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 <[email protected]> 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 <[email protected]> > 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 <[email protected]> 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/%[email protected]%3E >>> >>> [2] >>> http://mail-archives.apache.org/mod_mbox/ctakes-user/201403.mbox/%3CCAPqz87oUZ=hpzc_fo_zlaef3pvqcm9xsyums15iymgapsxx...@mail.gmail.com%3E >>> >>> On Wed, Jan 28, 2015 at 3:46 PM, Weiwei Zhang <[email protected]> >>> 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. <[email protected]> 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 < >>>>> [email protected]> 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 >>>>>> [email protected] >>>>>> >>>>>> On Jan 28, 2015, at 2:25 PM, Tol O. <[email protected]> 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! >>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> >
