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From Weiwei Zhang <wzhan...@dons.usfca.edu>
Subject Re: Collection Processing Engine (CPE) Exception, User Install
Date Thu, 29 Jan 2015 19:28:59 GMT
Hi Pei,

I used the example test file listed on the User Install Guide
- testpatient_cn_1.xml. So I guess it is XML/CDA file. The problem occurred
in CPE, not CVD, just to clarify.

Thanks,
Vivian

On Thu, Jan 29, 2015 at 11:16 AM, Pei Chen <chenpei@apache.org> wrote:

> Vivian,
>
> Just curious - Are your input files XML/CDA format or plaintext?
>
>
>
> --Pei
>
> On Thu, Jan 29, 2015 at 2:04 PM, Weiwei Zhang <wzhang41@dons.usfca.edu>
> wrote:
>
>> Hi Pei,
>>
>> Thank you for your response. I added the imports to the
>> CdaCasInitializer descriptor but I am still getting the same error as
>> follows,
>>
>> [image: Inline image 1]
>>
>> There might be something going wrong with "AggregateCdaProcessor".
>>
>> Thank you,
>> Vivian
>>
>>
>> On Thu, Jan 29, 2015 at 9:37 AM, Pei Chen <chenpei@apache.org> wrote:
>>
>>> Try adding the below to the earliest defined primitive descriptor? [1][2]
>>>
>>> <typeSystemDescription>
>>>
>>>        <imports>
>>>
>>> <import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
>>>
>>>      </imports>
>>>
>>> </typeSystemDescription>
>>>
>>>
>>>
>>> Normally I think this is already added in SegementAnnotator…  Feel free
>>> to create a Jira (steps to replicate the issue, and where you placed the
>>> fix so it can be addressed in the next patch).
>>>
>>> Side note: I think we should DELETE all existing xml Descriptors (very
>>> difficult to maintain and test all combinations).  And recreate only the
>>> necessary ones via uimaFIT.
>>>
>>>
>>>
>>> [1]
>>> http://mail-archives.apache.org/mod_mbox/ctakes-user/201311.mbox/%3C1384464005.90860.YahooMailNeo@web140301.mail.bf1.yahoo.com%3E
>>>
>>> [2]
>>> http://mail-archives.apache.org/mod_mbox/ctakes-user/201403.mbox/%3CCAPqz87oUZ=hPzc_Fo_ZLaEf3PVQcm9xSYuMs15iyMgapsxX9gg@mail.gmail.com%3E
>>>
>>> On Wed, Jan 28, 2015 at 3:46 PM, Weiwei Zhang <wzhang41@dons.usfca.edu>
>>> wrote:
>>>
>>>> Hello there,
>>>>
>>>> I encountered the same error as Tol when running CPE in Apache cTakes.
>>>>
>>>> Thank you,
>>>> Vivian
>>>>
>>>> On Wed, Jan 28, 2015 at 12:04 PM, Tol O. <toltox@gmail.com> wrote:
>>>>
>>>>> I just tried this test_plaintext.xml file as the CPE descriptor with
>>>>> the sample file placed in the testdata folder mentioned in the tutorial
and
>>>>> (set the input directory in the GUI to the testdata folder):
>>>>>
>>>>> https://svn.apache.org/repos/asf/ctakes/branches/ctakes-3.1.0/ctakes-clinical-pipeline/src/test/data/testpatient_cn_1.xml
>>>>>
>>>>> The Error window I am getting states
>>>>> "org.apache.uima.cas.CASRuntimeException: Jcas type
>>>>> "org.apache.ctakes.typesystem.type.structured.DocumentID" used in Java
>>>>> code, but was not declared in the XML type descriptor.
>>>>>
>>>>> So still no luck, do you have any other suggestions?
>>>>>
>>>>> Tol
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Wed, Jan 28, 2015 at 1:42 PM, britt fitch <
>>>>> britt.fitch@wiredinformatics.com> wrote:
>>>>>
>>>>>> Hi Tol, you might prefer to try the test_plaintext.xml CPE instead
of
>>>>>> the CDA one:
>>>>>>
>>>>>> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml
>>>>>>
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Britt
>>>>>>
>>>>>>     Britt Fitch
>>>>>> Wired Informatics
>>>>>> 265 Franklin St Ste 1702
>>>>>> Boston, MA 02110
>>>>>> http://wiredinformatics.com
>>>>>> Britt.Fitch@wiredinformatics.com
>>>>>>
>>>>>> On Jan 28, 2015, at 2:25 PM, Tol O. <toltox@gmail.com> wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I am following the cTAKES 3.2 User Install Guide with cTAKES 3.2.1
>>>>>> using Linux and Java 8.
>>>>>>
>>>>>> At step 8 of the Collection Processing Engine (CPE) (click the play
>>>>>> button) I am get an error message:
>>>>>> "org.apache.uima.resource.ResourceInitializationException:
>>>>>> Initialization of CAS Processor with name "AggregateCdaProcessor"
failed.
>>>>>> [...] Caused by: java.lang.IllegalArgumentException: URI is not
>>>>>> hierarchical."
>>>>>>
>>>>>> I read a bit on this mailing list and saw that other people also
>>>>>> encountered such or a similar error. I followed the install guide
step by
>>>>>> step and extracted/copied the cTAKES resources folder over the already
>>>>>> existing resources folder of cTAKES.
>>>>>>
>>>>>> Does anybody know how to fix this Exception problem to run the
>>>>>> Collection Processing Engine (CPE)?
>>>>>>
>>>>>> Many thanks!
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

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