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domeo / DomeoClient

Domeo Annotator GWT client
Apache License 2.0
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Unhandled exception in annotation mode with Firefox but not Chrome #2

Closed rkboyce closed 10 years ago

rkboyce commented 11 years ago

When testing revision da687f5 in Firefox 23.0 (Canonical for Ubuntu 1.0) I find that the annotation tool does not load when either 1) text is selected and then use selects the "Annotate" option or 2) the "Annotate" option is selected and then text is selected. The only way it works is when I have the "Annotate" option selected and then double click on some text. This problem does not go away when I unregister my custom plugin (SPLs) so I think it a bug that applies to DomeoClient in general. All is functional in Chrome.

Details -- STS reports the following information about an Unhandled exception on both of the approaches to triggering the Annotate functionality that don't work in Firefox:

09:55:53.669 [ERROR] [domeo] Uncaught exception escaped
com.google.gwt.event.shared.UmbrellaException: One or more exceptions caught, see full set in UmbrellaException#getCauses
    at com.google.gwt.event.shared.HandlerManager.fireEvent(HandlerManager.java:129)
    at com.google.gwt.user.client.ui.Widget.fireEvent(Widget.java:129)
    at com.google.gwt.event.dom.client.DomEvent.fireNativeEvent(DomEvent.java:116)
    at com.google.gwt.user.client.ui.Widget.onBrowserEvent(Widget.java:177)
    at com.google.gwt.user.client.DOM.dispatchEventImpl(DOM.java:1351)
    at com.google.gwt.user.client.DOM.dispatchEvent(DOM.java:1307)
    at sun.reflect.GeneratedMethodAccessor35.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at com.google.gwt.dev.shell.MethodAdaptor.invoke(MethodAdaptor.java:103)
    at com.google.gwt.dev.shell.MethodDispatch.invoke(MethodDispatch.java:71)
    at com.google.gwt.dev.shell.OophmSessionHandler.invoke(OophmSessionHandler.java:172)
    at com.google.gwt.dev.shell.BrowserChannelServer.reactToMessagesWhileWaitingForReturn(BrowserChannelServer.java:337)
    at com.google.gwt.dev.shell.BrowserChannelServer.invokeJavascript(BrowserChannelServer.java:218)
    at com.google.gwt.dev.shell.ModuleSpaceOOPHM.doInvoke(ModuleSpaceOOPHM.java:136)
    at com.google.gwt.dev.shell.ModuleSpace.invokeNative(ModuleSpace.java:561)
    at com.google.gwt.dev.shell.ModuleSpace.invokeNativeObject(ModuleSpace.java:269)
    at com.google.gwt.dev.shell.JavaScriptHost.invokeNativeObject(JavaScriptHost.java:91)
    at com.google.gwt.core.client.impl.Impl.apply(Impl.java)
    at com.google.gwt.core.client.impl.Impl.entry0(Impl.java:213)
    at sun.reflect.GeneratedMethodAccessor25.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at com.google.gwt.dev.shell.MethodAdaptor.invoke(MethodAdaptor.java:103)
    at com.google.gwt.dev.shell.MethodDispatch.invoke(MethodDispatch.java:71)
    at com.google.gwt.dev.shell.OophmSessionHandler.invoke(OophmSessionHandler.java:172)
    at com.google.gwt.dev.shell.BrowserChannelServer.reactToMessages(BrowserChannelServer.java:292)
