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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject RE: [VOTE] Release Apache cTAKES 3.2.0
Date Tue, 08 Jul 2014 11:15:00 GMT
One other thing -- the User install guide says to download the -bin and the Dev install guide
has you checking out from trunk. And the README in the -src distribution has instructions
that only make sense for the -bin distribution.
Are there instructions somewhere for how to install the -src version or are they basically
the same as the dev install w/o the subversion checkout step?

Tim

________________________________________
From: Pei Chen [chenpei@apache.org]
Sent: Monday, July 07, 2014 12:06 PM
To: dev@ctakes.apache.org
Subject: Re: [VOTE] Release Apache cTAKES 3.2.0

Thanks for testing this Tim.  I could recreate this on my mac now (worked
previously on windows on luck because of the class load order).
Essentially, the old mitre assertion module and LVG resources still need to
be unpacked.  We don't have access to modify the underlying lib to read
from a stream, I'm just going to omit/exclude the redundant
ctakes-assertion-res.jar from the distro (as the assertion module will be
updated in the future release anyway).
Let me know if you encounter anything else, otherwise will plan to create
an RC-2.


On Fri, Jul 4, 2014 at 12:01 PM, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:

> I get an error when I try to run the CVD following the README instructions
> for the binary release:
>
> 7/4/14 11:56:03 AM - 12:
> org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE:
> Initialization of annotator class
> "org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine" failed.
>  (Descriptor:
> file:/home/tmill/Projects/sandbox/ctakes-rcs/apache-ctakes-3.2.0/desc/ctakes-assertion/desc/assertionAnalysisEngine.xml)
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of annotator class
> "org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine" failed.
>  (Descriptor:
> file:/home/tmill/Projects/sandbox/ctakes-rcs/apache-ctakes-3.2.0/desc/ctakes-assertion/desc/assertionAnalysisEngine.xml)
>         at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>         at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
>         at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>         at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>         at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>         at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
>         at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
>         at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
>         at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>         at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>         at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>         at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>         at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>         at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
>         at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
>         at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
>         at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>         at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>         at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>         at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>         at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>         at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
>         at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
>         at
> org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477)
>         at
> org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
>         at
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
>         at
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
>         at
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
>         at
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
>         at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
>         at
> javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
>         at
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
>         at java.awt.Component.processMouseEvent(Component.java:6505)
>         at javax.swing.JComponent.processMouseEvent(JComponent.java:3311)
>         at java.awt.Component.processEvent(Component.java:6270)
>         at java.awt.Container.processEvent(Container.java:2229)
>         at java.awt.Component.dispatchEventImpl(Component.java:4861)
>         at java.awt.Container.dispatchEventImpl(Container.java:2287)
>         at java.awt.Component.dispatchEvent(Component.java:4687)
>         at
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
>         at
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
>         at
> java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
>         at java.awt.Container.dispatchEventImpl(Container.java:2273)
>         at java.awt.Window.dispatchEventImpl(Window.java:2719)
>         at java.awt.Component.dispatchEvent(Component.java:4687)
>         at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
>         at java.awt.EventQueue.access$200(EventQueue.java:103)
>         at java.awt.EventQueue$3.run(EventQueue.java:694)
>         at java.awt.EventQueue$3.run(EventQueue.java:692)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at
> java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
>         at
> java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
>         at java.awt.EventQueue$4.run(EventQueue.java:708)
>         at java.awt.EventQueue$4.run(EventQueue.java:706)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at
> java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
>         at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
>         at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
>         at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
>         at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
>         at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
>         at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
>         at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
> Caused by: java.lang.RuntimeException: problem accessing resource
>         at
> org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.initialize(AssertionAnalysisEngine.java:114)
>         at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>         ... 62 more
> Caused by: org.apache.uima.resource.ResourceAccessException
>         at
> org.apache.uima.impl.UimaContext_ImplBase.getResourceFilePath(UimaContext_ImplBase.java:253)
>         at
> org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.initialize(AssertionAnalysisEngine.java:93)
>         ... 63 more
>
>
> ________________________________________
> From: Finan, Sean [Sean.Finan@childrens.harvard.edu]
> Sent: Wednesday, July 02, 2014 3:49 PM
> To: dev@ctakes.apache.org
> Subject: RE: [VOTE] Release Apache cTAKES 3.2.0
>
> +1
>
> Pulled fresh candidate, built, and ran Clinical using CPE without problem.
>  Other than that, no testing.  SVN gave me a problem initially (checked out
> as anonymous) asking for a password then flunking the checkout, but an
> update completed it.  I blame the heat.
> ________________________________________
> From: Masanz, James J. [Masanz.James@mayo.edu]
> Sent: Monday, June 30, 2014 10:24 PM
> To: dev@ctakes.apache.org
> Subject: RE: [VOTE] Release Apache cTAKES 3.2.0
>
> This is pretty obvious, but since this is a record of what was voted upon,
> note that some of the URLs contain an extra
>
> ctakes-3.2.0/
>
> For example
>
> http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/apache-ctakes-3.2.0-src.tar.gz
>
> should be just
>
> http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/apache-ctakes-3.2.0-src.tar.gz
>
> -- James
>
> ________________________________________
> From: Pei Chen [chenpei@apache.org]
> Sent: Friday, June 27, 2014 5:15 PM
> To: dev@ctakes.apache.org
> Subject: [VOTE] Release Apache cTAKES 3.2.0
>
> Hi all,
>
> This is a call for a vote on releasing the following candidate (rc1) as
> Apache cTAKES 3.2.0.
> The major changes include:
> - New optional YTEX component(s) (Yale Extensions to cTAKES)
> - New optional improved/faster dictionary lookup (dictionary-lookup-fast)
> - New optional Temporal component (Time + Event extraction.  Relations will
> be including in a future release.)
> - Other bug fixes/enhancements from Jira
>
> [TODO: Online documentation still needs to be updated on wiki for the abo]
>
> For more detailed information on the changes/release notes, please visit:
>
> https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12313621&version=12324066
>
> The release was made using the cTAKES release process documented here:
> http://ctakes.apache.org/ctakes-release-guide.html
>
> The candidate is available at:
>
> http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/apache-ctakes-3.2.0-src.tar.gz
> /.zip
>
> The tag to be voted on:
> http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.2.0-rc1/
>
> The MD5 checksum of the tarball can be found at:
>
> http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/apache-ctakes-3.2.0-src.tar.gz.md5
> /.zip.md5
>
> The signature of the tarball can be found at:
>
> http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/apache-ctakes-3.2.0-src.tar.gz.asc
> /.zip.asc
>
> Apache cTAKES' KEYS file, containing the PGP keys used to sign the release:
> https://dist.apache.org/repos/dist/release/ctakes/KEYS
>
> Please vote on releasing these packages as Apache cTAKES 3.2.0. The vote is
> open for at least the next 72 hours.
> Only votes from the cTAKES PMC are binding, but folks are welcome to check
> the release candidate and voice their approval or disapproval.
> The vote passes if at least three binding +1 votes are cast.
>
> [ ] +1 Release the packages as Apache cTAKES 3.2.0
> [ ] -1 Do not release the packages because...
>
> Also, the convenience binary can be found at:
>
> http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/apache-ctakes-3.2.0-bin.tar.gz
> /.zip
> Note: It's tempoarily on people.a.o because the artifacts were too large
> for https://dist.apache.org/repos/dist/dev/ctakes (Working with infra on
> increasing the limit).
>
>
> Thanks!
>

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