       |  106 +
 ...DataflowOutputPortContextualViewFactory.java |   55 +
 .../datalink/DatalinkContextualView.java        |  106 +
 .../datalink/DatalinkContextualViewFactory.java |   55 +
 .../impl/ContextualViewComponent.java           |  389 ++
 .../impl/ContextualViewComponentFactory.java    |   64 +
 .../inputport/InputPortContextualView.java      |   76 +
 .../InputPortContextualViewFactory.java         |   48 +
 .../merge/MergeConfigurationAction.java         |   79 +
 .../merge/MergeConfigurationView.java           |  233 ++
 .../merge/MergeContextualView.java              |  150 +
 .../merge/MergeContextualViewFactory.java       |   66 +
 .../outputport/OutputPortContextualView.java    |   76 +
 .../OutputPortContextualViewFactory.java        |   48 +
 ...ntextualviews.activity.ContextualViewFactory |    9 +
 ....t2.workbench.ui.zaria.UIComponentFactorySPI |    1 +
 .../contextual-views-impl-context-osgi.xml      |   31 +
 .../spring/contextual-views-impl-context.xml    |   43 +
 .../annotatedcontextualview.properties          |    4 +
 taverna-workbench-contextual-views/pom.xml      |   41 +
 .../ProcessorActivitiesContextualView.java      |  154 +
 ...rocessorActivitiesContextualViewFactory.java |   75 +
 ...rPredictedBehaviorContextualViewFactory.java |  177 +
 ...ntextualviews.activity.ContextualViewFactory |    4 +
 .../spring/contextual-views-context-osgi.xml    |   15 +
 .../spring/contextual-views-context.xml         |   12 +
 taverna-workbench-credential-manager-ui/pom.xml |   64 +
 .../ui/credentialmanager/CMStrings.java         |    7 +
 .../ChangeMasterPasswordDialog.java             |  234 ++
 .../ConfirmTrustedCertificateDialog.java        |  520 +++
 .../ConfirmTrustedCertificateUI.java            |   71 +
 .../credentialmanager/CredentialManagerUI.java  | 1512 ++++++++
 .../CredentialManagerUILauncher.java            |   96 +
 .../ui/credentialmanager/CryptoFileFilter.java  |   73 +
 .../GetMasterPasswordDialog.java                |  169 +
 .../ui/credentialmanager/GetPasswordDialog.java |  168 +
 .../credentialmanager/KeyPairsTableModel.java   |  213 ++
 .../NewEditPasswordEntryDialog.java             |  397 ++
 .../NewKeyPairEntryDialog.java                  |  304 ++
 .../credentialmanager/NewTrustCertsDialog.java  |  248 ++
 .../credentialmanager/PasswordsTableModel.java  |  227 ++
 .../SetMasterPasswordDialog.java                |  189 +
 .../ui/credentialmanager/TableCellRenderer.java |  113 +
 .../credentialmanager/TableHeaderRenderer.java  |  100 +
 .../TrustedCertsTableModel.java                 |  216 ++
 .../ViewCertDetailsDialog.java                  |  509 +++
 .../ViewUsernamePasswordEntryDialog.java        |  199 +
 .../WarnUserAboutJCEPolicyDialog.java           |  223 ++
 .../action/CredentialManagerAction.java         |   68 +
 .../menu/CredentialManagerMenu.java             |   72 +
 .../AskUserJavaTruststorePasswordProvider.java  |   46 +
 .../password/AskUserMasterPasswordProvider.java |   55 +
 ...kUserServiceUsernameAndPasswordProvider.java |   23 +
 .../AskUserTrustConfirmationProvider.java       |   35 +
 .../password/GetPasswordDialog.java             |  228 ++
 .../password/SimpleMasterPasswordProvider.java  |   54 +
 .../password/UIMasterPasswordProvider.java      |  126 +
 .../password/UIUsernamePasswordProvider.java    |   92 +
 .../startup/InitialiseSSLStartupHook.java       |   64 +
 .../SetCredManAuthenticatorStartupHook.java     |   24 +
 .../toolbar/CredentialManagerToolbarAction.java |   44 +
 .../CredentialManagerToolbarSection.java        |   38 +
 ...rity.credentialmanager.CredentialProviderSPI |    3 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |    3 +
 .../net.sf.taverna.t2.workbench.StartupSPI      |    2 +
 .../credential-manager-ui-context-osgi.xml      |   37 +
 .../spring/credential-manager-ui-context.xml    |   44 +
 .../src/main/resources/images/cred_manager.png  |  Bin 0 -> 10131 bytes
 .../main/resources/images/cred_manager16x16.png |  Bin 0 -> 3622 bytes
 .../images/cred_manager_transparent.png         |  Bin 0 -> 8376 bytes
 .../resources/images/table/entry_heading.png    |  Bin 0 -> 205 bytes
 .../main/resources/images/table/key_entry.png   |  Bin 0 -> 260 bytes
 .../resources/images/table/keypair_entry.png    |  Bin 0 -> 306 bytes
 .../resources/images/table/trustcert_entry.png  |  Bin 0 -> 551 bytes
 .../pom.xml                                     |   68 +
 .../DataManagementConfigurationPanel.java       |  304 ++
 .../DataManagementConfigurationUIFactory.java   |   64 +
 ...rkbench.configuration.ConfigurationUIFactory |    1 +
 .../data-management-config-ui-context-osgi.xml  |   14 +
 .../data-management-config-ui-context.xml       |   11 +
 taverna-workbench-design-ui/pom.xml             |   44 +
 .../design/actions/AddConditionAction.java      |   82 +
 .../design/actions/AddDataflowInputAction.java  |   96 +
 .../design/actions/AddDataflowOutputAction.java |   90 +
 .../design/actions/DataflowEditAction.java      |   57 +
 .../actions/EditDataflowInputPortAction.java    |  115 +
 .../actions/EditDataflowOutputPortAction.java   |   95 +
 .../design/actions/RemoveConditionAction.java   |   69 +
 .../actions/RemoveDataflowInputPortAction.java  |   85 +
 .../actions/RemoveDataflowOutputPortAction.java |   85 +
 .../design/actions/RemoveDatalinkAction.java    |   68 +
 .../design/actions/RemoveProcessorAction.java   |  136 +
 .../design/actions/RenameProcessorAction.java   |   97 +
 .../design/ui/DataflowInputPortPanel.java       |  203 +
 .../design/ui/DataflowOutputPortPanel.java      |  105 +
 .../t2/workbench/design/ui/ProcessorPanel.java  |  101 +
 taverna-workbench-edits-api/pom.xml             |   28 +
 .../t2/workbench/edits/CompoundEdit.java        |  118 +
 .../net/sf/taverna/t2/workbench/edits/Edit.java |   66 +
 .../t2/workbench/edits/EditException.java       |   42 +
 .../taverna/t2/workbench/edits/EditManager.java |  222 ++
 .../t2/workbench/edits/package-info.java        |   48 +
 .../taverna/t2/workflow/edits/AbstractEdit.java |  119 +
 .../t2/workflow/edits/AddActivityEdit.java      |   55 +
 .../edits/AddActivityInputPortMappingEdit.java  |   59 +
 .../edits/AddActivityOutputPortMappingEdit.java |   59 +
 .../taverna/t2/workflow/edits/AddChildEdit.java |   52 +
 .../t2/workflow/edits/AddDataLinkEdit.java      |   90 +
 .../edits/AddIterationStrategyEdit.java         |   49 +
 .../AddIterationStrategyInputPortEdit.java      |   50 +
 .../t2/workflow/edits/AddProcessorEdit.java     |   45 +
 .../edits/AddProcessorInputPortEdit.java        |   45 +
 .../edits/AddProcessorOutputPortEdit.java       |   46 +
 .../edits/AddWorkflowInputPortEdit.java         |  110 +
 .../edits/AddWorkflowOutputPortEdit.java        |  111 +
 .../t2/workflow/edits/ChangeDepthEdit.java      |  104 +
 .../workflow/edits/ChangeGranularDepthEdit.java |   49 +
 .../t2/workflow/edits/ChangeJsonEdit.java       |   50 +
 .../edits/ClearIterationStrategyStackEdit.java  |   50 +
 .../t2/workflow/edits/ConfigureEdit.java        |   55 +
 .../t2/workflow/edits/RemoveActivityEdit.java   |   55 +
 .../RemoveActivityInputPortMappingEdit.java     |   51 +
 .../RemoveActivityOutputPortMappingEdit.java    |   51 +
 .../t2/workflow/edits/RemoveChildEdit.java      |   48 +
 .../t2/workflow/edits/RemoveDataLinkEdit.java   |  111 +
 .../edits/RemoveProcessorInputPortEdit.java     |   31 +
 .../edits/RemoveProcessorOutputPortEdit.java    |   31 +
 .../edits/RemoveWorkflowInputPortEdit.java      |  107 +
 .../edits/RemoveWorkflowOutputPortEdit.java     |  105 +
 .../taverna/t2/workflow/edits/RenameEdit.java   |  136 +
 .../edits/ReorderMergePositionsEdit.java        |   57 +
 .../edits/SetIterationStrategyStackEdit.java    |   51 +
 .../UpdateDataflowInternalIdentifierEdit.java   |   48 +
 taverna-workbench-edits-impl/pom.xml            |   49 +
 .../workbench/edits/impl/EditManagerImpl.java   |  285 ++
 .../edits/impl/menu/AbstractUndoAction.java     |  166 +
 .../edits/impl/menu/RedoMenuAction.java         |   86 +
 .../edits/impl/menu/UndoMenuAction.java         |   86 +
 .../edits/impl/menu/UndoMenuSection.java        |   42 +
 .../edits/impl/toolbar/EditToolbarSection.java  |   36 +
 .../edits/impl/toolbar/RedoToolbarAction.java   |   46 +
 .../edits/impl/toolbar/UndoToolbarAction.java   |   46 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |    6 +
 ...et.sf.taverna.t2.workbench.edits.EditManager |    1 +
 .../META-INF/spring/edits-impl-context-osgi.xml |   20 +
 .../META-INF/spring/edits-impl-context.xml      |   33 +
 .../edits/impl/TestEditManagerImpl.java         |  258 ++
 taverna-workbench-file-api/pom.xml              |   31 +
 .../AbstractDataflowPersistenceHandler.java     |   69 +
 .../taverna/t2/workbench/file/DataflowInfo.java |  108 +
 .../file/DataflowPersistenceHandler.java        |  152 +
 .../taverna/t2/workbench/file/FileManager.java  |  573 +++
 .../sf/taverna/t2/workbench/file/FileType.java  |   67 +
 .../file/events/AbstractDataflowEvent.java      |   45 +
 .../file/events/ClosedDataflowEvent.java        |   34 +
 .../file/events/ClosingDataflowEvent.java       |   45 +
 .../workbench/file/events/FileManagerEvent.java |   39 +
 .../file/events/OpenedDataflowEvent.java        |   34 +
 .../file/events/SavedDataflowEvent.java         |   34 +
