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From Tim Miller <timothy.mil...@childrens.harvard.edu>
Subject Re: Failure on unpack-dependencies?
Date Thu, 10 Jan 2013 22:42:09 GMT
I'm having some trouble with this issue on trunk using eclipse. When I 
try to run the default pipeline in the cvd it can't find the rxnorm_index:

    Caused by: java.io.FileNotFoundException:
    org/apache/ctakes/dictionary/lookup/rxnorm_index
         at
    org.apache.ctakes.core.resource.FileLocator.locateExplicitly(FileLocator.java:69)
         at
    org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:44)
         at
    org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:58)
         ... 59 more

When I try to compile from the command line it says:

    [INFO]
    ------------------------------------------------------------------------
    [INFO] Building Apache cTAKES dictionary lookup
    3.1.0-incubating-SNAPSHOT
    [INFO]
    ------------------------------------------------------------------------
    [INFO]
    [INFO] --- maven-remote-resources-plugin:1.3:process (default) @
    ctakes-dictionary-lookup ---
    [INFO]
    [INFO] --- maven-resources-plugin:2.5:resources (default-resources)
    @ ctakes-dictionary-lookup ---
    [debug] execute contextualize
    [INFO] Using 'UTF-8' encoding to copy filtered resources.
    [INFO] Copying 54 resources
    [INFO] Copying 3 resources
    [INFO]
    [INFO] --- maven-dependency-plugin:2.6:unpack-dependencies
    (unpack-dependencies) @ ctakes-dictionary-lookup ---
    [INFO] ctakes-resources-umls2011ab-3.1.0.jar already exists in
    destination.
    [INFO]
    [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @
    ctakes-dictionary-lookup ---
    [INFO] Nothing to compile - all classes are up to date
    [INFO]


-- so it says the resources are there, and I can see the downloaded jar 
in my .m2 directory, but they're not being unpacked for some reason 
(they are not in target/classes/.../ of dictionary-lookup as I think 
they are supposed to be).  Anyone else with this problem? Any idea 
what's going on?
Tim


On 01/09/2013 05:20 PM, Karthik Sarma wrote:
> I was able to check out the 3.0.0 branch and build + run it without
> trouble. Will give the trunk another try
>
>
>
>
>
> --
> Karthik Sarma
> UCLA Medical Scientist Training Program Class of 20??
> Member, UCLA Medical Imaging & Informatics Lab
> Member, CA Delegation to the House of Delegates of the American Medical
> Association
> ksarma@ksarma.com
> gchat: ksarma@gmail.com
> linkedin: www.linkedin.com/in/ksarma
>
>
> On Wed, Jan 9, 2013 at 1:46 PM, Masanz, James J. <Masanz.James@mayo.edu>wrote:
>
>> I did not get this error when I used eclipse's miport feature with maven
>> from SCM.
>> Everything built fine (The second time I tried a build)
>> Note, I did a Maven->Update project... from within eclipse between the two
>> builds.
>>
>> -- James
>>
>>
>>> -----Original Message-----
>>> From: ksarma@gmail.com [mailto:ksarma@gmail.com] On Behalf Of Karthik
>>> Sarma
>>> Sent: Tuesday, January 08, 2013 6:30 PM
>>> To: cTAKES Developer List
>>> Subject: Failure on unpack-dependencies?
>>>
>>> Hi folks,
>>>
>>> I was trying to get the trunk up and running on a new windows 8 machine
>>> (completely clean). Installed jdk, eclipse (classic/juno), m2e, and
>>> subversive. I used eclipse's import feature with maven from SCM. Checkout
>>> was fine, but ctakes-dictionary-lookup was not able to build (as far as I
>>> could tell, everything else built just fine. Here is the error:
>>>
>>> Execution unpack-dependencies of goal
>>> org.apache.maven.plugins:maven-dependency-plugin:2.6:unpack-dependencies
>>> failed: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.6 or
>> one
>>> of its dependencies could not be resolved: Failed to collect dependencies
>>> for org.apache.maven.plugins:maven-dependency-plugin:jar:2.6 ()
>>> (org.apache.maven.plugins:maven-dependency-plugin:2.6:unpack-
>>> dependencies:unpack-dependencies:process-resources)
>>> pom.xml /ctakes-dictionary-lookup line 82
>>>
>>> I did a few checks to try to diagnose the issue -- the pom seems to be
>>> correct, and the m2e fix for unpack also seems to be correct. The plugin
>>> itself (for umls) exists in my local repository, as does
>> maven-dependency-
>>> plugin 2.6. There aren't any spaces or other oddities in any of the
>> paths.
>>> I tried cleaning, re-acquiring the source, and even deleting eclipse and
>>> starting from scratch, but alas, no dice.
>>>
>>> Is anyone else having a similar issue? Jenkins says everything should be
>>> working fine. I should probably just try building without involving
>>> eclipse at all, which I will do next.
>>>
>>>
>>> Karthik
>>>
>>>
>>> --
>>> Karthik Sarma
>>> UCLA Medical Scientist Training Program Class of 20??
>>> Member, UCLA Medical Imaging & Informatics Lab Member, CA Delegation to
>>> the House of Delegates of the American Medical Association
>>> ksarma@ksarma.com
>>> gchat: ksarma@gmail.com
>>> linkedin: www.linkedin.com/in/ksarma


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