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Posted to dev@ctakes.apache.org by "Dligach, Dmitriy" <dd...@luc.edu> on 2017/04/11 16:36:26 UTC
dictionary lookup error
Hello,
After a recent ‘svn up’, a simple pipeline involving dictionary lookup started to fail. It fails to locate a file: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml.
The pipeline is here:
https://github.com/dmitriydligach/ctakes-misc/blob/master/src/main/java/org/apache/ctakes/pipelines/BasicAnnotations.java
Any thoughts on what might be going wrong?
Thank you in advance.
Here’s the full error message:
Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: <unknown>)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
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:279)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186)
at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711)
at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207)
at org.apache.ctakes.pipelines.BasicAnnotations.main(BasicAnnotations.java:67)
Caused by: org.apache.uima.resource.ResourceInitializationException
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:131)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266)
... 12 more
Caused by: java.io.FileNotFoundException: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml (No such file or directory)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.<init>(FileInputStream.java:138)
at org.apache.ctakes.core.resource.FileLocator.getAsStream(FileLocator.java:61)
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:128)
... 13 more
Dima
RE: dictionary lookup error
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Excellent! Thanks
-----Original Message-----
From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
Sent: Friday, April 14, 2017 11:11 AM
To: dev@ctakes.apache.org
Subject: Re: dictionary lookup error
Sean, thank you very much for your help.
I just wanted to inform everybody that after I did an ‘svn up’ this morning, dictionary lookup started to work without doing the additional steps Sean describes below.
Dima
> On Apr 11, 2017, at 11:50, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>
> Hi Dima,
>
> Great question. This is part of the change for v.4.0
>
> You will need to pick up the new dictionary (sno_rx_16ab.zip) from sourceforge:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=KmGEki1TU4BZLjRQjWCDwkDqhnTRLKVS3khDyoY-oDg&s=ZFumv_GSAUDMgrBdJQRHcgBV6WuUqOlErCxewLGAE6E&e=
> and unzip it in your resources/ directory.
>
> Sno_rx_16ab is a new database in hsqldb 2.3.4 format containing the standard ctakes tuis, cuis, snomedct and rxnorm from the umls 2016ab release.
>
> The ctakes.apache.org website will have an updated dictionary-fast link when we are ready to release 4.0.
> The pom in trunk will be switched to automatically grab that resource when you compile as soon as it is published from sourceforge (i.e. maven can find it).
>
> I apologize for not sending out this information earlier. A few items have fallen through the cracks wrt the 4.0 rc, trunk 4.0.1 updates, sourceforge publication, etc.
>
> There are running edits on the instructions for future releases ... I hope that we capture everything.
>
> Sean
>
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> Sent: Tuesday, April 11, 2017 12:36 PM
> To: cTAKES Developer list
> Subject: dictionary lookup error
>
> Hello,
>
>
>
> After a recent ‘svn up’, a simple pipeline involving dictionary lookup started to fail. It fails to locate a file: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml.
>
>
>
> The pipeline is here:
>
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_org_apache_ctakes_pipelines_BasicAnnotations.java&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UlWU5Cj26g3v3pPKCjO8HMaLfwabkSR_pSDvc7er58A&s=DJO0GqRKzDgpx_rGUTN6yTFJX5xeB7B4oAiJoNRfNno&e=
>
>
>
> Any thoughts on what might be going wrong?
>
>
>
> Thank you in advance.
>
>
>
> Here’s the full error message:
>
>
>
> Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: <unknown>)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
>
> 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:279)
>
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407)
>
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256)
>
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429)
>
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373)
>
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186)
>
> at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711)
>
> at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207)
>
> at org.apache.ctakes.pipelines.BasicAnnotations.main(BasicAnnotations.java:67)
>
> Caused by: org.apache.uima.resource.ResourceInitializationException
>
> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:131)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266)
>
> ... 12 more
>
> Caused by: java.io.FileNotFoundException: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml (No such file or directory)
>
> at java.io.FileInputStream.open0(Native Method)
>
> at java.io.FileInputStream.open(FileInputStream.java:195)
>
> at java.io.FileInputStream.<init>(FileInputStream.java:138)
>
> at org.apache.ctakes.core.resource.FileLocator.getAsStream(FileLocator.java:61)
>
> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:128)
>
> ... 13 more
>
>
>
>
>
> Dima
>
>
>
>
>
>
>
Re: dictionary lookup error
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
Sean, thank you very much for your help.
I just wanted to inform everybody that after I did an ‘svn up’ this morning, dictionary lookup started to work without doing the additional steps Sean describes below.