    at com.google.gwt.dev.shell.BrowserChannelServer.processConnection(BrowserChannelServer.java:546)
    at com.google.gwt.dev.shell.BrowserChannelServer.run(BrowserChannelServer.java:363)
    at java.lang.Thread.run(Thread.java:724)
Caused by: java.lang.NullPointerException: null
    at org.mindinformatics.gwt.domeo.client.ui.content.AnnotationFrameWrapper$1.onMouseUp(AnnotationFrameWrapper.java:512)
    at com.google.gwt.event.dom.client.MouseUpEvent.dispatch(MouseUpEvent.java:54)
    at com.google.gwt.event.dom.client.MouseUpEvent.dispatch(MouseUpEvent.java:1)
    at com.google.gwt.event.shared.GwtEvent.dispatch(GwtEvent.java:1)
    at com.google.web.bindery.event.shared.EventBus.dispatchEvent(EventBus.java:40)
    at com.google.web.bindery.event.shared.SimpleEventBus.doFire(SimpleEventBus.java:193)
    at com.google.web.bindery.event.shared.SimpleEventBus.fireEvent(SimpleEventBus.java:88)
    at com.google.gwt.event.shared.HandlerManager.fireEvent(HandlerManager.java:127)
    at com.google.gwt.user.client.ui.Widget.fireEvent(Widget.java:129)
    at com.google.gwt.event.dom.client.DomEvent.fireNativeEvent(DomEvent.java:116)
    at com.google.gwt.user.client.ui.Widget.onBrowserEvent(Widget.java:177)
    at com.google.gwt.user.client.DOM.dispatchEventImpl(DOM.java:1351)
    at com.google.gwt.user.client.DOM.dispatchEvent(DOM.java:1307)
    at sun.reflect.GeneratedMethodAccessor35.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at com.google.gwt.dev.shell.MethodAdaptor.invoke(MethodAdaptor.java:103)
    at com.google.gwt.dev.shell.MethodDispatch.invoke(MethodDispatch.java:71)
    at com.google.gwt.dev.shell.OophmSessionHandler.invoke(OophmSessionHandler.java:172)
    at com.google.gwt.dev.shell.BrowserChannelServer.reactToMessagesWhileWaitingForReturn(BrowserChannelServer.java:337)
    at com.google.gwt.dev.shell.BrowserChannelServer.invokeJavascript(BrowserChannelServer.java:218)
    at com.google.gwt.dev.shell.ModuleSpaceOOPHM.doInvoke(ModuleSpaceOOPHM.java:136)
    at com.google.gwt.dev.shell.ModuleSpace.invokeNative(ModuleSpace.java:561)
    at com.google.gwt.dev.shell.ModuleSpace.invokeNativeObject(ModuleSpace.java:269)
    at com.google.gwt.dev.shell.JavaScriptHost.invokeNativeObject(JavaScriptHost.java:91)
    at com.google.gwt.core.client.impl.Impl.apply(Impl.java)
    at com.google.gwt.core.client.impl.Impl.entry0(Impl.java:213)
    at sun.reflect.GeneratedMethodAccessor25.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at com.google.gwt.dev.shell.MethodAdaptor.invoke(MethodAdaptor.java:103)
    at com.google.gwt.dev.shell.MethodDispatch.invoke(MethodDispatch.java:71)
    at com.google.gwt.dev.shell.OophmSessionHandler.invoke(OophmSessionHandler.java:172)
    at com.google.gwt.dev.shell.BrowserChannelServer.reactToMessages(BrowserChannelServer.java:292)
    at com.google.gwt.dev.shell.BrowserChannelServer.processConnection(BrowserChannelServer.java:546)
    at com.google.gwt.dev.shell.BrowserChannelServer.run(BrowserChannelServer.java:363)
    at java.lang.Thread.run(Thread.java:724)
paolociccarese commented 11 years ago