 .../file/events/SetCurrentDataflowEvent.java    |   35 +
 .../file/exceptions/FileException.java          |   44 +
 .../file/exceptions/OpenException.java          |   40 +
 .../file/exceptions/OverwriteException.java     |   36 +
 .../file/exceptions/SaveException.java          |   40 +
 .../file/exceptions/UnsavedException.java       |   38 +
 taverna-workbench-file-impl/pom.xml             |  104 +
 .../DataflowFromDataflowPersistenceHandler.java |   49 +
 .../DataflowPersistenceHandlerRegistry.java     |  238 ++
 .../workbench/file/impl/FileDataflowInfo.java   |   67 +
 .../t2/workbench/file/impl/FileManagerImpl.java |  601 +++
 .../workbench/file/impl/FileTypeFileFilter.java |   55 +
 .../workbench/file/impl/MultipleFileTypes.java  |   58 +
 .../file/impl/OpenDataflowInProgressDialog.java |   88 +
 .../workbench/file/impl/OpenDataflowInfo.java   |   93 +
 .../file/impl/OpenDataflowRunnable.java         |   71 +
 .../file/impl/OpenDataflowSwingWorker.java      |   67 +
 .../workbench/file/impl/T2DataflowOpener.java   |  144 +
 .../t2/workbench/file/impl/T2FileFilter.java    |   40 +
 .../t2/workbench/file/impl/T2FlowFileType.java  |   42 +
 .../file/impl/WorkflowBundleFileFilter.java     |   40 +
 .../file/impl/WorkflowBundleFileType.java       |   42 +
 .../file/impl/WorkflowBundleOpener.java         |  143 +
 .../file/impl/WorkflowBundleSaver.java          |  145 +
 .../impl/actions/CloseAllWorkflowsAction.java   |   85 +
 .../file/impl/actions/CloseWorkflowAction.java  |  107 +
 .../file/impl/actions/NewWorkflowAction.java    |   58 +
 .../impl/actions/OpenNestedWorkflowAction.java  |   76 +
 .../file/impl/actions/OpenWorkflowAction.java   |  395 ++
 .../impl/actions/OpenWorkflowFromURLAction.java |  139 +
 .../file/impl/actions/PasswordInput.java        |  221 ++
 .../impl/actions/SaveAllWorkflowsAction.java    |  104 +
 .../file/impl/actions/SaveWorkflowAction.java   |  175 +
 .../file/impl/actions/SaveWorkflowAsAction.java |  219 ++
 .../impl/hooks/CloseWorkflowsOnShutdown.java    |   56 +
 .../file/impl/menu/FileCloseAllMenuAction.java  |   51 +
 .../file/impl/menu/FileCloseMenuAction.java     |   50 +
 .../file/impl/menu/FileNewMenuAction.java       |   47 +
 .../impl/menu/FileOpenFromURLMenuAction.java    |   48 +
 .../file/impl/menu/FileOpenMenuAction.java      |   47 +
 .../file/impl/menu/FileOpenMenuSection.java     |   36 +
 .../impl/menu/FileOpenRecentMenuAction.java     |  418 ++
 .../file/impl/menu/FileSaveAllMenuAction.java   |   47 +
 .../file/impl/menu/FileSaveAsMenuAction.java    |   43 +
 .../file/impl/menu/FileSaveMenuAction.java      |   46 +
 .../file/impl/menu/FileSaveMenuSection.java     |   36 +
 .../workbench/file/impl/menu/WorkflowsMenu.java |  163 +
 .../file/impl/toolbar/CloseToolbarAction.java   |   55 +
 .../impl/toolbar/FileToolbarMenuSection.java    |   36 +
 .../file/impl/toolbar/NewToolbarAction.java     |   47 +
 .../file/impl/toolbar/OpenToolbarAction.java    |   47 +
 .../OpenWorkflowFromURLToolbarAction.java       |   47 +
 .../file/impl/toolbar/SaveToolbarAction.java    |   50 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |   20 +
 .../net.sf.taverna.t2.workbench.ShutdownSPI     |    1 +
 ...t2.workbench.file.DataflowPersistenceHandler |    2 +
 ...net.sf.taverna.t2.workbench.file.FileManager |    1 +
 .../META-INF/spring/file-impl-context-osgi.xml  |  100 +
 .../META-INF/spring/file-impl-context.xml       |  123 +
 .../t2/workbench/file/impl/FileManagerTest.java |  385 ++
 .../workbench/file/impl/dummy-workflow.t2flow   |  157 +
 taverna-workbench-graph-model/pom.xml           |  129 +
 .../models/graph/DefaultGraphEventManager.java  |  271 ++
 .../t2/workbench/models/graph/DotWriter.java    |  253 ++
 .../t2/workbench/models/graph/Graph.java        |  165 +
 .../models/graph/GraphColorManager.java         |   75 +
 .../workbench/models/graph/GraphController.java | 1276 +++++++
 .../t2/workbench/models/graph/GraphEdge.java    |  137 +
 .../t2/workbench/models/graph/GraphElement.java |  430 +++
 .../models/graph/GraphEventManager.java         |   47 +
 .../t2/workbench/models/graph/GraphNode.java    |  153 +
 .../models/graph/GraphShapeElement.java         |  119 +
 .../workbench/models/graph/dot/GraphLayout.java |  326 ++
 .../t2/workbench/models/graph/svg/SVGGraph.java |  439 +++
 .../models/graph/svg/SVGGraphController.java    |  555 +++
 .../models/graph/svg/SVGGraphEdge.java          |  311 ++
 .../graph/svg/SVGGraphElementDelegate.java      |  178 +
 .../models/graph/svg/SVGGraphNode.java          |  611 +++
 .../models/graph/svg/SVGGraphSettings.java      |   28 +
 .../models/graph/svg/SVGMonitorShape.java       |   40 +
 .../t2/workbench/models/graph/svg/SVGShape.java |   29 +
 .../t2/workbench/models/graph/svg/SVGUtil.java  |  477 +++
 .../graph/svg/event/SVGEventListener.java       |   56 +
 .../svg/event/SVGMouseClickEventListener.java   |   45 +
 .../svg/event/SVGMouseDownEventListener.java    |   45 +
 .../svg/event/SVGMouseMovedEventListener.java   |   46 +
 .../svg/event/SVGMouseOutEventListener.java     |   46 +
 .../svg/event/SVGMouseOverEventListener.java    |   46 +
 .../svg/event/SVGMouseUpEventListener.java      |   46 +
 .../src/main/jjtree/NamedNode.java              |   65 +
 .../src/main/jjtree/dotparser.jjt               |  289 ++
 .../models/graph/GraphControllerTest.java       |   81 +
 .../workbench/models/graph/GraphEdgeTest.java   |  129 +
 .../models/graph/GraphElementTest.java          |  148 +
 .../workbench/models/graph/GraphNodeTest.java   |  179 +
 .../t2/workbench/models/graph/GraphTest.java    |  138 +
 .../src/test/resources/nested_iteration.xml     |  121 +
 taverna-workbench-graph-view/pom.xml            |   88 +
 .../views/graph/AutoScrollInteractor.java       |  181 +
 .../views/graph/GraphViewComponent.java         |  548 +++
 .../views/graph/GraphViewComponentFactory.java  |  100 +
 .../views/graph/actions/AddWFInputAction.java   |   69 +
 .../views/graph/actions/AddWFOutputAction.java  |   69 +
 .../actions/DeleteGraphComponentAction.java     |  180 +
 .../RenameWFInputOutputProcessorAction.java     |  184 +
 .../graph/config/GraphViewConfiguration.java    |   80 +
 .../config/GraphViewConfigurationPanel.java     |  360 ++
 .../config/GraphViewConfigurationUIFactory.java |   55 +
 .../views/graph/menu/AddWFInputMenuAction.java  |   60 +
 .../views/graph/menu/AddWFOutputMenuAction.java |   60 +
 .../menu/DeleteGraphComponentMenuAction.java    |   61 +
 .../workbench/views/graph/menu/DiagramMenu.java |   44 +
 .../graph/menu/DiagramSaveMenuSection.java      |   39 +
 .../graph/menu/DiagramZoomMenuSection.java      |   40 +
 .../views/graph/menu/GraphCopyMenuSection.java  |   39 +
 .../graph/menu/GraphDeleteMenuSection.java      |   39 +
 .../graph/menu/GraphDetailsMenuSection.java     |   40 +
 .../views/graph/menu/GraphEditMenuSection.java  |   39 +
 .../views/graph/menu/GraphMenuSection.java      |   39 +
 .../workbench/views/graph/menu/InsertMenu.java  |   30 +
 .../RenameWFInputOutputProcessorMenuAction.java |   62 +
 .../views/graph/menu/ResetDiagramAction.java    |   64 +
 .../graph/menu/ResetDiagramMenuAction.java      |   50 +
 .../views/graph/menu/SaveGraphImageSubMenu.java |  315 ++
 .../views/graph/menu/ZoomInAction.java          |   72 +
 .../views/graph/menu/ZoomInMenuAction.java      |   50 +
 .../views/graph/menu/ZoomOutAction.java         |   65 +
 .../views/graph/menu/ZoomOutMenuAction.java     |   50 +
 .../graph/toolbar/AddWFInputToolbarAction.java  |   60 +
 .../graph/toolbar/AddWFOutputToolbarAction.java |   60 +
 .../DeleteGraphComponentToolbarAction.java      |   60 +
 .../toolbar/GraphDeleteToolbarSection.java      |   39 +
 .../graph/toolbar/GraphEditToolbarSection.java  |   39 +
 ...nameWFInputOutputProcessorToolbarAction.java |   63 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |   29 +
 ...rkbench.configuration.ConfigurationUIFactory |    1 +
 ....t2.workbench.ui.zaria.UIComponentFactorySPI |    1 +
 ...taverna.t2.workbench.ui.zaria.UIComponentSPI |    1 +
 .../META-INF/spring/graph-view-context-osgi.xml |   46 +
 .../META-INF/spring/graph-view-context.xml      |  107 +
 .../src/test/resources/nested_iteration.t2flow  |  111 +
 .../src/test/resources/nested_iteration.xml     |  120 +
 taverna-workbench-helper-api/pom.xml            |   58 +
 .../t2/workbench/helper/HelpCollator.java       |  307 ++
 .../t2/workbench/helper/HelpEnabledDialog.java  |  101 +
 .../sf/taverna/t2/workbench/helper/Helper.java  |  187 +
 .../helper/NonBlockedHelpEnabledDialog.java     |   40 +
 taverna-workbench-helper/pom.xml                |   19 +
 taverna-workbench-httpproxy-config/pom.xml      |   30 +
 .../config/HttpProxyConfigurationPanel.java     |  582 +++
 .../config/HttpProxyConfigurationUIFactory.java |   56 +
 ...rkbench.configuration.ConfigurationUIFactory |    1 +
 .../spring/httpproxy-config-context-osgi.xml    |   13 +
 .../spring/httpproxy-config-context.xml         |   10 +
 taverna-workbench-iteration-strategy-ui/pom.xml |   63 +
 .../IterationStrategyIcons.java                 |   48 +
 .../IterationStrategyConfigurationDialog.java   |  148 +
 .../IterationStrategyContextualView.java        |  231 ++
 .../IterationStrategyContextualViewFactory.java |   54 +
 .../editor/IterationStrategyCellRenderer.java   |   74 +
 .../editor/IterationStrategyEditor.java         |  247 ++
