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From Jeff Headley <jeffun...@gmail.com>
Subject Re: Running cTAKES through Java
Date Sat, 27 Jun 2015 16:45:19 GMT
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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