I would try by changing line 394 from: if (anchorNode==null) return; to if (anchorNode==null || focusNode==null) return; and see if that solves the problem for that configuration.

The modified line seems working fine in my Firefox 23.0.1

rkboyce commented 11 years ago

I tested with the change and the exception does go away. However, the usability bug remains. The Annotation form will not show unless I select "Annotate" first and the double click on some text somewhere in the page. Here is a dump of the logs from a session where I did the following:

1) started the client in hosted mode running in Firefox (see above for version)

2) loaded a page from those within the DomeoClient project's 'war/tests' subfolder

3) selected a block of text and clicked "Annotate", waithin for ~10 seconds for something to happen

4) When the form did not appear, I double clicked on a word ("Annotate" was still selected)

INFO 2013 Aug 28 08:17:33 org.mindinformatics.gwt.domeo.client.Domeo Creating Domeo in real mode
INFO 2013 Aug 28 08:17:33 org.mindinformatics.gwt.domeo.client.Domeo Creating Application Framework...
DEBUG 2013 Aug 28 08:17:33 org.mindinformatics.gwt.domeo.client.Domeo Storage enabled: true
DEBUG 2013 Aug 28 08:17:33 org.mindinformatics.gwt.domeo.client.Domeo Definition of shortcut keys
DEBUG 2013 Aug 28 08:17:33 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline Parametrizing pipeline
DEBUG 2013 Aug 28 08:17:33 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline Starting pipeline
DEBUG 2013 Aug 28 08:17:33 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline Executing pipeline stage org.mindinformatics.gwt.framework.src.commands.InitUserInfoCommand
DEBUG 2013 Aug 28 08:17:33 org.mindinformatics.gwt.framework.src.commands.InitUserInfoCommand Initializing user info...
DEBUG 2013 Aug 28 08:17:33 org.mindinformatics.gwt.domeo.client.Domeo Loaded User Manager org.mindinformatics.gwt.framework.component.users.src.testing.JsonUserManager
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline TERMINATED STAGE 0 in 1754ms
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline EXECUTING STAGE 1
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline Executing pipeline stage org.mindinformatics.gwt.framework.src.commands.InitUserGroupsCommand
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.commands.InitUserGroupsCommand Initializing user groups...
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline TERMINATED STAGE 1 in 292ms
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline EXECUTING STAGE 2
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline Executing pipeline stage org.mindinformatics.gwt.framework.src.commands.InitUserPersonCommand
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.commands.InitUserPersonCommand Initializing user person info...
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.domeo.client.Domeo Loaded Agent Manager org.mindinformatics.gwt.framework.component.agents.src.testing.JsonAgentManager
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.component.agents.src.testing.JsonAgentManager Added person urn:person:uuid:8a70347a4096d318014096d369480000-Dr. John Doe (total agents 0)
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline TERMINATED STAGE 2 in 101ms
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline EXECUTING STAGE 3
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline Executing pipeline stage org.mindinformatics.gwt.framework.src.commands.InitSoftwareCommand
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.commands.InitSoftwareCommand Initializing software info...
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.component.agents.src.testing.JsonAgentManager Added software 2.0alpha-urn:domeo:software:id:Domeo-2.0alpha-030-Domeo Annotation Toolkit (total agents 0)
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline TERMINATED STAGE 3 in 24ms
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline EXECUTING STAGE 4
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline Executing pipeline stage org.mindinformatics.gwt.framework.src.commands.InitReportCommand
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.commands.InitReportCommand Initializing report manager...
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.domeo.client.Domeo Loaded Reports Manager org.mindinformatics.gwt.framework.component.reporting.src.testing.JsonReportManager
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline TERMINATED STAGE 4 in 11ms
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline EXECUTING STAGE 5
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline Executing pipeline stage org.mindinformatics.gwt.framework.src.commands.InitUserProfileCommand
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.commands.InitUserProfileCommand Initializing user profile info...
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.domeo.client.Domeo Loaded Profile Manager org.mindinformatics.gwt.framework.component.profiles.src.testing.JsonProfileManager
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline TERMINATED STAGE 5 in 112ms
