Re: Collection Processing Engine (CPE) Exception, User Install

[Pei Chen <ch...@apache.org>]

Hi Weiwei,
The "URI is not hierarchical" error from the CdaCasInitializer has been
fixed in 3.2.2 (rc2).
If you like to help test/verify, feel free to try the release candidate and
cast your vote [1] for the release.

[1]
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201505.mbox/%3cCAPqz87p-=6DEmsxG5AMgHhetmG7=h+-TU2F_+_yn7BcbUhMrjw@mail.gmail.com%3e

On Thu, Jan 29, 2015 at 2:04 PM, Weiwei Zhang <wz...@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 <ch...@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 <wz...@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. <to...@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. <to...@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!
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>