 .../editor/IterationStrategyEditorControl.java  |  439 +++
 .../editor/IterationStrategyTree.java           |  106 +
 .../IterationStrategyConfigureMenuAction.java   |   65 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |    1 +
 ...ntextualviews.activity.ContextualViewFactory |    1 +
 .../iteration-strategy-ui-context-osgi.xml      |   14 +
 .../spring/iteration-strategy-ui-context.xml    |   11 +
 .../icons/crossproducticon.png                  |  Bin 0 -> 831 bytes
 .../iterationstrategy/icons/dotproducticon.png  |  Bin 0 -> 663 bytes
 .../iterationstrategy/icons/leafnodeicon.png    |  Bin 0 -> 507 bytes
 .../editor/RunIterationStrategyEditor.java      |   56 +
 taverna-workbench-loop-ui/pom.xml               |   71 +
 .../t2/workbench/loop/ActivityGenerator.java    |  195 +
 .../t2/workbench/loop/AddLoopFactory.java       |  125 +
 .../t2/workbench/loop/LoopAddMenuAction.java    |   73 +
 .../workbench/loop/LoopConfigurationPanel.java  |  588 +++
 .../t2/workbench/loop/LoopConfigureAction.java  |  262 ++
 .../workbench/loop/LoopConfigureMenuAction.java |   97 +
 .../t2/workbench/loop/LoopContextualView.java   |  172 +
 .../loop/LoopContextualViewFactory.java         |   53 +
 .../t2/workbench/loop/LoopRemoveMenuAction.java |   92 +
 .../workbench/loop/comparisons/Comparison.java  |   47 +
 .../t2/workbench/loop/comparisons/EqualTo.java  |   40 +
 .../loop/comparisons/IsGreaterThan.java         |   40 +
 .../workbench/loop/comparisons/IsLessThan.java  |   40 +
 .../t2/workbench/loop/comparisons/Matches.java  |   40 +
 .../workbench/loop/comparisons/NotEqualTo.java  |   40 +
 .../workbench/loop/comparisons/NotMatches.java  |   40 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |    3 +
 ....ui.views.contextualviews.AddLayerFactorySPI |    1 +
 ...ntextualviews.activity.ContextualViewFactory |    1 +
 .../META-INF/spring/loop-ui-context-osgi.xml    |   21 +
 .../META-INF/spring/loop-ui-context.xml         |   32 +
 .../t2/workbench/loop/ShowContextualView.java   |  121 +
 .../src/test/resources/log4j.properties         |   10 +
 taverna-workbench-menu-api/pom.xml              |   28 +
 .../ui/menu/AbstractContextualMenuAction.java   |   64 +
 .../net/sf/taverna/t2/ui/menu/AbstractMenu.java |  123 +
 .../taverna/t2/ui/menu/AbstractMenuAction.java  |  135 +
 .../taverna/t2/ui/menu/AbstractMenuCustom.java  |  144 +
 .../sf/taverna/t2/ui/menu/AbstractMenuItem.java |  144 +
 .../t2/ui/menu/AbstractMenuOptionGroup.java     |   79 +
 .../taverna/t2/ui/menu/AbstractMenuSection.java |  113 +
 .../taverna/t2/ui/menu/AbstractMenuToggle.java  |  132 +
 .../sf/taverna/t2/ui/menu/AbstractToolBar.java  |   74 +
 .../t2/ui/menu/ContextualMenuComponent.java     |   35 +
 .../taverna/t2/ui/menu/ContextualSelection.java |   48 +
 .../t2/ui/menu/DefaultContextualMenu.java       |   53 +
 .../sf/taverna/t2/ui/menu/DefaultMenuBar.java   |   50 +
 .../sf/taverna/t2/ui/menu/DefaultToolBar.java   |   51 +
 .../sf/taverna/t2/ui/menu/DesignOnlyAction.java |   32 +
 .../t2/ui/menu/DesignOrResultsAction.java       |   32 +
 .../sf/taverna/t2/ui/menu/MenuComponent.java    |  277 ++
 .../net/sf/taverna/t2/ui/menu/MenuManager.java  |  339 ++
 .../net/sf/taverna/t2/ui/menu/package-info.java |  141 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |    4 +
 .../META-INF/spring/menu-api-context-osgi.xml   |   13 +
 .../META-INF/spring/menu-api-context.xml        |   10 +
 taverna-workbench-menu-impl/pom.xml             |   66 +
 .../t2/ui/menu/impl/MenuManagerImpl.java        |  880 +++++
 .../t2/workbench/ui/impl/menu/AdvancedMenu.java |   44 +
 .../t2/workbench/ui/impl/menu/EditMenu.java     |   43 +
 .../ui/impl/menu/FeedbackMenuAction.java        |   75 +
 .../t2/workbench/ui/impl/menu/FileMenu.java     |   48 +
 .../t2/workbench/ui/impl/menu/HelpMenu.java     |   44 +
 .../ui/impl/menu/OnlineHelpMenuAction.java      |   68 +
 .../ui/impl/menu/ShowLogsAndDataMenuAction.java |   89 +
 .../ui/impl/menu/ViewShowMenuSection.java       |   40 +
 .../net.sf.taverna.t2.ui.menu.MenuManager       |    1 +
 .../META-INF/spring/menu-impl-context-osgi.xml  |   26 +
 .../META-INF/spring/menu-impl-context.xml       |   25 +
 taverna-workbench-menu-items/pom.xml            |   73 +
 .../AbstractConnectPortMenuActions.java         |  268 ++
 .../activityport/ActivityInputPortSection.java  |   67 +
 .../activityport/ActivityOutputPortSection.java |   67 +
 .../AddInputPortDefaultValueAction.java         |  150 +
 .../ConnectInputPortMenuActions.java            |   41 +
 .../ConnectOutputPortMenuActions.java           |   41 +
 .../items/activityport/ConnectPortsAction.java  |   68 +
 .../CreateAndConnectDataflowPortAction.java     |  226 ++
 .../SetConstantInputPortValueMenuAction.java    |   73 +
 .../SetDefaultInputPortValueAction.java         |  171 +
 .../annotated/AnnotatedConfigureMenuAction.java |   77 +
 .../ConfigureRunningContextualMenuSection.java  |   50 +
 .../items/contextualviews/ConfigureSection.java |   61 +
 .../menu/items/contextualviews/EditSection.java |   73 +
 .../items/contextualviews/InsertSection.java    |   63 +
 .../items/contextualviews/PasteMenuAction.java  |   74 +
 .../ShowConfigureMenuAction.java                |  165 +
 .../ShowDetailsContextualMenuAction.java        |   65 +
 .../contextualviews/ShowDetailsMenuAction.java  |   81 +
 .../ShowReportsContextualMenuAction.java        |  103 +
 .../items/controllink/ConditionSection.java     |   71 +
 .../controllink/RemoveConditionMenuAction.java  |   67 +
 .../t2/ui/menu/items/datalink/LinkSection.java  |   73 +
 .../items/datalink/RemoveLinkMenuAction.java    |   66 +
 .../ConnectDataflowInputPortMenuActions.java    |   42 +
 .../ConnectDataflowOutputPortMenuActions.java   |   42 +
 .../ports/EditDataflowInputPortMenuAction.java  |   68 +
 .../ports/EditDataflowOutputPortMenuAction.java |   68 +
 .../RemoveDataflowInputPortMenuAction.java      |   68 +
 .../RemoveDataflowOutputPortMenuAction.java     |   68 +
 .../items/ports/WorkflowInputPortSection.java   |   73 +
 .../items/ports/WorkflowOutputPortSection.java  |   73 +
 .../items/processor/ConditionMenuActions.java   |  118 +
 .../menu/items/processor/ProcessorSection.java  |   58 +
 .../processor/RemoveProcessorMenuAction.java    |   67 +
 .../processor/RenameProcessorMenuAction.java    |   68 +
 .../items/workflow/CreateInputMenuAction.java   |   62 +
 .../items/workflow/CreateOutputMenuAction.java  |   62 +
 .../WorkflowServiceTemplatesSection.java        |   76 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |   46 +
 .../META-INF/spring/menu-items-context-osgi.xml |   57 +
 .../META-INF/spring/menu-items-context.xml      |  124 +
 taverna-workbench-monitor-view/pom.xml          |   67 +
 .../views/monitor/MonitorViewComponent.java     |  168 +
 .../views/monitor/graph/GraphMonitor.java       |  140 +
 .../views/monitor/graph/GraphMonitorNode.java   |  115 +
 .../monitor/graph/MonitorGraphComponent.java    |  378 ++
 .../progressreport/TableMonitorComponent.java   |  100 +
 .../WorkflowRunProgressTreeCellRenderer.java    |   96 +
 .../WorkflowRunProgressTreeTable.java           |  112 +
 .../WorkflowRunProgressTreeTableModel.java      |  279 ++
 ....t2.workbench.ui.zaria.UIComponentFactorySPI |    1 +
 ...taverna.t2.workbench.ui.zaria.UIComponentSPI |    1 +
 .../spring/monitor-view-context-osgi.xml        |    9 +
 .../META-INF/spring/monitor-view-context.xml    |    6 +
 taverna-workbench-parallelize-ui/pom.xml        |   42 +
 .../ParallelizeConfigurationPanel.java          |   99 +
 .../parallelize/ParallelizeConfigureAction.java |  185 +
 .../ParallelizeConfigureMenuAction.java         |   77 +
 .../parallelize/ParallelizeContextualView.java  |  130 +
 .../ParallelizeContextualViewFactory.java       |   56 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |    1 +
 ...ntextualviews.activity.ContextualViewFactory |    1 +
 .../spring/parallelize-ui-context-osgi.xml      |   16 +
 .../META-INF/spring/parallelize-ui-context.xml  |   16 +
 .../LocalTestLauncher.bat                       |   14 +
 .../lib/core-renderer.jar                       |  Bin 0 -> 1079323 bytes
 .../log4j.properties                            |    4 +
 .../pom.xml                                     |  183 +
 .../move_scomp_results_into_project.bat         |   29 +
 .../scomp_compile_from_web.bat                  |    9 +
 .../scomp_compile_from_web_to_jar.bat           |    9 +
 .../doc/BioCatalogue Plugin Documentation.odt   |  Bin 0 -> 77721 bytes
 .../src/main/help/Index-TOC-Map-Additions.txt   |   20 +
 .../main/help/biocatalogue-plugin-features.html |  113 +
 .../main/help/biocatalogue-plugin-feedback.html |   28 +
 .../src/main/help/biocatalogue-plugin.html      |   54 +
 .../model/BioCataloguePluginConstants.java      |   77 +
 .../model/HTTPMethodInterpreter.java            |   46 +
 .../model/LoadingExpandedResource.java          |   41 +
 .../biocatalogue/model/LoadingResource.java     |   39 +
 .../net/sf/taverna/biocatalogue/model/Pair.java |   30 +
 .../sf/taverna/biocatalogue/model/Resource.java |  506 +++
 .../biocatalogue/model/ResourceManager.java     |  326 ++
 .../model/ResourcePreviewContent.java           |   38 +
 .../model/SoapOperationIdentity.java            |   77 +
 .../model/SoapOperationPortIdentity.java        |   26 +
