ctakes-user mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Tol O." <tol...@gmail.com>
Subject Re: Collection Processing Engine (CPE) Exception, User Install
Date Thu, 29 Jan 2015 23:34:05 GMT
Hi,

In the file desc/ctakes-preprocessor/desc/CdaCasInitializer.xml, I also
replaced the empty typeSystemDescription tags (lines 35-38) with the
proposed changes. The Exception is still happening, it did not work. I am
also using the testpatient_cn_1.xml file.

On Thu, Jan 29, 2015 at 1:28 PM, Weiwei Zhang <wzhang41@dons.usfca.edu>
wrote:

> 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!
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

Mime
View raw message