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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 17:58:19 GMT
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
>>>>>
>>>>> [2]
>>>>> http://mail-archives.apache.org/mod_mbox/ctakes-user/201403.mbox/%3CCAPqz87oUZ=hPzc_Fo_ZLaEf3PVQcm9xSYuMs15iyMgapsxX9gg@mail.gmail.com%3E
>>>>>
>>>>> 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
>>>>>>>
>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>>
>>>>>>>> Britt
>>>>>>>>
>>>>>>>>     Britt Fitch
>>>>>>>> Wired Informatics
>>>>>>>> 265 Franklin St Ste 1702
>>>>>>>> Boston, MA 02110
>>>>>>>> http://wiredinformatics.com
>>>>>>>> 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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