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From Dmitriy Dligach <dmitriy.dlig...@childrens.harvard.edu>
Subject Re: latest build instructions
Date Wed, 17 Oct 2012 20:02:16 GMT
Thank you, Pei!

After a few more fixes I think I got one of the relation extraction 
pipelines to work!

Dima

On 10/17/2012 03:36 PM, Chen, Pei wrote:
> FYI:
> I reverted the main pom.xml back to use Lucene 3.0.2 instead of 3.5.0.
> (whoever needs 3.5.0 will need to work around this until someone rebuilds the OrangeBook
index- JIRA issue #38).
> --Pei
>
>> -----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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