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline EXECUTING STAGE 6
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline Executing pipeline stage org.mindinformatics.gwt.framework.src.commands.InitAvailableProfilesCommand
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.commands.InitAvailableProfilesCommand Initializing user available profiles info...
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline TERMINATED STAGE 6 in 37ms
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.src.pipelines.init.InitializationPipeline Initialization pipeline completed in 2339ms
INFO 2013 Aug 28 08:17:35 org.mindinformatics.gwt.domeo.client.Domeo Application [Domeo Annotation Toolkit]
INFO 2013 Aug 28 08:17:35 org.mindinformatics.gwt.domeo.client.Domeo User [admin]
INFO 2013 Aug 28 08:17:35 org.mindinformatics.gwt.domeo.client.Domeo Profile [Complete Biomedical Profile]
INFO 2013 Aug 28 08:17:35 org.mindinformatics.gwt.domeo.client.Domeo Creation Application Framework completed
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.domeo.client.Domeo Persistence manager selected org.mindinformatics.gwt.domeo.plugins.annotation.persistence.testing.JsonPersistenceManager
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing components...
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.plugins.annotation.persistence.testing.JsonPersistenceManager
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.component.cache.images.src.ImagesCache
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.framework.component.resources.management.ResourcesManager
DEBUG 2013 Aug 28 08:17:35 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.client.Preferences
DEBUG 2013 Aug 28 08:17:36 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.client.feature.clipboard.ClipboardManager
DEBUG 2013 Aug 28 08:17:36 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.model.accesscontrol.AnnotationAccessManager
DEBUG 2013 Aug 28 08:17:36 org.mindinformatics.gwt.framework.component.ComponentsManager Initialization components completed
DEBUG 2013 Aug 28 08:17:36 org.mindinformatics.gwt.domeo.client.ui.toolbar.DomeoToolbarPanel Creating the Toolbar...
DEBUG 2013 Aug 28 08:17:36 org.mindinformatics.gwt.framework.component.ui.toolbar.ToolbarPanel Creating the Application Toolbar
DEBUG 2013 Aug 28 08:17:36 org.mindinformatics.gwt.framework.component.ui.toolbar.ToolbarPanel Creation of the Application Toolbar completed
DEBUG 2013 Aug 28 08:17:50 org.mindinformatics.gwt.framework.component.ui.east.SideTabsContainer Creating the sidebar
DEBUG 2013 Aug 28 08:17:50 org.mindinformatics.gwt.framework.component.ui.east.SidePanelsContainer Creating the sidepanel
DEBUG 2013 Aug 28 08:17:52 org.mindinformatics.gwt.domeo.client.ui.east.annotation.AnnotationSideTab Initializing the Application Sidebar
DEBUG 2013 Aug 28 08:17:52 org.mindinformatics.gwt.domeo.client.ui.east.resource.ResourceSideTab Initializing the Application Sidebar
DEBUG 2013 Aug 28 08:17:52 org.mindinformatics.gwt.domeo.client.ui.east.sets.AnnotationSetSideTab Initializing the Application Sidebar
DEBUG 2013 Aug 28 08:17:52 org.mindinformatics.gwt.domeo.client.feature.clipboard.ui.east.ClipboardSideTab Initializing the Application Sidebar
DEBUG 2013 Aug 28 08:17:52 org.mindinformatics.gwt.domeo.plugins.annotation.comment.ui.east.CommentSideTab Initializing the Application Sidebar
INFO 2013 Aug 28 08:17:53 org.mindinformatics.gwt.framework.component.ui.east.SidePanelsFacade Registration of side component Resource
INFO 2013 Aug 28 08:17:53 org.mindinformatics.gwt.framework.component.ui.east.SidePanelsFacade Registration of side component Annotations
INFO 2013 Aug 28 08:17:53 org.mindinformatics.gwt.framework.component.ui.east.SidePanelsFacade Registration of side component Sets
INFO 2013 Aug 28 08:17:53 org.mindinformatics.gwt.framework.component.ui.east.SidePanelsFacade Registration of side component Discussion
INFO 2013 Aug 28 08:17:53 org.mindinformatics.gwt.framework.component.ui.east.SidePanelsFacade Registration of side component Clipboard
DEBUG 2013 Aug 28 08:17:53 org.mindinformatics.gwt.domeo.client.ui.east.debug.AnnotationDebugSideTab Initializing the Application Sidebar
INFO 2013 Aug 28 08:17:53 org.mindinformatics.gwt.framework.component.ui.east.SidePanelsFacade Registration of side component Debug
INFO 2013 Aug 28 08:17:53 org.mindinformatics.gwt.domeo.component.textmining.src.TextMiningRegistry Registration of text mining service org.mindinformatics.gwt.domeo.plugins.resource.bioportal.service.BioPortalManager
INFO 2013 Aug 28 08:17:53 org.mindinformatics.gwt.domeo.component.textmining.src.TextMiningRegistry Registration of text mining service org.mindinformatics.gwt.domeo.plugins.resource.nif.service.NifManager
INFO 2013 Aug 28 08:17:53 org.mindinformatics.gwt.domeo.client.Domeo Domeo Creation completed
INFO 2013 Aug 28 08:17:53 org.mindinformatics.gwt.domeo.client.Domeo -------------------------------------
DEBUG 2013 Aug 28 08:17:53 org.mindinformatics.gwt.domeo.services.extractors.ContentExtractorsManager Initializing the content extractor manager