 .../model/SoapProcessorIdentity.java            |   27 +
 .../biocatalogue/model/SoapServiceIdentity.java |   45 +
 .../net/sf/taverna/biocatalogue/model/Tag.java  |  218 ++
 .../net/sf/taverna/biocatalogue/model/Util.java |  793 ++++
 .../BeanForPOSTToFilteredIndex.java             |   12 +
 .../model/connectivity/BeansForJSONLiteAPI.java |   84 +
 .../connectivity/BioCatalogueAPIRequest.java    |   47 +
 .../model/connectivity/BioCatalogueClient.java  |  785 ++++
 .../model/connectivity/ServerResponse.java      |   40 +
 .../connectivity/ServerResponseStream.java      |   30 +
 .../biocatalogue/model/search/SearchEngine.java |  221 ++
 .../model/search/SearchInstance.java            |  490 +++
 .../model/search/SearchInstanceTracker.java     |   57 +
 .../model/search/SearchOptions.java             |   70 +
 .../model/search/SearchResults.java             |  214 ++
 .../model/search/ServiceFilteringSettings.java  |  184 +
 .../biocatalogue/test/AnnotationBean.java       |   52 +
 .../biocatalogue/test/DrawDefaultIconTest.java  |   38 +
 .../sf/taverna/biocatalogue/test/GSONTest.java  |   19 +
 .../test/GSONTest_exportingJSON.java            |   30 +
 .../test/GSONTest_forSoapOperationsIndex.java   |   27 +
 .../biocatalogue/test/JWaitDialogTest.java      |   36 +
 .../biocatalogue/test/LinkedListEqualsTest.java |   25 +
 .../biocatalogue/test/TestAPICaller.java        |  241 ++
 .../test/TestDoubleUsageOfSameSwingElement.java |   32 +
 .../biocatalogue/test/TestUtilURLHandling.java  |   87 +
 .../biocatalogue/test/TestXHTMLRenderer.java    |   42 +
 .../biocatalogue/test/WrappableJLabelTest.java  |   35 +
 .../taverna/biocatalogue/test/XStreamTest.java  |   32 +
 .../ui/BioCatalogueExplorationTab.java          |  131 +
 .../ui/HasDefaultFocusCapability.java           |   15 +
 .../biocatalogue/ui/JClickableLabel.java        |  172 +
 .../sf/taverna/biocatalogue/ui/JWaitDialog.java |  234 ++
 .../biocatalogue/ui/SearchOptionsPanel.java     |  167 +
 .../ui/filtertree/FilterTreeNode.java           |   91 +
 .../ui/filtertree/FilterTreePane.java           |  348 ++
 .../biocatalogue/ui/filtertree/JFilterTree.java |   69 +
 ...xpandableOnDemandLoadedListCellRenderer.java |  220 ++
 .../RESTMethodListCellRenderer.java             |  248 ++
 .../SOAPOperationListCellRenderer.java          |  257 ++
 .../SearchResultsListingPanel.java              |  870 +++++
 .../search_results/SearchResultsMainPanel.java  |  498 +++
 .../search_results/SearchResultsRenderer.java   |   47 +
 .../search_results/ServiceListCellRenderer.java |  291 ++
 .../ui/tristatetree/JTriStateTree.java          |  631 ++++
 .../tristatetree/Swing - Tristate CheckBox.7z   |  Bin 0 -> 108419 bytes
 .../biocatalogue/ui/tristatetree/Test.java      |   67 +
 .../ui/tristatetree/TriStateCheckBox.java       |  172 +
 .../TriStateCheckBoxTreeCellRenderer.java       |   62 +
 .../TriStateTreeCheckingListener.java           |   12 +
 .../ui/tristatetree/TriStateTreeNode.java       |  246 ++
 .../biocatalogue/BioCataloguePerspective.java   |   70 +
 .../biocatalogue/MainComponent.java             |  285 ++
 .../biocatalogue/MainComponentFactory.java      |   46 +
 .../biocatalogue/MainComponentShutdownHook.java |   49 +
 .../biocatalogue/TestJFrameForLocalLaunch.java  |   68 +
 .../biocatalogue/integration/Integration.java   |  518 +++
 .../config/BioCataloguePluginConfiguration.java |   68 +
 .../BioCataloguePluginConfigurationPanel.java   |  448 +++
 ...ioCataloguePluginConfigurationUIFactory.java |   27 +
 ...aloguePluginInputPortContextViewFactory.java |   45 +
 ...loguePluginOutputPortContextViewFactory.java |   45 +
 ...aloguePluginProcessorContextViewFactory.java |   43 +
 .../ProcessorInputPortView.java                 |   52 +
 .../ProcessorOutputPortView.java                |   52 +
 .../contextual_views/ProcessorView.java         |  229 ++
 .../BioCatalogueWSDLActivityHealthCheck.java    |   40 +
 ...ueWSDLActivityHealthCheckVisitExplainer.java |  111 +
 .../BioCatalogueWSDLActivityHealthChecker.java  |  199 +
 .../health_check/ServiceHealthChecker.java      |  280 ++
 .../ServiceMonitoringStatusInterpreter.java     |   77 +
 .../BioCatalogueContextualMenuSection.java      |   62 +
 .../integration/menus/MenuActionInputPort.java  |   43 +
 .../menus/MenuActionProcessorHealthCheck.java   |   51 +
 .../BioCatalogueRESTServiceProvider.java        |  117 +
 .../BioCatalogueServiceProvider.java            |  274 ++
 ...ioCatalogueWSDLOperationServiceProvider.java |  215 ++
 .../RESTFromBioCatalogueServiceDescription.java |  194 +
 ...ationFromBioCatalogueServiceDescription.java |  116 +
 ...rvicedescriptions.ServiceDescriptionProvider |    2 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |    2 +
 .../net.sf.taverna.t2.workbench.ShutdownSPI     |    1 +
 ...rkbench.configuration.ConfigurationUIFactory |    1 +
 ...t2.workbench.report.explainer.VisitExplainer |    1 +
 ...ntextualviews.activity.ContextualViewFactory |    3 +
 ...taverna.t2.workbench.ui.zaria.PerspectiveSPI |    1 +
 ....t2.workbench.ui.zaria.UIComponentFactorySPI |    1 +
 ...taverna.t2.workbench.ui.zaria.UIComponentSPI |    1 +
 ...averna.t2.workflowmodel.health.HealthChecker |    1 +
 .../ajax-loader-grey-bert2-still.png            |  Bin 0 -> 1271 bytes
 .../biocatalogue/ajax-loader-grey-bert2.gif     |  Bin 0 -> 3951 bytes
 .../ajax-loader-orange-bert2-still.png          |  Bin 0 -> 1214 bytes
 .../biocatalogue/ajax-loader-orange-bert2.gif   |  Bin 0 -> 3951 bytes
 .../biocatalogue/ajax-loader-still.gif          |  Bin 0 -> 889 bytes
 .../perspectives/biocatalogue/ajax-loader.gif   |  Bin 0 -> 1456 bytes
 .../biocatalogue/biocatalogue-perspective.xml   |   19 +
 .../biocatalogue/biocatalogue_styles.css        | 2673 +++++++++++++
 .../biocatalogue/blue-sphere-50.png             |  Bin 0 -> 1936 bytes
 .../biocatalogue/cross-sphere-35.png            |  Bin 0 -> 2748 bytes
 .../biocatalogue/cross-sphere-50.png            |  Bin 0 -> 7161 bytes
 .../biocatalogue/famfamfam_silk/accept.png      |  Bin 0 -> 781 bytes
 .../biocatalogue/famfamfam_silk/add - tick.pdn  |  Bin 0 -> 5367 bytes
 .../biocatalogue/famfamfam_silk/add - tick.png  |  Bin 0 -> 784 bytes
 .../biocatalogue/famfamfam_silk/add.png         |  Bin 0 -> 733 bytes
 .../famfamfam_silk/application_form_add.png     |  Bin 0 -> 592 bytes
 .../arrow_join (flipped vertically).png         |  Bin 0 -> 669 bytes
 .../biocatalogue/famfamfam_silk/arrow_left.png  |  Bin 0 -> 557 bytes
 .../famfamfam_silk/arrow_refresh.png            |  Bin 0 -> 685 bytes
 .../biocatalogue/famfamfam_silk/arrow_right.png |  Bin 0 -> 596 bytes
 .../famfamfam_silk/chart_organisation.png       |  Bin 0 -> 444 bytes
 .../biocatalogue/famfamfam_silk/cross.png       |  Bin 0 -> 655 bytes
 .../biocatalogue/famfamfam_silk/disk.png        |  Bin 0 -> 620 bytes
 .../biocatalogue/famfamfam_silk/error.png       |  Bin 0 -> 666 bytes
 .../biocatalogue/famfamfam_silk/exclamation.png |  Bin 0 -> 701 bytes
 .../external_link_listing_small.png             |  Bin 0 -> 456 bytes
 .../famfamfam_silk/folder_explore.png           |  Bin 0 -> 679 bytes
 .../biocatalogue/famfamfam_silk/grey_circle.png |  Bin 0 -> 586 bytes
 .../biocatalogue/famfamfam_silk/help.png        |  Bin 0 -> 786 bytes
 .../biocatalogue/famfamfam_silk/information.png |  Bin 0 -> 778 bytes
 .../biocatalogue/famfamfam_silk/lightbulb.png   |  Bin 0 -> 782 bytes
 .../biocatalogue/famfamfam_silk/lock.png        |  Bin 0 -> 749 bytes
 .../biocatalogue/famfamfam_silk/lock_open.png   |  Bin 0 -> 727 bytes
 .../biocatalogue/famfamfam_silk/magnifier.png   |  Bin 0 -> 615 bytes
 .../famfamfam_silk/multiple_star.png            |  Bin 0 -> 676 bytes
 .../famfamfam_silk/page_white_code.png          |  Bin 0 -> 603 bytes
 .../biocatalogue/famfamfam_silk/plugin.png      |  Bin 0 -> 591 bytes
 .../famfamfam_silk/remote_resource.png          |  Bin 0 -> 957 bytes
 .../biocatalogue/famfamfam_silk/server.png      |  Bin 0 -> 530 bytes
 .../biocatalogue/famfamfam_silk/star.png        |  Bin 0 -> 670 bytes
 .../biocatalogue/famfamfam_silk/style.png       |  Bin 0 -> 813 bytes
 .../biocatalogue/famfamfam_silk/sum.png         |  Bin 0 -> 289 bytes
 .../biocatalogue/famfamfam_silk/tag_blue.png    |  Bin 0 -> 586 bytes
 .../text_linespacing (collapse).png             |  Bin 0 -> 371 bytes
 .../famfamfam_silk/text_linespacing.png         |  Bin 0 -> 363 bytes
 .../famfamfam_silk/text_list_numbers.png        |  Bin 0 -> 357 bytes
 .../biocatalogue/famfamfam_silk/tick.png        |  Bin 0 -> 537 bytes
 .../biocatalogue/famfamfam_silk/user.png        |  Bin 0 -> 741 bytes
 .../t2/ui/perspectives/biocatalogue/favicon.png |  Bin 0 -> 1336 bytes
 .../ui/perspectives/biocatalogue/folds/fold.png |  Bin 0 -> 331 bytes
 .../biocatalogue/folds/fold_16x16.png           |  Bin 0 -> 361 bytes
 .../perspectives/biocatalogue/folds/unfold.png  |  Bin 0 -> 334 bytes
 .../biocatalogue/folds/unfold_16x16.png         |  Bin 0 -> 354 bytes
 .../biocatalogue/info-sphere-35.png             |  Bin 0 -> 2492 bytes
 .../biocatalogue/info-sphere-50.png             |  Bin 0 -> 2439 bytes
 .../biocatalogue/open_in_BioCatalogue.pdn       |  Bin 0 -> 5128 bytes
 .../biocatalogue/open_in_BioCatalogue.png       |  Bin 0 -> 663 bytes
 .../biocatalogue/pling-sphere-35.png            |  Bin 0 -> 2275 bytes
