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From Weiwei Zhang <wzhan...@dons.usfca.edu>
Subject Re: Collection Processing Engine (CPE) Exception, User Install
Date Mon, 02 Feb 2015 18:36:38 GMT
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 <Pei.Chen@childrens.harvard.edu>
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:wzhang41@dons.usfca.edu]
> *Sent:* Monday, February 02, 2015 1:02 PM
> *To:* user@ctakes.apache.org
> *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. <toltox@gmail.com> 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 <wzhang41@dons.usfca.edu>
> 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 <chenpei@apache.org> 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 <wzhang41@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 <chenpei@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
> <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_ZLaEf3PVQcm9xSYuMs15iyMgapsxX9gg@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 <wzhang41@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. <toltox@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
> <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 <
> 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
> <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=>
> Britt.Fitch@wiredinformatics.com
>
>
>
>  On Jan 28, 2015, at 2:25 PM, Tol O. <toltox@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!
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>

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