Dima
> On Apr 11, 2017, at 11:50, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>
> Hi Dima,
>
> Great question. This is part of the change for v.4.0
>
> You will need to pick up the new dictionary (sno_rx_16ab.zip) from sourceforge:
> https://sourceforge.net/projects/ctakesresources/files/
> and unzip it in your resources/ directory.
>
> Sno_rx_16ab is a new database in hsqldb 2.3.4 format containing the standard ctakes tuis, cuis, snomedct and rxnorm from the umls 2016ab release.
>
> The ctakes.apache.org website will have an updated dictionary-fast link when we are ready to release 4.0.
> The pom in trunk will be switched to automatically grab that resource when you compile as soon as it is published from sourceforge (i.e. maven can find it).
>
> I apologize for not sending out this information earlier. A few items have fallen through the cracks wrt the 4.0 rc, trunk 4.0.1 updates, sourceforge publication, etc.
>
> There are running edits on the instructions for future releases ... I hope that we capture everything.
>
> Sean
>
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> Sent: Tuesday, April 11, 2017 12:36 PM
> To: cTAKES Developer list
> Subject: dictionary lookup error
>
> Hello,
>
>
>
> After a recent ‘svn up’, a simple pipeline involving dictionary lookup started to fail. It fails to locate a file: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml.
>
>
>
> The pipeline is here:
>
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_org_apache_ctakes_pipelines_BasicAnnotations.java&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UlWU5Cj26g3v3pPKCjO8HMaLfwabkSR_pSDvc7er58A&s=DJO0GqRKzDgpx_rGUTN6yTFJX5xeB7B4oAiJoNRfNno&e=
>
>
>
> Any thoughts on what might be going wrong?
>
>
>
> Thank you in advance.
>
>
>
> Here’s the full error message:
>
>
>
> Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: <unknown>)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
>
> 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:279)
>
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407)
>
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256)
>
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429)
>
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373)
>
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186)
>
> at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711)
>
> at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207)
>
> at org.apache.ctakes.pipelines.BasicAnnotations.main(BasicAnnotations.java:67)
>
> Caused by: org.apache.uima.resource.ResourceInitializationException
>
> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:131)
>
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266)
>
> ... 12 more
>
> Caused by: java.io.FileNotFoundException: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml (No such file or directory)
>
> at java.io.FileInputStream.open0(Native Method)
>
> at java.io.FileInputStream.open(FileInputStream.java:195)
>
> at java.io.FileInputStream.<init>(FileInputStream.java:138)
>
> at org.apache.ctakes.core.resource.FileLocator.getAsStream(FileLocator.java:61)
>
> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:128)
>
> ... 13 more
>
>
>
>
>
> Dima
>
>
>
>
>
>
>
RE: dictionary lookup error
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Dima,
Great question. This is part of the change for v.4.0
You will need to pick up the new dictionary (sno_rx_16ab.zip) from sourceforge:
https://sourceforge.net/projects/ctakesresources/files/
and unzip it in your resources/ directory.
Sno_rx_16ab is a new database in hsqldb 2.3.4 format containing the standard ctakes tuis, cuis, snomedct and rxnorm from the umls 2016ab release.
The ctakes.apache.org website will have an updated dictionary-fast link when we are ready to release 4.0.
The pom in trunk will be switched to automatically grab that resource when you compile as soon as it is published from sourceforge (i.e. maven can find it).
I apologize for not sending out this information earlier. A few items have fallen through the cracks wrt the 4.0 rc, trunk 4.0.1 updates, sourceforge publication, etc.
There are running edits on the instructions for future releases ... I hope that we capture everything.
Sean
-----Original Message-----
From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
Sent: Tuesday, April 11, 2017 12:36 PM
To: cTAKES Developer list
Subject: dictionary lookup error
Hello,
After a recent ‘svn up’, a simple pipeline involving dictionary lookup started to fail. It fails to locate a file: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml.
The pipeline is here:
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_org_apache_ctakes_pipelines_BasicAnnotations.java&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UlWU5Cj26g3v3pPKCjO8HMaLfwabkSR_pSDvc7er58A&s=DJO0GqRKzDgpx_rGUTN6yTFJX5xeB7B4oAiJoNRfNno&e=
Any thoughts on what might be going wrong?
Thank you in advance.
Here’s the full error message:
Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: <unknown>)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
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:279)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186)
at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711)
at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207)
at org.apache.ctakes.pipelines.BasicAnnotations.main(BasicAnnotations.java:67)
Caused by: org.apache.uima.resource.ResourceInitializationException
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:131)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266)
... 12 more
Caused by: java.io.FileNotFoundException: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml (No such file or directory)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.<init>(FileInputStream.java:138)
at org.apache.ctakes.core.resource.FileLocator.getAsStream(FileLocator.java:61)
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:128)
... 13 more
Dima