 .../biocatalogue/pling-sphere-50.png            |  Bin 0 -> 1724 bytes
 .../biocatalogue/query-sphere-35.png            |  Bin 0 -> 2473 bytes
 .../biocatalogue/query-sphere-50.png            |  Bin 0 -> 1854 bytes
 .../service_icons/service_type_multitype.png    |  Bin 0 -> 1133 bytes
 .../service_icons/service_type_rest.png         |  Bin 0 -> 1137 bytes
 .../service_icons/service_type_soap.png         |  Bin 0 -> 1131 bytes
 .../service_icons/service_type_unknown.png      |  Bin 0 -> 1076 bytes
 .../soap_rest_multitype_unknown.pdn             |  Bin 0 -> 6693 bytes
 .../t2/ui/perspectives/biocatalogue/styles.css  |  290 ++
 .../t2/ui/perspectives/biocatalogue/test.html   |   78 +
 .../biocatalogue/tick-sphere-35.png             |  Bin 0 -> 2479 bytes
 .../biocatalogue/tick-sphere-50.png             |  Bin 0 -> 1909 bytes
 .../t2/ui/perspectives/biocatalogue/trash.png   |  Bin 0 -> 460 bytes
 .../tristate_checkbox_checked.png               |  Bin 0 -> 1050 bytes
 .../tristate_checkbox_partial.png               |  Bin 0 -> 1042 bytes
 .../tristate_checkbox_partial_green.png         |  Bin 0 -> 993 bytes
 .../tristate_checkbox_unchecked.png             |  Bin 0 -> 1033 bytes
 .../ui/perspectives/biocatalogue/unchecked.png  |  Bin 0 -> 3636 bytes
 .../src/main/xsd/dc.xsd                         |  119 +
 .../src/main/xsd/dcterms.xsd                    |  137 +
 .../src/main/xsd/schema-v1.xsd                  | 3557 ++++++++++++++++++
 .../src/main/xsd/xlink.xsd                      |   83 +
 taverna-workbench-perspective-design/pom.xml    |   83 +
 .../perspectives/design/DesignPerspective.java  |  118 +
 .../design/DesignPerspectiveComponent.java      |  115 +
 .../design/WorkflowBundleSelectorComponent.java |  113 +
 .../design/WorkflowSelectorComponent.java       |  167 +
 .../t2/ui/perspectives/design/WorkflowTab.java  |  133 +
 ...taverna.t2.workbench.ui.zaria.PerspectiveSPI |    1 +
 .../spring/perspective-design-context-osgi.xml  |   21 +
 .../spring/perspective-design-context.xml       |   18 +
 .../pom.xml                                     |   85 +
 .../myexperiment/AddCommentDialog.java          |  330 ++
 .../myexperiment/AddRemoveFavouriteDialog.java  |  277 ++
 .../myexperiment/ExampleWorkflowsPanel.java     |  153 +
 .../HistoryBrowserTabContentPanel.java          |  541 +++
 .../myexperiment/JClickableLabel.java           |  127 +
 .../myexperiment/MainComponent.java             |  645 ++++
 .../myexperiment/MainComponentFactory.java      |   60 +
 .../myexperiment/MainComponentShutdownHook.java |   84 +
 .../myexperiment/MyExperimentPerspective.java   |  190 +
 .../myexperiment/MyStuffContributionsPanel.java |  370 ++
 .../myexperiment/MyStuffSidebarPanel.java       |  359 ++
 .../myexperiment/MyStuffTabContentPanel.java    |  342 ++
 .../myexperiment/PluginPreferencesDialog.java   |  372 ++
 .../myexperiment/PluginStatusBar.java           |  195 +
 .../myexperiment/ResourceListPanel.java         |  182 +
 .../myexperiment/ResourcePreviewBrowser.java    |  711 ++++
 .../myexperiment/ResourcePreviewContent.java    |   78 +
 .../myexperiment/ResourcePreviewFactory.java    | 1359 +++++++
 .../myexperiment/SearchOptionsPanel.java        |  317 ++
 .../myexperiment/SearchResultsPanel.java        |  201 +
 .../myexperiment/SearchTabContentPanel.java     |  450 +++
 .../myexperiment/StyledHTMLEditorKit.java       |   19 +
 .../myexperiment/TagBrowserTabContentPanel.java |  226 ++
 .../myexperiment/TagCloudPanel.java             |  342 ++
 .../myexperiment/TestJFrameForLocalLaunch.java  |   48 +
 .../myexperiment/UploadWorkflowDialog.java      |  849 +++++
 .../myexperiment/model/Base64$InputStream.class |  Bin 0 -> 2083 bytes
 .../model/Base64$OutputStream.class             |  Bin 0 -> 2307 bytes
 .../myexperiment/model/Base64.class             |  Bin 0 -> 15458 bytes
 .../perspectives/myexperiment/model/Base64.java | 1813 +++++++++
 .../myexperiment/model/Comment.java             |  141 +
 .../perspectives/myexperiment/model/File.java   |  237 ++
 .../perspectives/myexperiment/model/Group.java  |  222 ++
 .../myexperiment/model/License.java             |   62 +
 .../myexperiment/model/MyExperimentClient.class |  Bin 0 -> 3174 bytes
 .../myexperiment/model/MyExperimentClient.java  | 1218 ++++++
 .../perspectives/myexperiment/model/Pack.java   |  232 ++
 .../myexperiment/model/PackItem.java            |  186 +
 .../myexperiment/model/Resource.java            |  683 ++++
 .../myexperiment/model/SearchEngine.java        |  321 ++
 .../myexperiment/model/ServerResponse.java      |   59 +
 .../ui/perspectives/myexperiment/model/Tag.java |  125 +
 .../myexperiment/model/TagCloud.java            |   47 +
 .../perspectives/myexperiment/model/User.java   |  297 ++
 .../perspectives/myexperiment/model/Util.java   |  624 +++
 .../myexperiment/model/Workflow.java            |  420 +++
 .../config/MyExperimentConfiguration.java       |   68 +
 .../config/MyExperimentConfigurationPanel.java  |  305 ++
 .../MyExperimentConfigurationUIFactory.java     |   62 +
 .../TestJFrameForPreferencesLocalLaunch.java    |   46 +
 .../net.sf.taverna.t2.workbench.ShutdownSPI     |    1 +
 ...rkbench.configuration.ConfigurationUIFactory |    1 +
 ...taverna.t2.workbench.ui.zaria.PerspectiveSPI |    1 +
 ....t2.workbench.ui.zaria.UIComponentFactorySPI |    1 +
 ...taverna.t2.workbench.ui.zaria.UIComponentSPI |    1 +
 .../perspective-myexperiment-context-osgi.xml   |   20 +
 .../spring/perspective-myexperiment-context.xml |   20 +
 .../myexperiment/ajax-loader-still.gif          |  Bin 0 -> 889 bytes
 .../perspectives/myexperiment/ajax-loader.gif   |  Bin 0 -> 1456 bytes
 .../ui/perspectives/myexperiment/arrow_left.png |  Bin 0 -> 557 bytes
 .../perspectives/myexperiment/arrow_refresh.png |  Bin 0 -> 685 bytes
 .../perspectives/myexperiment/arrow_right.png   |  Bin 0 -> 596 bytes
 .../perspectives/myexperiment/comment_add.png   |  Bin 0 -> 530 bytes
 .../myexperiment/comment_delete.png             |  Bin 0 -> 548 bytes
 .../t2/ui/perspectives/myexperiment/cross.png   |  Bin 0 -> 655 bytes
 .../t2/ui/perspectives/myexperiment/denied.png  |  Bin 0 -> 701 bytes
 .../myexperiment/dummy-workflow.t2flow          |  157 +
 .../external_link_listing_small.png             |  Bin 0 -> 456 bytes
 .../perspectives/myexperiment/favourite_add.png |  Bin 0 -> 701 bytes
 .../myexperiment/favourite_delete.png           |  Bin 0 -> 722 bytes
 .../t2/ui/perspectives/myexperiment/file.png    |  Bin 0 -> 562 bytes
 .../t2/ui/perspectives/myexperiment/group.png   |  Bin 0 -> 753 bytes
 .../t2/ui/perspectives/myexperiment/login.png   |  Bin 0 -> 693 bytes
 .../t2/ui/perspectives/myexperiment/logout.png  |  Bin 0 -> 688 bytes
 .../ui/perspectives/myexperiment/myexp_icon.png |  Bin 0 -> 1611 bytes
 .../myexperiment/myexp_icon16x16.png            |  Bin 0 -> 1057 bytes
 .../myexperiment/myexperiment-perspective.xml   |   17 +
 .../myexperiment/open_in_myExperiment.png       |  Bin 0 -> 621 bytes
 .../t2/ui/perspectives/myexperiment/pack.png    |  Bin 0 -> 565 bytes
 .../myexperiment/remote_resource.png            |  Bin 0 -> 957 bytes
 .../t2/ui/perspectives/myexperiment/star.png    |  Bin 0 -> 670 bytes
 .../t2/ui/perspectives/myexperiment/styles.css  |  380 ++
 .../ui/perspectives/myexperiment/tag_blue.png   |  Bin 0 -> 586 bytes
 .../t2/ui/perspectives/myexperiment/tick.png    |  Bin 0 -> 537 bytes
 .../myexperiment/transparent_icon.png           |  Bin 0 -> 1172 bytes
 .../t2/ui/perspectives/myexperiment/user.png    |  Bin 0 -> 741 bytes
 .../ui/perspectives/myexperiment/workflow.png   |  Bin 0 -> 975 bytes
 taverna-workbench-perspective-results/pom.xml   |   64 +
 .../results/ResultsPerspective.java             |  158 +
 .../results/ResultsPerspectiveComponent.java    |  221 ++
 .../t2/ui/perspectives/results/RunMonitor.java  |  171 +
 .../results/RunSelectorComponent.java           |   72 +
 .../t2/ui/perspectives/results/RunTab.java      |  133 +
 .../t2/ui/perspectives/results/WorkflowRun.java |   54 +
 .../results/WorkflowRunListCellRenderer.java    |   59 +
 .../results/WorkflowRunListModel.java           |   66 +
 ...taverna.t2.workbench.ui.zaria.PerspectiveSPI |    1 +
 .../spring/perspective-results-context-osgi.xml |   27 +
 .../spring/perspective-results-context.xml      |   19 +
 taverna-workbench-plugin-manager/pom.xml        |   49 +
 .../plugin/impl/AvailablePluginPanel.java       |   72 +
 .../plugin/impl/InstalledPluginPanel.java       |   66 +
 .../plugin/impl/PluginManagerPanel.java         |  210 ++
 .../plugin/impl/PluginManagerView.java          |   71 +
 .../t2/workbench/plugin/impl/PluginPanel.java   |  166 +
 .../plugin/impl/UpdatePluginPanel.java          |   72 +
 .../plugin/impl/menu/PluginMenuAction.java      |   56 +
 .../spring/plugin-manager-context-osgi.xml      |   20 +
 .../META-INF/spring/plugin-manager-context.xml  |   15 +
 taverna-workbench-plugins-gui/pom.xml           |   46 +
 .../raven/plugins/ui/AddPluginSiteFrame.java    |  273 ++
 .../plugins/ui/CheckForNoticeStartupHook.java   |  143 +
 .../raven/plugins/ui/CheckForUpdatesDialog.java |  122 +
 .../plugins/ui/CheckForUpdatesStartupHook.java  |   94 +
 .../plugins/ui/PluginListCellRenderer.java      |  214 ++
 .../raven/plugins/ui/PluginListModel.java       |  108 +
 .../raven/plugins/ui/PluginManagerFrame.java    |  516 +++
