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From Jeff Headley <jeffun...@gmail.com>
Subject Re: Running cTAKES through Java
Date Sun, 28 Jun 2015 03:08:47 GMT
I was able to get by the error by modifying my installation's
DictionaryLookupAnnotatorUMLS.xml file. I changed:
<fileUrl>file:org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml</fileUrl>

to
<fileUrl>file:resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml</fileUrl>

and that seemed to work.

I saw only a slight performance improvement however. Would anyone be able
to tell me what is going on between these two log statements that takes
about 12 minutes?

2015-06-27 22:45:02.374  INFO 8972 --- [           main]
.a.c.d.l.a.UmlsDictionaryLookupAnnotator : process(JCas)
2015-06-27 22:57:39.385  INFO 8972 --- [           main]
o.a.c.c.parser.MaxentParserWrapper       : Started processing: null

On Sat, Jun 27, 2015 at 12:45 PM, Jeff Headley <jeffunf96@gmail.com> wrote:

> I have changed my cTAKES dependencies in my pom back to
> <scope>provided</scope> and I think I have the classpath set correctly as
> it seems to start out ok but eventually gets this new error. I'm hoping
> maybe someone has seen this before and can help me out. I believe my cTAKES
> is installed correctly. I followed the guide and can use the CVD. The
> analysis engine I'm attempting to load
> is desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml.
>
> 2015-06-27 12:36:07.425 DEBUG 10332 --- [           main]
> o.a.ctakes.core.ae.OverlapAnnotator      : Overlap bitset: {3}
> 2015-06-27 12:36:07.453  INFO 10332 --- [           main]
> o.a.c.d.p.ae.ClearNLPDependencyParserAE  : using Morphy analysis? true
> Loading configuration.
> Loading feature templates.
> Loading lexica.
> Loading model:
>
> ........................................................................................
> 2015-06-27 12:36:16.930  INFO 10332 --- [           main]
> org.apache.ctakes.chunker.ae.Chunker     : Chunker model file:
> org/apache/ctakes/chunker/models/chunker-model.zip
> 2015-06-27 12:36:17.952  INFO 10332 --- [           main]
> c.c.a.ContextDependentTokenizerAnnotator : Finite state machines loaded.
> 2015-06-27 12:36:17.959  INFO 10332 --- [           main]
> o.a.c.c.parser.ae.ConstituencyParser     : Initializing parser...
> 2015-06-27 12:36:20.616  INFO 10332 --- [           main]
> o.a.ctakes.necontexts.ContextAnnotator   : SCOPE ORDER: [1, 3]
> 2015-06-27 12:36:20.619  INFO 10332 --- [           main]
> o.a.c.n.n.NegationContextAnalyzer        : initBoundaryData() called for
> ContextInitializer
> 2015-06-27 12:36:20.758  INFO 10332 --- [           main]
> org.apache.ctakes.postagger.POSTagger    : POS tagger model file:
> org/apache/ctakes/postagger/models/mayo-pos.zip
> 2015-06-27 12:36:21.061 ERROR 10332 --- [           main]
> c.e.c.processors.CommandLineProcessor    : ResourceInitializationException:
>
> org.apache.uima.resource.ResourceInitializationException: Error
> initializing "org.apache.uima.resource.impl.DataResource_impl" from
> descriptor
> file:/D:/java/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml.
> at
> org.apache.uima.util.SimpleResourceFactory.produceResource(SimpleResourceFactory.java:144)
> 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:243)
> at
> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:565)
> 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
> .
> .
> .
> Caused by: org.apache.uima.resource.ResourceInitializationException: Could
> not access the resource data at
> file:org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml.
> at
> org.apache.uima.resource.impl.DataResource_impl.initialize(DataResource_impl.java:127)
> at
> org.apache.uima.util.SimpleResourceFactory.produceResource(SimpleResourceFactory.java:123)
> ... 35 common frames omitted
>
> On Fri, Jun 26, 2015 at 9:46 AM, Bruce Tietjen <
> bruce.tietjen@perfectsearchcorp.com> wrote:
>
>> I'm sorry I don't have any current numbers for running that pipeline
>> because we need more than just entity recognition. We also need polarity,
>> certainty, etc.
>>
>> We have done a lot of optimization work in the more expensive parts of
>> the pipeline and have made modifications to some areas to make them thread
>> safe to enable running multiple pipelines concurrently within the same
>> process. We have also made changes so most of the models that are loaded
>> can be shared across multiple pipelines.
>>
>> We have not had time and resources to share these changes with the
>> community yet, but intend to make our changes available to the community as
>> soon as we feel they are ready.
>>
>>
>>  [image: IMAT Solutions] <http://imatsolutions.com>
>>  Bruce Tietjen
>> Senior Software Engineer
>> [image: Mobile:] 801.634.1547
>> bruce.tietjen@imatsolutions.com
>>
>> On Thu, Jun 25, 2015 at 11:43 PM, Sai Anuroop <sai.anuroop@abzooba.com>
>> wrote:
>>
>>> Hi All,
>>> I am presently working with developer version of cTAKES in Windows
>>> through eclipse.
>>> @Jeff:Thanks for your reply.
>>> @Lance:I am new to cTAKES and Java.So please Can you give me the code
>>> which runs cTAKES CPE in background without opening the CUI and produces
>>> XML output.If the code given does the same then can you please tell where
>>> to create above java class(in which project).
>>> @Bruce:Thanks for your posts.Can you tell What is the average and best
>>> time of cTAKES analyzing say a 20 line discharge report
>>> using AggregatePlaintextFastUMLSProcessor.
>>>
>>> Regards,
>>>
>>> Vetsa Sai Anuroop
>>>
>>>
>>>
>>
>

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