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From Kim Ebert <kim.eb...@perfectsearchcorp.com>
Subject Re: managing ctakes resources on classpath
Date Mon, 08 Sep 2014 17:04:14 GMT
Hi Pei,

I was finally able to get around to testing this. I am running into the
same issue that Tim has encountered.

Thanks for making the fix and logging the ticket for the xdl.xsd issue.

Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/

On 08/26/2014 12:30 AM, Tim O'Connell wrote:
> 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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
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