INFO 2013 Aug 28 08:17:53 org.mindinformatics.gwt.domeo.services.extractors.ContentExtractorsManager PLUGIN::EXTRACTOR::OMIM Extractor registered for prefix http://omim.org/entry/
INFO 2013 Aug 28 08:17:53 org.mindinformatics.gwt.domeo.services.extractors.ContentExtractorsManager PLUGIN::EXTRACTOR::PUBMED Extractor registered for prefix http://www.ncbi.nlm.nih.gov/pubmed/
INFO 2013 Aug 28 08:17:53 org.mindinformatics.gwt.domeo.services.extractors.ContentExtractorsManager PLUGIN::EXTRACTOR::PUBMEDCENTRAL Extractor registered for prefix http://www.ncbi.nlm.nih.gov/pmc/articles/
INFO 2013 Aug 28 08:17:53 org.mindinformatics.gwt.domeo.services.extractors.ContentExtractorsManager PLUGIN::EXTRACTOR::GENERIC Extractor registered for prefix http://
COMMAND 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo Attempt loading of http://127.0.0.1:8888/tests/SPL-annotation/section-pages/03bec9ad-cd22-44d3-9b82-2796157de1d1-boxedWarning.html
INFO 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo Re-initializing environment
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing components...
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.client.ui.east.sets.AnnotationSetsSidePanel
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.services.extractors.ContentExtractorsManager
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.client.ui.east.resource.ResourceSidePanel
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.component.cache.images.src.ImagesCache
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.framework.component.resources.management.ResourcesManager
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.client.feature.clipboard.ClipboardManager
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.plugins.annotation.persistence.testing.JsonPersistenceManager
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.client.feature.clipboard.ui.east.ClipboardSidePanel
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.feature.clipboard.ui.east.ClipboardSidePanel Initializing...
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.client.ui.east.annotation.AnnotationSidePanel
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.ui.east.annotation.AnnotationSidePanel Initializing...
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.plugins.annotation.comment.ui.east.CommentSidePanel
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.annotation.comment.ui.east.CommentSidePanel Initializing...
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.client.Preferences
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.client.ui.toolbar.DomeoToolbarPanel
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ui.toolbar.ToolbarPanel Activating group: Document commands
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.framework.component.ui.east.SidePanelsFacade
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ui.east.SidePanelsFacade Initializing...
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initializing component... org.mindinformatics.gwt.domeo.model.accesscontrol.AnnotationAccessManager
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Initialization components completed
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.ui.content.AnnotationFrameWrapper Setting up url http://127.0.0.1:8888/http://dbmi-icode-01.dbmi.pitt.edu:2020/SPL-annotation/section-pages//03bec9ad-cd22-44d3-9b82-2796157de1d1-boxedWarning.html
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo:AFTER DOCUMENT Executing notifyDocumentLoadedStageOne()
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo Resource Metadata extractor
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo Persistence manager setup
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.annotation.persistence.testing.JsonPersistenceManager Resource org.mindinformatics.gwt.domeo.model.MOnlineResource
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.persistance.src.PersistenceManager Document loaded true
INFO 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.persistance.src.PersistenceManager Current document http://127.0.0.1:8888/http://dbmi-icode-01.dbmi.pitt.edu:2020/SPL-annotation/section-pages//03bec9ad-cd22-44d3-9b82-2796157de1d1-boxedWarning.html
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo:AFTER DOCUMENT Completed Execution of notifyDocumentLoadedStageOne() in 52ms
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo:AFTER DOCUMENT Executing startExtraction()
INFO 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.services.extractors.ContentExtractorsManager Extractor 'Generic Document Extractor' selected for prefix http://127.0.0.1:8888/http://dbmi-icode-01.dbmi.pitt.edu:2020/SPL-annotation/section-pages//03bec9ad-cd22-44d3-9b82-2796157de1d1-boxedWarning.html
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.resource.document.extractor.GenericDocumentPipeline Parametrizing pipeline
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.resource.document.extractor.GenericDocumentPipeline Starting pipeline
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.resource.document.extractor.GenericDocumentPipeline Executing pipeline stage org.mindinformatics.gwt.domeo.plugins.resource.document.extractor.GenericDocumentExtractMetadataCommand