 .../plugins/ui/PluginRepositoryListener.java    |  148 +
 .../raven/plugins/ui/PluginSiteFrame.java       |  542 +++
 .../raven/plugins/ui/UpdatesAvailableIcon.java  |  205 +
 .../profile/ui/ProfileVersionCellRenderer.java  |  177 +
 .../profile/ui/ProfileVersionListFrame.java     |  260 ++
 .../profile/ui/ProfileVersionListModel.java     |  101 +
 .../net.sf.taverna.t2.workbench.StartupSPI      |    2 +
 .../spring/plugins-gui-context-osgi.xml         |   11 +
 .../META-INF/spring/plugins-gui-context.xml     |    8 +
 .../net/sf/taverna/raven/plugins/ui/update.png  |  Bin 0 -> 689 bytes
 .../raven/plugins/ui/updateRecommended.png      |  Bin 0 -> 731 bytes
 taverna-workbench-reference-ui/pom.xml          |   66 +
 .../t2/reference/ui/CheckWorkflowStatus.java    |   97 +
 .../ui/CopyWorkflowInProgressDialog.java        |   91 +
 .../reference/ui/CopyWorkflowSwingWorker.java   |   51 +
 .../t2/reference/ui/InvalidDataflowReport.java  |   95 +
 .../t2/reference/ui/RegistrationPanel.java      |  808 ++++
 .../sf/taverna/t2/reference/ui/UrlPanel.java    |  100 +
 .../t2/reference/ui/WorkflowLaunchWindow.java   |  626 +++
 .../net/sf/taverna/t2/reference/ui/package.html |    4 +
 .../ui/referenceactions/LoadInputsFromXML.java  |  120 +
 .../ui/referenceactions/ReferenceActionSPI.java |   38 +
 .../ui/referenceactions/SaveInputsAsXML.java    |  207 +
 .../reference/ui/tree/PreRegistrationTree.java  |  217 ++
 .../tree/PreRegistrationTreeCellRenderer.java   |  115 +
 .../ui/tree/PreRegistrationTreeDnDHandler.java  |  268 ++
 .../ui/tree/PreRegistrationTreeModel.java       |  310 ++
 .../taverna/t2/reference/ui/tree/package.html   |    6 +
 ...rence.ui.referenceactions.ReferenceActionSPI |    2 +
 .../spring/reference-ui-context-osgi.xml        |   12 +
 .../META-INF/spring/reference-ui-context.xml    |    9 +
 .../src/main/resources/icons/addtext_co.gif     |  Bin 0 -> 335 bytes
 .../main/resources/icons/complete_status.gif    |  Bin 0 -> 76 bytes
 .../src/main/resources/icons/deadlock_view.gif  |  Bin 0 -> 239 bytes
 .../src/main/resources/icons/delete_obj.gif     |  Bin 0 -> 351 bytes
 .../src/main/resources/icons/det_pane_hide.gif  |  Bin 0 -> 370 bytes
 .../src/main/resources/icons/error_tsk.gif      |  Bin 0 -> 353 bytes
 .../main/resources/icons/errorwarning_tab.gif   |  Bin 0 -> 577 bytes
 .../resources/icons/genericregister_obj.gif     |  Bin 0 -> 115 bytes
 .../src/main/resources/icons/information.gif    |  Bin 0 -> 267 bytes
 .../main/resources/icons/invalid_build_tool.gif |  Bin 0 -> 339 bytes
 .../src/main/resources/icons/newfolder_wiz.gif  |  Bin 0 -> 349 bytes
 .../src/main/resources/icons/repo_rep.gif       |  Bin 0 -> 588 bytes
 .../src/main/resources/icons/start_task.gif     |  Bin 0 -> 318 bytes
 .../src/main/resources/icons/topic.gif          |  Bin 0 -> 354 bytes
 .../src/main/resources/icons/web.gif            |  Bin 0 -> 362 bytes
 .../src/main/resources/icons/wordassist_co.gif  |  Bin 0 -> 152 bytes
 .../src/main/resources/icons/write_obj.gif      |  Bin 0 -> 210 bytes
 taverna-workbench-renderers-api/pom.xml         |   27 +
 .../net/sf/taverna/t2/renderers/Renderer.java   |   33 +
 .../taverna/t2/renderers/RendererException.java |   46 +
 .../taverna/t2/renderers/RendererRegistry.java  |   48 +
 .../sf/taverna/t2/renderers/RendererUtils.java  |   89 +
 taverna-workbench-renderers-exts/pom.xml        |   62 +
 .../t2/renderers/HTMLBrowserRenderer.java       |   95 +
 .../sf/taverna/t2/renderers/JMolRenderer.java   |  178 +
 .../sf/taverna/t2/renderers/PDFRenderer.java    |  124 +
 .../sf/taverna/t2/renderers/SVGRenderer.java    |  154 +
 .../taverna/t2/renderers/SeqVistaRenderer.java  |  167 +
 .../net.sf.taverna.t2.renderers.Renderer        |    5 +
 .../spring/renderers-exts-context-osgi.xml      |   15 +
 .../META-INF/spring/renderers-exts-context.xml  |   12 +
 .../taverna/t2/renderers/TestRendererSPI.java   |  153 +
 taverna-workbench-renderers-impl/pom.xml        |   65 +
 .../t2/renderers/impl/AbstractRenderer.java     |  124 +
 .../renderers/impl/AdvancedImageRenderer.java   |   94 +
 .../t2/renderers/impl/ExtensionFileFilter.java  |   77 +
 .../t2/renderers/impl/HexBinaryRenderer.java    |   77 +
 .../t2/renderers/impl/RendererConstants.java    |   13 +
 .../t2/renderers/impl/RendererRegistryImpl.java |   54 +
 .../taverna/t2/renderers/impl/TextRenderer.java |  137 +
 .../t2/renderers/impl/TextRtfRenderer.java      |   85 +
 .../t2/renderers/impl/TextXMLRenderer.java      |   86 +
 .../sf/taverna/t2/renderers/impl/XMLTree.java   |  329 ++
 .../net.sf.taverna.t2.renderers.Renderer        |    7 +
 .../spring/renderers-impl-context-osgi.xml      |   19 +
 .../META-INF/spring/renderers-impl-context.xml  |   17 +
 .../taverna/t2/renderers/TestRendererSPI.java   |  154 +
 taverna-workbench-report-api/pom.xml            |   59 +
 .../t2/workbench/report/ProfileReportEvent.java |   21 +
 .../t2/workbench/report/ReportManager.java      |   44 +
 .../t2/workbench/report/ReportManagerEvent.java |   10 +
 .../config/ReportManagerConfiguration.java      |   44 +
 .../services/net.sf.taverna.t2.visit.VisitKind  |    1 +
 ....taverna.t2.visit.fragility.FragilityChecker |    1 +
 .../META-INF/spring/report-api-context-osgi.xml |   13 +
 .../META-INF/spring/report-api-context.xml      |   10 +
 taverna-workbench-report-explainer/pom.xml      |  102 +
 .../report/explainer/BasicExplainer.java        | 1294 +++++++
 ...t2.workbench.report.explainer.VisitExplainer |    1 +
 .../spring/report-explainer-context-osgi.xml    |   19 +
 .../spring/report-explainer-context.xml         |   15 +
 taverna-workbench-report-impl/pom.xml           |   40 +
 .../impl/ReportManagerConfigurationImpl.java    |   71 +
 .../report/impl/ReportManagerImpl.java          |  564 +++
 .../spring/report-impl-context-osgi.xml         |   23 +
 .../META-INF/spring/report-impl-context.xml     |   21 +
 taverna-workbench-report-view/pom.xml           |   84 +
 .../ui/ReportManagerConfigurationPanel.java     |  363 ++
 .../ui/ReportManagerConfigurationUIFactory.java |   55 +
 .../ReportOnObjectContextualMenuAction.java     |  189 +
 .../report/view/ReportOnWorkflowAction.java     |  177 +
 .../report/view/ReportViewComponent.java        |  574 +++
 .../report/view/ReportViewComponentFactory.java |   75 +
 .../report/view/ReportViewConfigureAction.java  |   45 +
 .../report/view/ReportViewTableModel.java       |  284 ++
 .../workbench/report/view/StatusRenderer.java   |   46 +
 .../report/view/ValidateInProgressDialog.java   |   92 +
 .../view/ValidateObjectInProgressDialog.java    |   93 +
 .../report/view/ValidateObjectSwingWorker.java  |   71 +
 .../report/view/ValidateSwingWorker.java        |  123 +
 .../workbench/report/view/VisitReportProxy.java |   42 +
 .../report/view/VisitReportProxySet.java        |   36 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |    1 +
 ...rkbench.configuration.ConfigurationUIFactory |    1 +
 ....t2.workbench.ui.zaria.UIComponentFactorySPI |    1 +
 .../spring/report-view-context-osgi.xml         |   25 +
 .../META-INF/spring/report-view-context.xml     |   28 +
 taverna-workbench-results-view/pom.xml          |  112 +
 .../views/results/InvocationTreeModel.java      |  103 +
 .../views/results/InvocationTreeNode.java       |  100 +
 .../workbench/views/results/InvocationView.java |  136 +
 .../t2/workbench/views/results/ReportView.java  |  420 +++
 .../views/results/ResultsComponent.java         |  233 ++
 .../views/results/SimpleFilteredTreeModel.java  |   68 +
 .../processor/FilteredIterationTreeModel.java   |   91 +
 .../FilteredProcessorValueTreeModel.java        |   70 +
 .../IntermediateValuesInProgressDialog.java     |   89 +
 .../IntermediateValuesSwingWorker.java          |   47 +
 .../results/processor/IterationTreeNode.java    |   99 +
 .../processor/ProcessorEnactmentsTreeModel.java |  189 +
 .../processor/ProcessorEnactmentsTreeNode.java  |   84 +
 .../processor/ProcessorPortResultsViewTab.java  |  229 ++
 .../processor/ProcessorResultCellRenderer.java  |   89 +
 .../processor/ProcessorResultTreeNode.java      |  181 +
 .../processor/ProcessorResultsComponent.java    | 1004 +++++
 .../processor/ProcessorResultsTreeModel.java    |   73 +
 .../RenderedProcessorResultComponent.java       |  575 +++
 .../saveactions/SaveAllResultsAsExcel.java      |  296 ++
 .../saveactions/SaveAllResultsAsXML.java        |   80 +
 .../results/saveactions/SaveAllResultsSPI.java  |  193 +
 .../saveactions/SaveAllResultsToFileSystem.java |   94 +
 .../saveactions/SaveIndividualResult.java       |  186 +
 .../saveactions/SaveIndividualResultSPI.java    |   48 +
 .../results/workflow/DataBundleTreeModel.java   |  136 +
 .../workflow/FilteredDataBundleTreeModel.java   |  147 +
 .../FilteredWorkflowResultTreeModel.java        |  126 +
 .../workflow/PortResultCellRenderer.java        |  100 +
 .../results/workflow/PortResultsViewTab.java    |  283 ++
 .../workflow/RenderedResultComponent.java       |  601 +++
 .../workflow/WorkflowResultTreeModel.java       |  197 +
 .../workflow/WorkflowResultTreeNode.java        |  120 +
 .../workflow/WorkflowResultsComponent.java      |  352 ++
 ...taverna.t2.workbench.ui.zaria.UIComponentSPI |    1 +
 ....views.results.saveactions.SaveAllResultsSPI |    3 +
 ....results.saveactions.SaveIndividualResultSPI |    1 +
