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From Bhaskar B <bhaskarb.2...@gmail.com>
Subject Re: YTEX cTAKES 3.1.1 ready
Date Wed, 08 Jan 2014 12:41:44 GMT
Hi Vijay,

Thank you for this update.  In order to evaluate the YTEX port into cTAKES, 
I wanted to do the following (goals):

(a) Compile the ctakes/branches/ytex to create apache-ctakes-3.1.2-SNAPSHOT.
(b) Validate that the just compiled binary works by running either the 
AggregatePlaintextProcessor.xml or AggregatePlaintextUMLSProcessor.xml 
pipelines (basically following instructions at 
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide).
(c) Follow instructions at 
https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_1 to explore YTEX 
specific features, e.g. pipelines, writing annotations to database, etc.

So I took the following steps:

1) Followed the instructions at 
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+Developer+Install+Guide 
and 
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Developer+Install+Guide 
to successfully (i) configure Eclipse (Juno) environment for building 
cTAKES, and (ii) pull the source code from the SVN repository branch: 
https://svn.apache.org/repos/asf/ctakes/branches/ytex.

2) In Eclipse, right clicked on the top-most (or root level) pom.xml, 
selected Run As -> Maven build, typed in "compile" as the goal, and hit 
Run.  This successfully compiled all the projects.

3) In Eclipse, repeated step (2) but selected Run As -> Maven install to 
create a distribution.  However this is where I started to encounter few 
problems.  I was eventually able to get Maven install to complete and 
create the binaries (i.e. in ctakes-distribution/target/) but by manually 
doing the following:

3.1) in pom.xml of ctakes-ytex-uima: excluded all tests
3.2) in pom.xml of ctakes-core: excluded 2 tests
3.3) in ctakes-ytex: modified scripts/build-classpath.xml and 
scripts/build-setup.xml to hardcode path to ANT library
3.4) in ctakes-dependency-parser: excluded 1 unit test

4) After this step, I extracted apache-ctakes-3.1.2-SNAPSHOT-bin.zip and 
attempted to verify (i.e. step (b)) above.  However when I attempted to 
load AggregatePlaintextProcessor, I am getting exception (below).

While I continue to look to resolve this, any tips/hints that you could 
provide to get this build functional would be highly appreciated.  I think 
I may be missing one or more key steps/configuration.  My workstation is 
Windows 7 and I use Eclipse Juno.

-------------------------
java.lang.Error: Unresolved compilation problems:
        The import org.apache.ctakes.core.fsm.machine cannot be resolved
        The import org.apache.ctakes.core.fsm.machine cannot be resolved
        The import org.apache.ctakes.core.fsm.machine cannot be resolved
        The import org.apache.ctakes.core.fsm.machine cannot be resolved
        The import org.apache.ctakes.core.fsm.machine cannot be resolved
        The import org.apache.ctakes.core.fsm.machine cannot be resolved
        The import org.apache.ctakes.core.fsm.machine cannot be resolved
        The import org.apache.ctakes.core.fsm.output cannot be resolved
        The import org.apache.ctakes.core.fsm.output cannot be resolved
        The import org.apache.ctakes.core.fsm.output cannot be resolved
        The import org.apache.ctakes.core.fsm.output cannot be resolved
        The import org.apache.ctakes.core.fsm.output cannot be resolved
        The import org.apache.ctakes.core.fsm.output cannot be resolved
        The import org.apache.ctakes.core.fsm.output cannot be resolved
        The import org.apache.ctakes.core.fsm.token.BaseToken cannot be 
resolved

        The import org.apache.ctakes.core.fsm.token.EolToken cannot be 
resolved
        DateFSM cannot be resolved to a type
        TimeFSM cannot be resolved to a type
        FractionFSM cannot be resolved to a type
        RomanNumeralFSM cannot be resolved to a type
        RangeFSM cannot be resolved to a type
        MeasurementFSM cannot be resolved to a type
        PersonTitleFSM cannot be resolved to a type
        DateFSM cannot be resolved to a type
        DateFSM cannot be resolved to a type
        TimeFSM cannot be resolved to a type
        TimeFSM cannot be resolved to a type
        FractionFSM cannot be resolved to a type
        FractionFSM cannot be resolved to a type
        RomanNumeralFSM cannot be resolved to a type
        RomanNumeralFSM cannot be resolved to a type
        RangeFSM cannot be resolved to a type
        RangeFSM cannot be resolved to a type
        MeasurementFSM cannot be resolved to a type
        MeasurementFSM cannot be resolved to a type
        PersonTitleFSM cannot be resolved to a type
        PersonTitleFSM cannot be resolved to a type
        BaseToken cannot be resolved to a type
        BaseToken cannot be resolved to a type
        BaseToken cannot be resolved to a type
        The method adaptToBaseToken(BaseToken) from the type 
ContextDependentTok
enizerAnnotator refers to the missing type BaseToken
        EolToken cannot be resolved to a type
        BaseToken cannot be resolved to a type
        DateToken cannot be resolved to a type
        DateFSM cannot be resolved to a type
        DateToken cannot be resolved to a type
        DateToken cannot be resolved to a type
        TimeToken cannot be resolved to a type
        TimeFSM cannot be resolved to a type
        TimeToken cannot be resolved to a type
        TimeToken cannot be resolved to a type
        RomanNumeralToken cannot be resolved to a type
        RomanNumeralFSM cannot be resolved to a type
        RomanNumeralToken cannot be resolved to a type
        RomanNumeralToken cannot be resolved to a type
        FractionToken cannot be resolved to a type
        FractionFSM cannot be resolved to a type
        FractionToken cannot be resolved to a type
        FractionToken cannot be resolved to a type
        RangeToken cannot be resolved to a type
        RangeFSM cannot be resolved to a type
        RangeToken cannot be resolved to a type
        RangeToken cannot be resolved to a type
        MeasurementToken cannot be resolved to a type
        MeasurementFSM cannot be resolved to a type
        MeasurementToken cannot be resolved to a type
        MeasurementToken cannot be resolved to a type
        PersonTitleToken cannot be resolved to a type
        PersonTitleFSM cannot be resolved to a type
        PersonTitleToken cannot be resolved to a type
        PersonTitleToken cannot be resolved to a type
        BaseToken cannot be resolved to a type

