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Posted to dev@ctakes.apache.org by Kim Ebert <ki...@perfectsearchcorp.com> on 2014/08/20 19:24:45 UTC
Re: managing ctakes resources on classpath
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.TestClearNLPAnalysisEngines
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.TestClearNLPAnalysisEngines):
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 <sh...@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.java: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.
>>
>>
>>
>>
Re: managing ctakes resources on classpath
Posted by Pei Chen <ch...@apache.org>.
I'm not too privy to the ytex config details, but yes you're right,
it's caused by the xdl.xsd being null. However it looks like it
exists in ytex-res.jar but the call being made uses Class.getResource
which won't be able to read in from the jar as an InputStream.
1) We can make ytex read in resources directly from jars (as maven
central artifacts). We can make AppJdl.class.getResourceAsStream()
instead of getResource(). However, are there any other local physical
File dependencies?
2) Alternatively, we can add a step to have maven unpack res.jar if required.
I think 1 would be nice, but not sure how involved it will be.
Caused by: java.io.FileNotFoundException:
/Users/pei/workspace/apache-ctakes/trunk/ctakes-ytex/file:/Users/pei/workspace/apache-ctakes/trunk/ctakes-ytex-res/target/ctakes-ytex-res-3.2.1-SNAPSHOT.jar!/org/apache/ctakes/jdl/xdl.xsd
(No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:146)
at java.io.FileInputStream.<init>(FileInputStream.java:101)
at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:90)
Anyhow- https://issues.apache.org/jira/browse/CTAKES-308 opened to track this
On Tue, Aug 26, 2014 at 3:01 AM, vijay garla <vn...@gmail.com> wrote:
> Hi
>
> The test that is failing has nothing to do with the MRCONSO not found
> warning.
>
> ValidationTest failed because it couldn't find the XSD.
>
> The XSD is in the ctakes-ytex-resources, but the corresponding maven
> artifact is an empty jar.
>
> I think it would be best to modify the resource jars to actually contain
> resources.
Re: managing ctakes resources on classpath
Posted by vijay garla <vn...@gmail.com>.
Hi
The test that is failing has nothing to do with the MRCONSO not found
warning.
ValidationTest failed because it couldn't find the XSD.
The XSD is in the ctakes-ytex-resources, but the corresponding maven
artifact is an empty jar.
I think it would be best to modify the resource jars to actually contain
resources.
Re: managing ctakes resources on classpath
Posted by Kim Ebert <ki...@perfectsearchcorp.com>.
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 <Pe...@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"
>>>>>> <ki...@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
>>>>>> <sh...@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.
>>>>
Re: managing ctakes resources on classpath
Posted by Tim O'Connell <ti...@gmail.com>.
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 <Pe...@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"
> > > >> <ki...@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
> > > >> <sh...@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.
> > > >
> > >
> > >
>
RE: managing ctakes resources on classpath
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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"
> > >> <ki...@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
> > >> <sh...@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.
> > >
> >
> >
Re: managing ctakes resources on classpath
Posted by Tim O'Connell <ti...@gmail.com>.
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"
> >> <ki...@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.TestClearNLPAnalysisEngin
> >>>> 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.TestCle
> >> 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
> >> <sh...@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.
> >
>
>
Re: managing ctakes resources on classpath
Posted by Kim Ebert <ki...@perfectsearchcorp.com>.
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"
>> <ki...@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.TestClearNLPAnalysisEngin
>>>> 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.TestCle
>> 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
>> <sh...@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.
>
RE: managing ctakes resources on classpath
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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"
> <ki...@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.TestClearNLPAnalysisEngin
> >> 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.TestCle
> 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
> <sh...@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.
Re: managing ctakes resources on classpath
Posted by Kim Ebert <ki...@perfectsearchcorp.com>.
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" <ki...@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.TestClearNLPAnalysisEngines
>> 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.TestClearNLPAnalysisEngines):
>> 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 <sh...@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.java: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.
Re: managing ctakes resources on classpath
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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" <ki...@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.TestClearNLPAnalysisEngines
> 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.TestClearNLPAnalysisEngines):
> 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 <sh...@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.java: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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>