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_+_yn7bcbuhm...@mail.gmail.com%3e 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! >>>>> >>>>> >>>>> >>>> >>> >> >