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.annotation.persistence.testing.JsonPersistenceManager Resource org.mindinformatics.gwt.domeo.plugins.resource.document.model.MDocumentResource
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.resource.document.extractor.GenericDocumentPipeline TERMINATED STAGE 0 in 0ms
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.resource.document.extractor.GenericDocumentPipeline EXECUTING STAGE 1
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.resource.document.extractor.GenericDocumentPipeline Executing pipeline stage org.mindinformatics.gwt.domeo.plugins.resource.document.extractor.GenericDocumentExtractImagesCommand
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.resource.document.extractor.GenericDocumentExtractImagesCommand PLUGIN::ANALYZER::PUBMEDCENTRAL Extracting document images
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.resource.document.extractor.GenericDocumentPipeline TERMINATED STAGE 1 in 1ms
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.resource.document.extractor.GenericDocumentPipeline Extraction pipeline completed in 2ms
INFO 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo Document extraction completed
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo:AFTER DOCUMENT Completed Document Pipeline Execution in 3ms
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo:AFTER DOCUMENT Executing endExtraction()
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo Document handlers setup
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.ui.content.AnnotationFrameWrapper Registering Highlight Handlers
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.ui.content.AnnotationFrameWrapper Registered Highlight Handlers
INFO 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.ui.content.AnnotationFrameWrapper Content type: text/html
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo CSS injection
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo Refresh components
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Refreshing components...
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Refreshing component org.mindinformatics.gwt.domeo.client.ui.east.debug.AnnotationDebugSidePanel
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.ui.east.debug.AnnotationDebugSummaryTable Annotation debug summary panel refreshed in (ms):11
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Refreshing component org.mindinformatics.gwt.domeo.client.ui.east.sets.AnnotationSetsSidePanel
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.ui.east.sets.AnnotationSetsSidePanel Annotation sets summary panel refreshed in (ms):1
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Refreshing component org.mindinformatics.gwt.domeo.client.feature.clipboard.ui.east.ClipboardSidePanel
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.feature.clipboard.ui.east.ClipboardSidePanel Refreshing...
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Refreshing component org.mindinformatics.gwt.domeo.client.ui.east.resource.ResourceSidePanel
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.resource.document.lenses.LDocumentResourceCardPanel Creating Images Visualization
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Refreshing component org.mindinformatics.gwt.domeo.plugins.annotation.comment.ui.east.CommentSidePanel
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.annotation.comment.ui.east.CommentSidePanel Refreshing...
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Refreshing component org.mindinformatics.gwt.domeo.client.ui.east.annotation.AnnotationSidePanel
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.ui.east.annotation.AnnotationSidePanel Refreshing...
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.ui.east.annotation.AnnotationSummaryTable Annotation summary panel with search term refreshed in (ms):0
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.framework.component.ComponentsManager Refreshing components completed
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.resource.document.lenses.LDocumentResourceCardPanel Creating Images Visualization
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo:AFTER DOCUMENT Completed Execution of endExtraction() in 173ms
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo:AFTER DOCUMENT Document url:
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo:AFTER DOCUMENT Annotation set id:
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo:AFTER DOCUMENT Executing checkForExistingAnnotationSets()
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.plugins.annotation.persistence.testing.JsonPersistenceManager Beginning retrieving annotation...
DEBUG 2013 Aug 28 08:18:16 org.mindinformatics.gwt.domeo.client.Domeo Completed Execution of checkForExistingAnnotationSets() in 16ms
COMMAND 2013 Aug 28 08:18:20 org.mindinformatics.gwt.domeo.client.ui.toolbar.DomeoToolbarPanel$6 Enabling manual annotation