 .../spring/results-view-context-osgi.xml        |   14 +
 .../META-INF/spring/results-view-context.xml    |   11 +
 taverna-workbench-retry-ui/pom.xml              |   42 +
 .../retry/RetryConfigurationPanel.java          |  172 +
 .../workbench/retry/RetryConfigureAction.java   |  183 +
 .../retry/RetryConfigureMenuAction.java         |   77 +
 .../t2/workbench/retry/RetryContextualView.java |  165 +
 .../retry/RetryContextualViewFactory.java       |   58 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |    1 +
 ...ntextualviews.activity.ContextualViewFactory |    1 +
 .../META-INF/spring/retry-ui-context-osgi.xml   |   16 +
 .../META-INF/spring/retry-ui-context.xml        |   16 +
 taverna-workbench-run-ui/pom.xml                |   55 +
 .../run/actions/OpenWorkflowRunAction.java      |  135 +
 .../run/actions/RunWorkflowAction.java          |  299 ++
 .../run/actions/ValidateWorkflowAction.java     |   56 +
 .../WorkflowRunStatusShutdownDialog.java        |  153 +
 .../cleanup/WorkflowRunStatusShutdownHook.java  |  110 +
 .../run/menu/FileOpenRunMenuAction.java         |   63 +
 .../workbench/run/menu/FileRunMenuAction.java   |   82 +
 .../workbench/run/menu/FileRunMenuSection.java  |   36 +
 .../run/menu/FileValidateMenuAction.java        |   70 +
 .../workbench/run/toolbar/RunToolbarAction.java |   82 +
 .../run/toolbar/RunToolbarSection.java          |   36 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |    6 +
 .../net.sf.taverna.t2.workbench.ShutdownSPI     |    5 +
 .../net.sf.taverna.t2.workbench.StartupSPI      |    1 +
 ....t2.workbench.ui.zaria.UIComponentFactorySPI |    1 +
 ...taverna.t2.workbench.ui.zaria.UIComponentSPI |    1 +
 .../META-INF/spring/run-ui-context-osgi.xml     |   28 +
 .../META-INF/spring/run-ui-context.xml          |   41 +
 taverna-workbench-selection-api/pom.xml         |   53 +
 .../selection/DataflowSelectionModel.java       |   85 +
 .../workbench/selection/SelectionManager.java   |  113 +
 .../events/DataflowSelectionMessage.java        |   66 +
 .../events/PerspectiveSelectionEvent.java       |   59 +
 .../selection/events/ProfileSelectionEvent.java |   57 +
 .../selection/events/SelectionManagerEvent.java |   34 +
 .../events/WorkflowBundleSelectionEvent.java    |   59 +
 .../events/WorkflowRunSelectionEvent.java       |   51 +
 .../events/WorkflowSelectionEvent.java          |   57 +
 taverna-workbench-selection-impl/pom.xml        |   35 +
 .../impl/DataflowSelectionModelImpl.java        |  116 +
 .../selection/impl/SelectionManagerImpl.java    |  367 ++
 .../spring/selection-impl-context-osgi.xml      |   17 +
 .../META-INF/spring/selection-impl-context.xml  |   12 +
 taverna-workbench-update-manager/pom.xml        |   26 +
 .../update/impl/UpdateManagerView.java          |   45 +
 .../update/impl/menu/UpdateMenuAction.java      |   92 +
 .../updatemanager/PluginMenuAction.java         |   52 +
 .../UpdatesAvailableMenuAction.java             |   19 +
 .../updatemanager/UpdatesToolbarSection.java    |   16 +
 .../spring/update-manager-context-osgi.xml      |   13 +
 .../META-INF/spring/update-manager-context.xml  |   12 +
 taverna-workbench-workbench-api/pom.xml         |   15 +
 .../net/sf/taverna/t2/workbench/MainWindow.java |   16 +
 .../taverna/t2/workbench/ModelMapConstants.java |   28 +
 .../sf/taverna/t2/workbench/ShutdownSPI.java    |   72 +
 .../net/sf/taverna/t2/workbench/StartupSPI.java |   65 +
 .../t2/workbench/icons/WorkbenchIcons.java      |  214 ++
 .../ui/SwingWorkerCompletionWaiter.java         |   33 +
 .../sf/taverna/t2/workbench/ui/Updatable.java   |   32 +
 .../net/sf/taverna/t2/workbench/ui/Utils.java   |   20 +
 .../sf/taverna/t2/workbench/ui/Workbench.java   |   33 +
 .../t2/workbench/ui/zaria/PerspectiveSPI.java   |   77 +
 .../ui/zaria/UIComponentFactorySPI.java         |   56 +
 .../t2/workbench/ui/zaria/UIComponentSPI.java   |   56 +
 .../t2/workbench/icons/explorer/biomoby.png     |  Bin 0 -> 1218 bytes
 .../t2/workbench/icons/explorer/constraint.gif  |  Bin 0 -> 144 bytes
 .../t2/workbench/icons/explorer/dataflow.png    |  Bin 0 -> 814 bytes
 .../t2/workbench/icons/explorer/datalink.gif    |  Bin 0 -> 124 bytes
 .../t2/workbench/icons/explorer/input.png       |  Bin 0 -> 396 bytes
 .../t2/workbench/icons/explorer/inputport.png   |  Bin 0 -> 251 bytes
 .../t2/workbench/icons/explorer/localworker.png |  Bin 0 -> 706 bytes
 .../t2/workbench/icons/explorer/merge.png       |  Bin 0 -> 422 bytes
 .../t2/workbench/icons/explorer/output.png      |  Bin 0 -> 425 bytes
 .../t2/workbench/icons/explorer/outputport.png  |  Bin 0 -> 235 bytes
 .../t2/workbench/icons/explorer/rserv.png       |  Bin 0 -> 1235 bytes
 .../t2/workbench/icons/explorer/seqhound.png    |  Bin 0 -> 3603 bytes
 .../t2/workbench/icons/explorer/soaplab.png     |  Bin 0 -> 701 bytes
 .../workbench/icons/explorer/stringconstant.png |  Bin 0 -> 733 bytes
 .../t2/workbench/icons/explorer/talisman.png    |  Bin 0 -> 1214 bytes
 .../icons/explorer/unknownprocessor.png         |  Bin 0 -> 1060 bytes
 .../icons/explorer/workflow-explorer-old.png    |  Bin 0 -> 255 bytes
 .../icons/explorer/workflow-explorer.png        |  Bin 0 -> 267 bytes
 .../t2/workbench/icons/explorer/workflow.png    |  Bin 0 -> 1213 bytes
 .../icons/explorer/workflowInputPort.png        |  Bin 0 -> 718 bytes
 .../icons/explorer/workflowOutputPort.png       |  Bin 0 -> 636 bytes
 .../t2/workbench/icons/explorer/wsdl.png        |  Bin 0 -> 748 bytes
 .../taverna/t2/workbench/icons/generic/bin.png  |  Bin 0 -> 393 bytes
 .../t2/workbench/icons/generic/break.gif        |  Bin 0 -> 1120 bytes
 .../t2/workbench/icons/generic/close.gif        |  Bin 0 -> 351 bytes
 .../t2/workbench/icons/generic/closeAll.gif     |  Bin 0 -> 380 bytes
 .../t2/workbench/icons/generic/configure.png    |  Bin 0 -> 610 bytes
 .../taverna/t2/workbench/icons/generic/copy.png |  Bin 0 -> 389 bytes
 .../taverna/t2/workbench/icons/generic/cut.png  |  Bin 0 -> 710 bytes
 .../t2/workbench/icons/generic/database.gif     |  Bin 0 -> 1032 bytes
 .../t2/workbench/icons/generic/delete.png       |  Bin 0 -> 565 bytes
 .../t2/workbench/icons/generic/down-arrow.png   |  Bin 0 -> 331 bytes
 .../taverna/t2/workbench/icons/generic/edit.gif |  Bin 0 -> 579 bytes
 .../t2/workbench/icons/generic/fileimport.png   |  Bin 0 -> 851 bytes
 .../taverna/t2/workbench/icons/generic/find.gif |  Bin 0 -> 346 bytes
 .../workbench/icons/generic/folder-closed.png   |  Bin 0 -> 621 bytes
 .../t2/workbench/icons/generic/folder-open.png  |  Bin 0 -> 626 bytes
 .../t2/workbench/icons/generic/greentick.png    |  Bin 0 -> 331 bytes
 .../t2/workbench/icons/generic/import.gif       |  Bin 0 -> 929 bytes
 .../t2/workbench/icons/generic/inputValue.gif   |  Bin 0 -> 561 bytes
 .../t2/workbench/icons/generic/janus.png        |  Bin 0 -> 395 bytes
 .../taverna/t2/workbench/icons/generic/leaf.gif |  Bin 0 -> 194 bytes
 .../t2/workbench/icons/generic/minus.png        |  Bin 0 -> 214 bytes
 .../t2/workbench/icons/generic/newinput.gif     |  Bin 0 -> 357 bytes
 .../t2/workbench/icons/generic/newlist.gif      |  Bin 0 -> 350 bytes
 .../t2/workbench/icons/generic/normalize.png    |  Bin 0 -> 580 bytes
 .../taverna/t2/workbench/icons/generic/open.gif |  Bin 0 -> 216 bytes
 .../t2/workbench/icons/generic/openmenu.gif     |  Bin 0 -> 251 bytes
 .../t2/workbench/icons/generic/openurl.gif      |  Bin 0 -> 362 bytes
 .../t2/workbench/icons/generic/opmIcon.png      |  Bin 0 -> 376 bytes
 .../t2/workbench/icons/generic/paste.png        |  Bin 0 -> 490 bytes
 .../t2/workbench/icons/generic/pause.png        |  Bin 0 -> 385 bytes
 .../taverna/t2/workbench/icons/generic/play.png |  Bin 0 -> 341 bytes
 .../taverna/t2/workbench/icons/generic/plus.png |  Bin 0 -> 345 bytes
 .../t2/workbench/icons/generic/rbreak.gif       |  Bin 0 -> 1161 bytes
 .../taverna/t2/workbench/icons/generic/redo.png |  Bin 0 -> 513 bytes
 .../t2/workbench/icons/generic/refresh.gif      |  Bin 0 -> 336 bytes
 .../t2/workbench/icons/generic/rename.png       |  Bin 0 -> 212 bytes
 .../icons/generic/results-perspective.png       |  Bin 0 -> 542 bytes
 .../taverna/t2/workbench/icons/generic/run.gif  |  Bin 0 -> 318 bytes
 .../taverna/t2/workbench/icons/generic/save.gif |  Bin 0 -> 639 bytes
 .../taverna/t2/workbench/icons/generic/save.png |  Bin 0 -> 631 bytes
 .../t2/workbench/icons/generic/saveAll.png      |  Bin 0 -> 624 bytes
 .../t2/workbench/icons/generic/saveAs.png       |  Bin 0 -> 529 bytes
 .../t2/workbench/icons/generic/savemenu.gif     |  Bin 0 -> 661 bytes
 .../t2/workbench/icons/generic/savepng.gif      |  Bin 0 -> 988 bytes
 .../t2/workbench/icons/generic/search.png       |  Bin 0 -> 1023 bytes
 .../taverna/t2/workbench/icons/generic/stop.gif |  Bin 0 -> 268 bytes
 .../taverna-wheel-message-dialog-error-icon.png |  Bin 0 -> 11424 bytes
 .../taverna-wheel-message-dialog-info-icon.png  |  Bin 0 -> 11383 bytes
 ...verna-wheel-message-dialog-question-icon.png |  Bin 0 -> 11312 bytes
 ...averna-wheel-message-dialog-warning-icon.png |  Bin 0 -> 11254 bytes
 .../icons/generic/taverna_cogs_32x32.png        |  Bin 0 -> 3094 bytes
 .../icons/generic/taverna_cogs_64x64.png        |  Bin 0 -> 11014 bytes
 .../taverna/t2/workbench/icons/generic/tick.png |  Bin 0 -> 537 bytes
 .../taverna/t2/workbench/icons/generic/undo.png |  Bin 0 -> 548 bytes
