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 <[email protected]> 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 <[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! >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
