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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: latest build instructions
Date Wed, 17 Oct 2012 16:47:26 GMT
> The stack trace is below.  However, if I run it using  ctakes-clinical-
> pipeline/resources/launch/UIMA_CPE_GUI--clinical_documents_
> pipeline.launch

The current dictionary lookup is still on Lucene 3.0.2.  Should we just revert the default
back to 3.0.2 at least until JIRA issue #38 is fixed?
ctakes/pom.xml:
			<dependency>
				<groupId>org.apache.lucene</groupId>
				<artifactId>lucene-core</artifactId>
				<version>3.5.0</version>
			</dependency>

> -----Original Message-----
> From: Wu, Stephen T., Ph.D. [mailto:Wu.Stephen@mayo.edu]
> Sent: Wednesday, October 17, 2012 12:41 PM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: latest build instructions
> 
> I get errors when I try what pei suggested, running the standard  /ctakes-
> clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProces
> sor.xml
> The stack trace is below.  However, if I run it using  ctakes-clinical-
> pipeline/resources/launch/UIMA_CPE_GUI--clinical_documents_
> pipeline.launch
> 
> then this doesn't come up, and I instead get problems like JIRA issue #38
> (lucene.index.IndexFormatTooOldException)
> 
> Do we need to run mvn install (or mvn compile as steve suggests) before a
> CVD/CPE, every time we change code?  If so, maven gurus, how do we
> change that?
> 
> stephen
> 
> 
>   Exception in thread "Thread-7" java.lang.NoClassDefFoundError:
> net/openai/util/fsm/State
>     at
> org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnota
> tor.ini
> tialize(ContextDependentTokenizerAnnotator.java:95)
>     at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize
> AnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>     at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize
> (PrimitiveAnalysisEngine_impl.java:156)
>     at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysi
> sEngi
> neFactory_impl.java:94)
>     ... 22 more
> Caused by: java.lang.ClassNotFoundException: net.openai.util.fsm.State
>     at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
>     at java.security.AccessController.doPrivileged(Native Method)
>     at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>     at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>     at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>     at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
>     ... 26 more
> 
> 
> 
> On 10/15/12 8:09 PM, "Chen, Pei" <Pei.Chen@childrens.harvard.edu> wrote:
> 
> > It should compile and test fine at minimum. Feel free to update the
> > instructions.
> > We can Make the runCVD mvn install optional as the exec scripts needs
> > the jars and its dependencies to be installed somewhere in order for
> > it to work.  We can revisit the optional scripts after the first
> > release to see what we want to do with snapshot repos and running scripts
> (using the jars and libs).
> >
> >
> > On Oct 15, 2012, at 6:01 PM, "Steven Bethard"
> > <steven.bethard@Colorado.EDU>
> > wrote:
> >
> >> On Oct 15, 2012, at 2:52 PM, "Chen, Pei"
> >> <Pei.Chen@childrens.harvard.edu>
> >> wrote:
> >>> Building and Running from Command Line:
> >>> Requirements: svn, java jdk 1.6+, maven 3.0.4+
> >>> 1) svn co http://svn.apache.org/repos/asf/incubator/ctakes/trunk
> >>> 2) mvn install
> >>
> >> Don't do this. Do `mvn compile` or `mvn test` instead.
> >>
> >> The only reason to do `mvn install` is if you do *not* intend to
> >> modify anything in the cTAKES source code, and you *just* want to
> >> depend on the current snapshot of cTAKES in some *other* project.
> >> Otherwise, `mvn install` is almost guaranteed to get your dependencies
> out of sync.
> >>
> >>> 3)Optional to run the UIMA CAS Visual Debugger or Collection
> >>> Processing Engine GUI:
> >>> cd ctakes-clincial-pipeline
> >>> mvn exec:exec -PrunCVD
> >>> or
> >>> mvn exec:exec -PrunCPE
> >>>
> >>>
> >>> Building and Running from Eclipse IDE:
> >>> Requirements: Eclipse IDE 4.2.1+, java jdk 1.6+, subversive plugin
> >>> (or svn equivalent with appropriate svn team provider connectors),
> >>> m2e plugin (or mvn equivalent) Import Project > Maven > Checkout
> >>> Maven Project from SCM
> >>> svn: http://svn.apache.org/repos/asf/incubator/ctakes/trunk
> >>> Select all projects
> >>> Wait until Eclipse downloads and builds all of your projects.  The
> >>> various build helpers should run jcasgen and builds the projects for
> >>> you (there shouldn't be a real need to run mvn install, etc.)
> >>> Finish.
> >>>
> >>>> -----Original Message-----
> >>>> From: Coarr, Matt [mailto:mcoarr@mitre.org]
> >>>> Sent: Monday, October 15, 2012 4:23 PM
> >>>> To: ctakes-dev@incubator.apache.org
> >>>> Subject: latest build instructions
> >>>>
> >>>> [I already read the thread "Update cTAKES Building and Running
> >>>> page?" that Pei started 2012-10-10T16:56.]
> >>>>
> >>>> iWhat are the latest build instructions for command-line and for
> eclipse?
> >>>>
> >>>> I have some changes to commit and need to get my system building
> >>>> from the latest apache svn code.
> >>>>
> >>>> I'm catching up on the recent emails about building, maven,
> >>>> command-line, eclipse, and target users.  Lots of discussions going
on!
> >>>>
> >>>> I already have a working copy checked out from svn.  And I've seen
> >>>> (the
> >>>> yet-to-be-completed) instructions here:
> >>>> http://incubator.apache.org/ctakes/source.html
> >>>> (I'd be happy to update this with a quick set of instructions once
> >>>> I go through the process.)
> >>>>
> >>>> I'm assuming it's something along the lines of:
> >>>>
> >>>> * for command-line
> >>>>   - checkout from svn
> >>>>   - run "mvn compile"/"mvn test"/"mvn package"
> >>>>     (I've been using maven for 8+ years and I've always run "mvn
> >>>> install", but I've been listening to Steve's advice and I'll switch
> >>>> to these commands :-)
> >>>> * for eclipse
> >>>>   - checkout from svn
> >>>>   - make sure you have m2e installed
> >>>>   - import the projects into eclipse
> >>>>   - ...trying to figure out what I should be doing here҆
> >>>>     Do I just let it build automatically?  (In the past I've always
> >>>> done right click on project -> choose "run as..." -> "mvn install"
> >>>> but now I know that this is
> >>>> evil.)
> >>>>
> >>>> Thanks!
> >>>> Matt
> >>>
> >>


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