 .../t2/workbench/icons/generic/uninstall.png    |  Bin 0 -> 639 bytes
 .../t2/workbench/icons/generic/untick.png       |  Bin 0 -> 664 bytes
 .../t2/workbench/icons/generic/up-arrow.png     |  Bin 0 -> 300 bytes
 .../t2/workbench/icons/generic/update.png       |  Bin 0 -> 689 bytes
 .../icons/generic/updateRecommended.png         |  Bin 0 -> 731 bytes
 .../t2/workbench/icons/generic/urlimport.png    |  Bin 0 -> 969 bytes
 .../taverna/t2/workbench/icons/generic/web.gif  |  Bin 0 -> 362 bytes
 .../workbench/icons/generic/workflowResults.png |  Bin 0 -> 736 bytes
 .../t2/workbench/icons/generic/working.gif      |  Bin 0 -> 673 bytes
 .../workbench/icons/generic/workingStopped.png  |  Bin 0 -> 258 bytes
 .../t2/workbench/icons/generic/xml_node.gif     |  Bin 0 -> 82 bytes
 .../taverna/t2/workbench/icons/generic/zoom.gif |  Bin 0 -> 545 bytes
 .../t2/workbench/icons/generic/zoomin.gif       |   78 +
 .../t2/workbench/icons/generic/zoomin.png       |  Bin 0 -> 659 bytes
 .../t2/workbench/icons/generic/zoomout.png      |  Bin 0 -> 607 bytes
 .../t2/workbench/icons/graph/allport.png        |  Bin 0 -> 652 bytes
 .../t2/workbench/icons/graph/allport.svg        |  124 +
 .../taverna/t2/workbench/icons/graph/blob.png   |  Bin 0 -> 468 bytes
 .../taverna/t2/workbench/icons/graph/blob.svg   |   72 +
 .../t2/workbench/icons/graph/expandnested.png   |  Bin 0 -> 718 bytes
 .../t2/workbench/icons/graph/expandnested.svg   |  130 +
 .../t2/workbench/icons/graph/horizontal.png     |  Bin 0 -> 380 bytes
 .../t2/workbench/icons/graph/horizontal.svg     |  152 +
 .../taverna/t2/workbench/icons/graph/noport.png |  Bin 0 -> 482 bytes
 .../taverna/t2/workbench/icons/graph/noport.svg |   82 +
 .../t2/workbench/icons/graph/saveAsDOT.png      |  Bin 0 -> 1105 bytes
 .../t2/workbench/icons/graph/saveAsPNG.png      |  Bin 0 -> 1337 bytes
 .../t2/workbench/icons/graph/saveAsPS.png       |  Bin 0 -> 1019 bytes
 .../t2/workbench/icons/graph/saveAsPS2.png      |  Bin 0 -> 1018 bytes
 .../t2/workbench/icons/graph/saveAsSVG.png      |  Bin 0 -> 1416 bytes
 .../taverna/t2/workbench/icons/graph/trash.png  |  Bin 0 -> 482 bytes
 .../t2/workbench/icons/graph/vertical.png       |  Bin 0 -> 383 bytes
 .../t2/workbench/icons/graph/vertical.svg       |  150 +
 taverna-workbench-workbench-impl/pom.xml        |  116 +
 .../ui/impl/DataflowEditsListener.java          |   93 +
 .../t2/workbench/ui/impl/LoggerStream.java      |  136 +
 .../ui/impl/SetConsoleLoggerStartup.java        |   62 +
 .../ui/impl/StoreWindowStateOnShutdown.java     |   58 +
 .../workbench/ui/impl/UserRegistrationData.java |  105 +
 .../workbench/ui/impl/UserRegistrationForm.java |  995 +++++
 .../workbench/ui/impl/UserRegistrationHook.java |  163 +
 .../t2/workbench/ui/impl/WorkbenchImpl.java     |  538 +++
 .../ui/impl/WorkbenchPerspectives.java          |  229 ++
 .../t2/workbench/ui/impl/menu/ExitAction.java   |   66 +
 .../net.sf.taverna.raven.launcher.Launchable    |    1 +
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |   18 +
 .../net.sf.taverna.t2.workbench.ShutdownSPI     |    1 +
 .../net.sf.taverna.t2.workbench.StartupSPI      |    2 +
 .../spring/workbench-impl-context-osgi.xml      |   38 +
 .../META-INF/spring/workbench-impl-context.xml  |   43 +
 .../src/main/resources/Map.jhm                  |   28 +
 .../resources/example-registration-form.xml     |   12 +
 .../src/main/resources/registration-form.xsd    |   27 +
 .../src/main/resources/registration.php         |  137 +
 .../src/main/resources/sample.hs                |   64 +
 .../workbench/ui/impl/UserRegistrationTest.java |  190 +
 .../src/test/resources/log4j.properties         |   10 +
 taverna-workbench-workflow-explorer/pom.xml     |   75 +
 .../ui/workflowexplorer/WorkflowExplorer.java   |  824 ++++
 .../WorkflowExplorerFactory.java                |   95 +
 .../WorkflowExplorerTreeCellRenderer.java       |  216 ++
 .../WorkflowExplorerTreeModel.java              |  404 ++
 .../WorkflowExplorerTreeSelectionModel.java     |   45 +
 ....t2.workbench.ui.zaria.UIComponentFactorySPI |    1 +
 ...taverna.t2.workbench.ui.zaria.UIComponentSPI |    1 +
 .../spring/workflow-explorer-context-osgi.xml   |   19 +
 .../spring/workflow-explorer-context.xml        |   18 +
 taverna-workbench-workflow-view/pom.xml         |   74 +
 .../ui/actions/CopyGraphComponentAction.java    |  143 +
 .../ui/actions/CopyProcessorAction.java         |   53 +
 .../ui/actions/CutGraphComponentAction.java     |  153 +
 .../ui/actions/CutProcessorAction.java          |   69 +
 .../ui/actions/PasteGraphComponentAction.java   |   98 +
 .../ui/dndhandler/ServiceTransferHandler.java   |  119 +
 .../ui/menu/CopyGraphComponentMenuAction.java   |   54 +
 .../ui/menu/CopyProcessorMenuAction.java        |   56 +
 .../ui/menu/CutGraphComponentMenuAction.java    |   60 +
 .../ui/menu/CutProcessorMenuAction.java         |   69 +
 .../ui/menu/PasteGraphComponentMenuAction.java  |   73 +
 .../workbench/ui/toolbar/CopyToolbarAction.java |   51 +
 .../workbench/ui/toolbar/CutToolbarAction.java  |   57 +
 .../ui/toolbar/PasteToolbarAction.java          |   70 +
 .../ui/workflowview/ShowExceptionRunnable.java  |   26 +
 .../workbench/ui/workflowview/WorkflowView.java |  414 ++
 .../net.sf.taverna.t2.ui.menu.MenuComponent     |   10 +
 .../spring/workflow-view-context-osgi.xml       |   23 +
 .../META-INF/spring/workflow-view-context.xml   |   38 +
 1364 files changed, 137101 insertions(+)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/8c4b365e/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..a23d348
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,91 @@
+<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.workbench</groupId>
+	<artifactId>taverna-workbench</artifactId>
+	<version>3.1.0-incubating-SNAPSHOT</version>
+	<packaging>pom</packaging>
+	<name>Apache Taverna Workbench</name>
+  <description>Graphical workbench for editing and running Apache Taverna workflows</description>
+  <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>
+    <taverna.commonactivities.version>2.1.0-incubating-SNAPSHOT</taverna.commonactivities.version>
+  </properties>
+	<modules>
+    <module>taverna-dataflow-activity-ui</module>
+    <module>taverna-disabled-activity-ui</module>
+    <module>taverna-stringconstant-activity-ui</module>
+    <module>taverna-unrecognized-activity-ui</module>
+    <module>taverna-workbench-activity-icons-api</module>
+    <module>taverna-workbench-activity-palette-api</module>
+    <module>taverna-workbench-activity-palette-impl</module>
+    <module>taverna-workbench-activity-palette-ui</module>
+    <module>taverna-workbench-activity-tools</module>
+    <module>taverna-workbench-configuration-api</module>
+    <module>taverna-workbench-configuration-impl</module>
+    <module>taverna-workbench-contextual-views</module>
+    <module>taverna-workbench-contextual-views-api</module>
+    <module>taverna-workbench-contextual-views-impl</module>
+    <module>taverna-workbench-credential-manager-ui</module>
+    <module>taverna-workbench-data-management-config-ui</module>
+    <module>taverna-workbench-design-ui</module>
+    <module>taverna-workbench-edits-api</module>
+    <module>taverna-workbench-edits-impl</module>
+    <module>taverna-workbench-file-api</module>
+    <module>taverna-workbench-file-impl</module>
+    <module>taverna-workbench-graph-model</module>
+    <module>taverna-workbench-graph-view</module>
+    <module>taverna-workbench-helper</module>
+    <module>taverna-workbench-helper-api</module>
+    <module>taverna-workbench-httpproxy-config</module>
+    <module>taverna-workbench-iteration-strategy-ui</module>
+    <module>taverna-workbench-loop-ui</module>
+    <module>taverna-workbench-menu-api</module>
+    <module>taverna-workbench-menu-impl</module>
+    <module>taverna-workbench-menu-items</module>
+    <module>taverna-workbench-monitor-view</module>
+    <module>taverna-workbench-parallelize-ui</module>
+    <module>taverna-workbench-perspective-biocatalogue</module>
+    <module>taverna-workbench-perspective-design</module>
+    <module>taverna-workbench-perspective-myexperiment</module>
+    <module>taverna-workbench-perspective-results</module>
+    <module>taverna-workbench-plugin-manager</module>
+    <module>taverna-workbench-plugins-gui</module>
+    <module>taverna-workbench-reference-ui</module>
+    <module>taverna-workbench-renderers-api</module>
+    <module>taverna-workbench-renderers-exts</module>
+    <module>taverna-workbench-renderers-impl</module>
+    <module>taverna-workbench-report-api</module>
+    <module>taverna-workbench-report-explainer</module>
+    <module>taverna-workbench-report-impl</module>
+    <module>taverna-workbench-report-view</module>
+    <module>taverna-workbench-results-view</module>
+    <module>taverna-workbench-retry-ui</module>
+    <module>taverna-workbench-run-ui</module>
+    <module>taverna-workbench-selection-api</module>
+    <module>taverna-workbench-selection-impl</module>
+    <module>taverna-workbench-update-manager</module>
+    <module>taverna-workbench-workbench-api</module>
+    <module>taverna-workbench-workbench-impl</module>
+    <module>taverna-workbench-workflow-explorer</module>
+    <module>taverna-workbench-workflow-view</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>