DEBUG 2013 Aug 28 08:19:00 org.mindinformatics.gwt.domeo.client.ui.content.AnnotationFrameWrapper$1 Before calibration(1): Effectiveness of clopidogrel bisulfate depends on activation to an active metabolite by the cytochrome P450 (CYP) system, principally CYP2C19. (5.1)
DEBUG 2013 Aug 28 08:19:00 org.mindinformatics.gwt.domeo.client.ui.content.AnnotationFrameWrapper$1 After calibration(1): Effectiveness of clopidogrel bisulfate depends on activation to an active metabolite by the cytochrome P450 (CYP) system, principally CYP2C19. (5.1)
COMMAND 2013 Aug 28 08:19:00 org.mindinformatics.gwt.domeo.client.ui.content.AnnotationFrameWrapper TEXT SELECTION $ Effectiveness $ of clopidogrel bisulfate depends on activation to an active metabolite by the cytochrome P450 (CYP) system, principally CYP2C19. (5.1)
INFO 2013 Aug 28 08:19:00 org.mindinformatics.gwt.domeo.client.ui.content.AnnotationFrameWrapper TEXT ANNOTATION $ Effectiveness $ of clopidogrel bisulfate depends on activation to an active metabolite by the cytochrome P450 (CYP) system, principally CYP2C19. (5.1)
COMMAND 2013 Aug 28 08:19:01 org.mindinformatics.gwt.domeo.plugins.annotation.persistence.testing.JsonPersistenceManager CREATED NEW SET with id 0
COMMAND 2013 Aug 28 08:19:01 org.mindinformatics.gwt.domeo.plugins.annotation.persistence.testing.JsonPersistenceManager Selected set with id 0
DEBUG 2013 Aug 28 08:19:02 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm SPL annotation widget bound to UI
DEBUG 2013 Aug 28 08:19:02 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm SPL annotation filter set refreshed
DEBUG 2013 Aug 28 08:19:02 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm 'Apply' button added
DEBUG 2013 Aug 28 08:19:02 org.mindinformatics.gwt.domeo.client.ui.annotation.forms.text.TextAnnotationFormsPanel 5
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm$1 SPL annotation content validated
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm$1 _item is null...
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm$1 quote selector initialized
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm$1 SPL annotation factory initialized
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm$1 SPL annotation 1
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm$1 SPL annotation 2
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm$1 SPL annotation 3
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm$1 SPL annotation 4
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm$1 SPL annotation 5
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm$1 SPL pharmgxUsage initialized and attached to the SPL annotation instance
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm$1 SPL comment set
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm$1 Annotation set is not empty, passing new SPL annotation to persistance manager
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm$1 Making the new SPL annotation visible in the content panel
INFO 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.client.ui.content.AnnotationFrameWrapper TEXT ANNOTATED null in (ms) 21
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.client.Domeo Refresh annotation components
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.framework.component.ComponentsManager Refreshing annotation components...
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.framework.component.ComponentsManager Refreshing annotation component org.mindinformatics.gwt.domeo.client.ui.east.debug.AnnotationDebugSidePanel
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.client.ui.east.debug.AnnotationDebugSummaryTable Annotation debug summary panel refreshed in (ms):16
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.framework.component.ComponentsManager Refreshing annotation component org.mindinformatics.gwt.domeo.client.ui.east.sets.AnnotationSetsSidePanel
DEBUG 2013 Aug 28 08:19:08 org.mindinformatics.gwt.domeo.client.ui.east.sets.AnnotationSetsSidePanel Creating lens for set 0
DEBUG 2013 Aug 28 08:19:09 org.mindinformatics.gwt.domeo.client.ui.east.sets.AnnotationSetsSidePanel Annotation sets summary panel refreshed in (ms):190
DEBUG 2013 Aug 28 08:19:09 org.mindinformatics.gwt.framework.component.ComponentsManager Refreshing annotation component org.mindinformatics.gwt.domeo.client.ui.east.annotation.AnnotationSidePanel
DEBUG 2013 Aug 28 08:19:09 org.mindinformatics.gwt.domeo.client.ui.east.annotation.AnnotationSidePanel Refreshing...
DEBUG 2013 Aug 28 08:19:09 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.tile.TSPLsTile org.mindinformatics.gwt.framework.component.agents.model.MAgentPerson@a3b7fa
DEBUG 2013 Aug 28 08:19:09 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.tile.TSPLsTile urn:person:uuid:8a70347a4096d318014096d369480000
DEBUG 2013 Aug 28 08:19:09 org.mindinformatics.gwt.domeo.client.ui.east.annotation.AnnotationSummaryTable Annotation summary panel with search term refreshed in (ms):122
DEBUG 2013 Aug 28 08:19:09 org.mindinformatics.gwt.framework.component.ComponentsManager Refreshing annotation components completed
DEBUG 2013 Aug 28 08:19:09 org.mindinformatics.gwt.domeo.plugins.annotation.spls.ui.form.FSPLsForm$1 SPL annotation data collected. widget should close now.