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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: Collection Processing Engine (CPE) Exception, User Install
Date Mon, 02 Feb 2015 18:15:26 GMT
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:///<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<mailto: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<mailto: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<mailto: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<mailto: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,

[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<mailto: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<mailto: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<mailto: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<mailto: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<mailto:Britt.Fitch@wiredinformatics.com>

On Jan 28, 2015, at 2:25 PM, Tol O. <toltox@gmail.com<mailto: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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