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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: managing ctakes resources on classpath
Date Mon, 25 Aug 2014 15:52:59 GMT
Tim/Kim,
After a quick debug, it looks like the DependencyParser Tests looks okay, however, the test
pipeline uses LVG.  And during maven 'install', these files are inside a jar which LVG explicitly
needs a File or Directory.  I just committed a step in the pom.xml to unpack the lvg-res.
 This should be fine for the junit test; but also keep that in mind when configuring for a
production environment.
If you have a chance, could you try trunk?  It should solve the parser issue (and any other
test components that depend on lvg-res), but not sure about potentially other test errors.

--Pei

> -----Original Message-----
> From: Tim O'Connell [mailto:tim.oconnell@gmail.com]
> Sent: Monday, August 25, 2014 12:38 AM
> To: dev@ctakes.apache.org
> Subject: Re: managing ctakes resources on classpath
> 
> Thanks Kim & Pei.  If it helps any, I'm getting the same error in Eclipse.
>  I just checked out the code this morning from SVN.
> 
> Using -DskipTests=true I was able to get it to build from the command line.
> 
> Tim
> 
> 
> 
> 
> On Wed, Aug 20, 2014 at 12:41 PM, Kim Ebert
> <kim.ebert@perfectsearchcorp.com
> > wrote:
> 
> > I've added issue 307.
> >
> > https://issues.apache.org/jira/browse/CTAKES-307
> >
> > Kim Ebert
> > 1.801.669.7342
> > Perfect Search Corp
> > http://www.perfectsearchcorp.com/
> >
> > On 08/20/2014 11:52 AM, Chen, Pei wrote:
> > > Thanks Kim- would you mind opening up a Jira to track this?
> > > The cTAKES ClearNLP Dependency Parser and/or Test Cases most likely
> > > need
> > to be updated to enable resources to be picked up from the jar.
> > >
> > >> -----Original Message-----
> > >> From: Kim Ebert [mailto:kim.ebert@perfectsearchcorp.com]
> > >> Sent: Wednesday, August 20, 2014 1:39 PM
> > >> To: dev@ctakes.apache.org
> > >> Subject: Re: managing ctakes resources on classpath
> > >>
> > >> I'm just using exactly what came out of SVN, so I haven't modified
> > >> the default classpath yet.
> > >>
> > >> Kim Ebert
> > >> 1.801.669.7342
> > >> Perfect Search Corp
> > >> http://www.perfectsearchcorp.com/
> > >>
> > >> On 08/20/2014 11:28 AM, Chen, Pei wrote:
> > >>> Do you happen to have both jars and unpacked in your cp?
> > >>> Temp workaround: -DskipTests=true?
> > >>>
> > >>> Sent from my iPhone
> > >>>
> > >>>> On Aug 20, 2014, at 1:25 PM, "Kim Ebert"
> > >> <kim.ebert@perfectsearchcorp.com> wrote:
> > >>>> I am encountering this same issue when I try to run mvn install
> > >>>> from the command line. Is there a way to get mvn install to work?
> > >>>>
> > >>>> -------------------------------------------------------
> > >>>> T E S T S
> > >>>> -------------------------------------------------------
> > >>>> Running
> > >>>> org.apache.ctakes.dependency.parser.ae.util.TestClearNLPAnalysisE
> > >>>> ngin
> > >>>> es
> > >>>> log4j: reset attribute= "false".
> > >>>> log4j: Threshold ="null".
> > >>>> log4j: Level value for root is  [INFO].
> > >>>> log4j: root level set to INFO
> > >>>> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> > >>>> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> > >>>> log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy
> > >>>> HH:mm:ss} %5p %c{1} - %m%n].
> > >>>> log4j: Adding appender named [consoleAppender] to category
> [root].
> > >>>> Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed:
> > >>>> 1.397 sec <<< FAILURE!
> > >>>>
> > >>>> Results :
> > >>>>
> > >>>> Tests in error:
> > >>>>
> > >>>>
> > >> TestClearNLPPipeLine(org.apache.ctakes.dependency.parser.ae.util.Te
> > >> stCle
> > >> arNLPAnalysisEngines):
> > >>>> URI is not hierarchical
> > >>>>
> > >>>> Kim Ebert
> > >>>> 1.801.669.7342
> > >>>> Perfect Search Corp
> > >>>> http://www.perfectsearchcorp.com/
> > >>>>
> > >>>>> On 09/10/2013 07:33 AM, Pei Chen wrote:
> > >>>>> Hi Steve,
> > >>>>> The URI is not hierarchical is most likely caused by the code
> > >>>>> trying to use the resources/models, but they are inside a jar
> > >>>>> instead of
> > >> unpacked.
> > >>>>> -Which version of cTAKES are you using?
> > >>>>> -Do you happen to have the resource file name that caused the
> above?
> > >>>>>
> > >>>>> --Pei
> > >>>>>
> > >>>>>
> > >>>>>> On Mon, Sep 9, 2013 at 9:48 PM, Steve Hookway
> > >> <shookway@cra.com> wrote:
> > >>>>>> Hi all,
> > >>>>>>
> > >>>>>> I'm trying to integrate ctakes into a webapp and am running
> > >>>>>> into issues getting the resources to load correctly. In
a
> > >>>>>> standalone version of the app, if I add the resources folder
to
> > >>>>>> the buildpath (as described in the install directions)
> > >>>>>> everything works as expected. However, if I add the folder
to
> > >>>>>> the project classpath instead, I get a URI is not hierarchical
> > >>>>>> exception from
> > >> FileResourceImpl.load:
> > >>>>>> java.lang.IllegalArgumentException: URI is not hierarchical
> > >>>>>>       at java.io.File.<init>(File.java:392)
> > >>>>>>       at
> > >>>>>>
> > >>
> > org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImpl
> > .ja
> > >> va:44)
> > >>>>>>       at
> > >>>>>>
> > >>
> org.apache.uima.resource.impl.ResourceManager_impl.registerResource
> > >>>>>> (ResourceManager_impl.java:603)
> > >>>>>>
> > >>>>>> Similarly if I try and run from a webapp - setting up tomcat's
> > >>>>>> classpath to include the ctakes resource folder, I get
the same
> > >>>>>> URI is not hierarchical error. I found this bug report:
> > >>>>>> https://issues.apache.org/jira/browse/CTAKES-89 but  it
> > >>>>>> suggests adding the resource folder to my classpath, which
> > >>>>>> isn't doing the
> > trick.
> > >>>>>>
> > >>>>>> If you can steer me in the right direction, I'd really
> > >>>>>> appreciate
> > it.
> > >>>>>>
> > >>>>>> Thanks,
> > >>>>>> Steve
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>> THIS MESSAGE IS INTENDED FOR THE USE OF THE PERSON TO
> WHOM IT
> > >> IS
> > >>>>>> ADDRESSED. IT MAY CONTAIN INFORMATION THAT IS PRIVILEGED,
> > >>>>>> CONFIDENTIAL AND EXEMPT FROM DISCLOSURE UNDER
> APPLICABLE
> > >> LAW. If
> > >>>>>> you are not the intended recipient, your use of this message
> > >>>>>> for any
> > >> purpose is strictly prohibited.
> > >>>>>> If you have received this communication in error, please
delete
> > >>>>>> the message and notify the sender so that we may correct
our
> records.
> > >
> >
> >
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