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From "Tim O'Connell" <tim.oconn...@gmail.com>
Subject Re: managing ctakes resources on classpath
Date Tue, 26 Aug 2014 06:30:52 GMT
Hi Pei,

Yes, I was able to get as far as it looks like you did - until I ran into
the same error with ytex:
2014-08-25 22:43:09,596 WARN  org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
 - sql exception - mrconso probably doesn't exist, check error

However, earlier in the ytex tests, I did get another error:
Running org.apache.ctakes.jdl.data.xml.ValidationTest
org.xml.sax.SAXParseException; schema_reference.4: Failed to read schema
document
'file:/C:/Users/oconnell/workspace/cTakes%20Projects/ctakes/ctakes-ytex/file:/C:/Users/oconnell/workspace/cTakes%2520Projects/ctakes/ctakes-ytex-res/target/ctakes-ytex-res-3.2.1-SNAPSHOT.jar!/org/apache/ctakes/jdl/xdl.xsd',
because 1) could not find the document; 2) the document could not be read;
3) the root element of the document is not <xsd:schema>.
at
com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:198)
...
Caused by: java.io.FileNotFoundException:
C:\Users\oconnell\workspace\cTakes
Projects\ctakes\ctakes-ytex\file:\C:\Users\oconnell\workspace\cTakes%20Projects\ctakes\ctakes-ytex-res\target\ctakes-ytex-res-3.2.1-SNAPSHOT.jar!\org\apache\ctakes\jdl\xdl.xsd
(The filename, directory name, or volume label syntax is incorrect)
...
Tests run: 3, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.624 sec
<<< FAILURE!

It then goes on to keep running tests, and finds the ytex UMLS/SQL error
above, but at the end of that error dump, it says:
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.539 sec

Results :

Tests in error:
  setSchema(org.apache.ctakes.jdl.data.xml.ValidationTest)

Tests run: 36, Failures: 0, Errors: 1, Skipped: 4

Which seems to point towards the earlier test error as being what is
stopping the build.  Any thoughts?

Tim



On Mon, Aug 25, 2014 at 8:52 AM, Chen, Pei <Pei.Chen@childrens.harvard.edu>
wrote:

> 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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