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From "Wu, Stephen T., Ph.D." <Wu.Step...@mayo.edu>
Subject Re: latest build instructions
Date Wed, 17 Oct 2012 16:39:46 GMT
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.ContextDependentTokenizerAnnotator.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(AnalysisEngi
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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