Hi Pei, I appreciate your quick response. I'd like to try the temporary solution you suggested in the email but could you also specify the name of the XML file that I need to modify and how I can modify it (maybe in an example)?
Many Thanks! Best, Vivian On Mon, Feb 2, 2015 at 10:15 AM, Chen, Pei <[email protected]> wrote: > Hi, > > I opened the below Jira to track this: > > https://issues.apache.org/jira/browse/CTAKES-347 > > > > Essentially, I believe the URI is not hierarchal error is due to the > config using physical file:/// instead of classpath [1]. > > I did not get a chance test or verify this. As a temp work around, you > can modify the xml to point those to physical files that exist if you like > (feel free to add comments/submit a patch if you like). > > Note: the CDA preprocessor is only intended for incoming documents that > are already well formed XML/CDA documents. If it’s plaintext, I would > suggest using the plaintext aggregates instead of CDA. > > > > [1] > > > http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-preprocessor/desc/CdaCasInitializer.xml > > > > *From:* Weiwei Zhang [mailto:[email protected]] > *Sent:* Monday, February 02, 2015 1:02 PM > *To:* [email protected] > *Subject:* Re: Collection Processing Engine (CPE) Exception, User Install > > > > Hi Pei, > > > > I want to follow up with you on the CPE Exception which was reported by me > and another user last week. Here I pasted the stacktrace on the terminal > when the error occurred to provide you with more clues of what could have > happened. Please let me know if you have any questions or need more > information to troubleshoot. Thanks a lot. > > > > Best, > > Vivian > > > > *Stacktrace*: > > > > log4j: reset attribute= "false". > > log4j: Threshold ="null". > > log4j: Level value for root is [INFO]. > > log4j: root level set to INFO > > log4j: Class name: [org.apache.log4j.ConsoleAppender] > > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" > > log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} > %5p %c{1} - %m%n]. > > log4j: Adding appender named [consoleAppender] to category [root]. > > 02 Feb 2015 09:50:51 INFO LvgCmdApiResourceImpl - Loading NLM Norm and > Lvg with config file = > /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/lvg/data/config/lvg.properties > > 02 Feb 2015 09:50:51 INFO LvgCmdApiResourceImpl - config file absolute > path = > /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/lvg/data/config/lvg.properties > > 02 Feb 2015 09:50:51 INFO LvgCmdApiResourceImpl - cwd = > /usr/local/apache-ctakes-3.2.0 > > 02 Feb 2015 09:50:51 INFO LvgCmdApiResourceImpl - cd > /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/lvg/ > > 02 Feb 2015 09:50:53 INFO LvgCmdApiResourceImpl - cd > /usr/local/apache-ctakes-3.2.0 > > org.apache.uima.resource.ResourceInitializationException: Initialization > of CAS Processor with name "AggregateCdaProcessor" failed. > > at > org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:83) > > at > org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessingEngine(UIMAFramework_impl.java:420) > > at > org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIMAFramework.java:864) > > at org.apache.uima.tools.cpm.CpmPanel.startProcessing(CpmPanel.java:573) > > at org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel.java:105) > > at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713) > > Caused by: org.apache.uima.resource.ResourceConfigurationException: > Initialization of CAS Processor with name "AggregateCdaProcessor" failed. > > at > org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1104) > > at > org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProcessors(CPEFactory.java:550) > > at > org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.java:253) > > at > org.apache.uima.collection.impl.cpm.BaseCPMImpl.<init>(BaseCPMImpl.java:127) > > at > org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:75) > > ... 5 more > > Caused by: java.lang.IllegalArgumentException: URI is not hierarchical > > at java.io.File.<init>(File.java:418) > > at > org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImpl.java:44) > > at > org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603) > > at > org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442) > > at > org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153) > > at > org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157) > > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123) > > at > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) > > at > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) > > at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) > > at > org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) > > at > org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) > > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) > > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) > > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) > > at > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) > > at > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) > > at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) > > at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314) > > at > org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425) > > at > org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088) > > ... 9 more > > > > > > On Thu, Jan 29, 2015 at 3:34 PM, Tol O. <[email protected]> wrote: > > 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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__mail-2Darchives.apache.org_mod-5Fmbox_ctakes-2Duser_201311.mbox_-253C1384464005.90860.YahooMailNeo-40web140301.mail.bf1.yahoo.com-253E&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=phDrlIb8RXczznm_ezqhWlv4EGIEnc2GYw0Fj4NMmuU&s=9u-Ny2tVLKjy8gWrOM8Da5NtKStucQ25e-he1GSrFc0&e=> > > [2] > http://mail-archives.apache.org/mod_mbox/ctakes-user/201403.mbox/%3CCAPqz87oUZ=hpzc_fo_zlaef3pvqcm9xsyums15iymgapsxx...@mail.gmail.com%3E > <https://urldefense.proofpoint.com/v2/url?u=http-3A__mail-2Darchives.apache.org_mod-5Fmbox_ctakes-2Duser_201403.mbox_-253CCAPqz87oUZ-3DhPzc-5FFo-5FZLaEf3PVQcm9xSYuMs15iyMgapsxX9gg-40mail.gmail.com-253E&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=phDrlIb8RXczznm_ezqhWlv4EGIEnc2GYw0Fj4NMmuU&s=t1X3ezcjSERYZ4_MyDNloaMuiV5Z1KFBwbTNa-TIRVM&e=> > > > > 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 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_branches_ctakes-2D3.1.0_ctakes-2Dclinical-2Dpipeline_src_test_data_testpatient-5Fcn-5F1.xml&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=phDrlIb8RXczznm_ezqhWlv4EGIEnc2GYw0Fj4NMmuU&s=kqXz4fH23jjkM0Fv9s20tNJtH03nyWe51sxRHMbcdUc&e=> > > 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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_repos_asf_ctakes_trunk_ctakes-2Dclinical-2Dpipeline_desc_collection-5Fprocessing-5Fengine_test-5Fplaintext.xml&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=phDrlIb8RXczznm_ezqhWlv4EGIEnc2GYw0Fj4NMmuU&s=NuPyO2DcLscxB6E0cq5WWSm_I5DJNgc9bO9Uoqgphlg&e=> > > > > > Cheers, > > > > Britt > > > > > > > > > > > > Britt Fitch > > Wired Informatics > 265 Franklin St Ste 1702 > Boston, MA 02110 > > http://wiredinformatics.com > <https://urldefense.proofpoint.com/v2/url?u=http-3A__wiredinformatics.com&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=phDrlIb8RXczznm_ezqhWlv4EGIEnc2GYw0Fj4NMmuU&s=BJl8sK_6O0Xd0mnWdV8aOJy7pXtg_PBFHwwjZd9QXNc&e=> > [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! > > > > > > > > > > > > > > > > > > >