        at 
org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnota
tor.<init>(ContextDependentTokenizerAnnotator.java:45)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native 
Method)

        at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown 
Source)

        at 
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Sou
rce)
        at java.lang.reflect.Constructor.newInstance(Unknown Source)
        at java.lang.Class.newInstance0(Unknown Source)
        at java.lang.Class.newInstance(Unknown Source)
        at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
tializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:227)
        at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
tialize(PrimitiveAnalysisEngine_impl.java:156)
        at 
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy
sisEngineFactory_impl.java:94)
        at 
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co
mpositeResourceFactory_impl.java:62)
        at 
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)

        at 
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav
a: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.ini
tASB(AggregateAnalysisEngine_impl.java:431)
        at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
        at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
tialize(AggregateAnalysisEngine_impl.java:185)
        at 
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy
sisEngineFactory_impl.java:94)
        at 
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co
mpositeResourceFactory_impl.java:62)
        at 
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)

        at 
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav
a:354)
        at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
        at 
org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:4
77)
        at 
org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPer
formed(AnnotatorOpenEventHandler.java:52)
        at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
        at javax.swing.AbstractButton$Handler.actionPerformed(Unknown 
Source)
        at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown 
Source)
        at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
        at javax.swing.AbstractButton.doClick(Unknown Source)
        at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
        at 
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
Source)
        at java.awt.Component.processMouseEvent(Unknown Source)
        at javax.swing.JComponent.processMouseEvent(Unknown Source)
        at java.awt.Component.processEvent(Unknown Source)
        at java.awt.Container.processEvent(Unknown Source)
        at java.awt.Component.dispatchEventImpl(Unknown Source)
        at java.awt.Container.dispatchEventImpl(Unknown Source)
        at java.awt.Component.dispatchEvent(Unknown Source)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
        at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
        at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
        at java.awt.Container.dispatchEventImpl(Unknown Source)
        at java.awt.Window.dispatchEventImpl(Unknown Source)
        at java.awt.Component.dispatchEvent(Unknown Source)
        at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
        at java.awt.EventQueue.access$200(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown 
Sour
ce)
        at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown 
Sour
ce)
        at java.awt.EventQueue$4.run(Unknown Source)
        at java.awt.EventQueue$4.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown 
Sour
ce)
        at java.awt.EventQueue.dispatchEvent(Unknown Source)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown 
Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown 
Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.run(Unknown Source)



On Saturday, January 4, 2014 9:06:52 AM UTC+5:45, vijay garla wrote:
>
> Hello All,
>
> I have finished an initial cut at the port of YTEX to cTAKES 3.1.1.  Most 
> of the YTEX functionality has been ported and integrated with cTAKES, and 
> I've tested with MySQL and MS SQL Server (oracle tests pending).
>
> Most of the changes were made in new projects - very little existing 
> cTAKES code has been modified.  The only non-trivial changes are 
> in /ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api 
> - here I modified CharacterOffsetToLineTokenConverterCtakesImpl & 
> SingleDocumentProcessorCtakes to deal with newlines within sentences 
> correctly.  Can somebody take a look at the changes in the ytex branch?
>
> I believe that the branch 
> https://svn.apache.org/repos/asf/ctakes/branches/ytex is ready to be 
> merged into ctakes trunk, but would like other users to test it as well. 
>  Questions:
>
> * How can I distribute the ctakes binary distribution to ytex users before 
> the merge? Can we make the branch build available somewhere?  The binary 
> distribution is too large to host on the ytex google code site (max 200 MB)
> * Non-ASF libraries - I have segregated these out into their own zip file 
> that can be distributed via sourceforge.  As a stopgap, I can upload this 
> to the ytex google code site, but would prefer to upload to sourceforge.
> * UMLS Derivatives - Ditto for these - would like to move to sourceforge.
> * Documentation - How can I update the confluence docs?  I would migrate 
> the documentation from the google code website.
>
> Here the installation instructions (putting the wagon in front of the 
> horse ...)
>
>
> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_1?ts=1388793998&updated=Installation_cTAKES_3_1
>
> Best,
>
> VJ
>
>
>
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