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Posted to dev@ctakes.apache.org by Jakob Rogstadius <Ja...@who-umc.org> on 2015/07/09 14:43:04 UTC
Cannot resolve lookup descriptor files for
UmlsDictionaryLookupAnnotator
Hi cTakes devs,
I am trying to use cTakes' UMLS Dictionary Lookup annotator (either the older one or the newer fast one) through uimaFIT, and I am running into problems with resources that can't be found. Please bear with me if my problem description omits any relevant details, as I don't have much experience neither with cTakes, UIMA, Java, Maven nor Eclipse.
cTakes is imported into my Eclipse project through Maven, and I have a very basic pipeline running with a few annotators from UIMA and cTakes, along with a few custom ones. I have specified the UMLS login details in the arguments of the Eclipse runtime configuration, which works. However, when I add either a UmlsDictionaryLookupAnnotator or its fast version, they fail to resolve their respective lookup descriptor files. I have included a stack trace for the first method, while the second method throws a null pointer exception on AbstractJCasTermAnnotator.initialize() (line 129), due to the fileResource variable being null.
I have noticed that since cTakes version 3.1.1, the lookup descriptor file referenced in UmlsDictionaryLookupAnnotator.createAnnotatorDescription() is no longer included in ctakes-dictionary-lookup-res-3.x.x.jar. I don't know if the same change took place for the fast dictionary, but I can see that the xml file referenced in DictionaryLookupFactory.createUmlsDictionaryLookupDescription() is not present in the ctakes-dictionary-lookup-fast-res-3.2.2.jar that I get through Maven. Have these files moved, so that I now need to include something else? Am I doing something else wrong?
Also, I have downloaded the UMLS dictionary resources from http://ctakes.apache.org/downloads.cgi, but where do I place them for cTakes to be able to find them?
Stack trace for UmlsDictionaryLookupAnnotator.createAnnotatorDescription():
java.io.FileNotFoundException: No File exists at org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:118)
at org.umc.research.social_media_adr_detection.pipelines.ExtractDrugAndAEMentions.main(ExtractDrugAndAEMentions.java:128)
Exception in thread "main" org.apache.uima.resource.ResourceInitializationException
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:156)
at org.umc.research.social_media_adr_detection.pipelines.ExtractDrugAndAEMentions.main(ExtractDrugAndAEMentions.java:128)
Caused by: java.io.FileNotFoundException: No File exists at org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:118)
... 1 more
Any pointers would be greatly appreciated.
Best regards,
Jakob Rogstadius
Research Engineer
Uppsala Monitoring Centre
WHO Collaborating Centre for International Drug Monitoring
RE: Cannot resolve lookup descriptor files for
UmlsDictionaryLookupAnnotator
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Jakob,
The LookupDesc.xml file is supposed to be editable by the user in order to enter umls username and password information. If the file was in a resource .jar that would be pretty difficult. Umls user information can also be specified on the command line, so perhaps the whole .xml scenario should be rethought. It could easily be changed as long as users all agree to stick to the command-line umls user specification only.
Do you feel like submitting a JIRA item?
Sean
-----Original Message-----
From: Jakob Rogstadius [mailto:Jakob.Rogstadius@who-umc.org]
Sent: Monday, July 20, 2015 4:41 AM
To: dev@ctakes.apache.org
Subject: RE: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi Sean,
Thanks for your response. I had to work on something else for a couple of days, but now I'm back at it.
As you say, I get UmlsDictionaryLookupAnnotator to work when I manually copy the files from the subversion repository to my local project. What I have now looks like this:
project-name
project-name/src/main/java/...
project-name/data/...
project-name/resources/...
project-name/org/apache/ctakes/dictionary/lookup/... (this folder was copied from cTakes svn and is where LookupDesc.xml and the others files are located)
However, this doesn't seem like the right approach at all. The other cTakes components that I have tried using have all imported neatly as jars from Maven central, together with their -res jars which contain the descriptor files and other resources that they reference. At no point have I previously downloaded the source project from the SVN server, and everything except the UMLS dictionary lookups have worked this way.
I am confused. You say that the -res jars are not supposed to contain these files, but then what are they supposed to contain? As I mentioned below, the current -res jar for UmlsDictionaryLookupAnnotator has no content, except for META-INF. And is this really the only way I can get the components to work? What am I missing?
In case it matters, I instantiate the annotator as follows using uimaFit:
AggregateBuilder aggregate = new AggregateBuilder();
...
aggregate.add(UmlsDictionaryLookupAnnotator.createAnnotatorDescription());
...
AnalysisEngine aggregateEngine = aggregate.createAggregate();
...
SimplePipeline.runPipeline(reader, aggregateEngine, writer, evaluator);
Best regards,
Jakob
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: den 10 juli 2015 18:29
To: dev@ctakes.apache.org
Subject: RE: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi Jakob,
The -res jars aren't supposed to contain those files. The files should be placed in the resources/ directory under the ctakes root parallel to lib/.
Can you take me through your checkout / installation and build / run steps? A list of your svn and maven commands might help me figure out what step is failing you.
Sean
-----Original Message-----
From: Jakob Rogstadius [mailto:Jakob.Rogstadius@who-umc.org]
Sent: Friday, July 10, 2015 3:04 AM
To: dev@ctakes.apache.org
Subject: RE: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi Sean,
Many thanks for your reply. Like you say, I see both the lookup descriptors and all other resources in the projects on the svn server (https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_trunk_&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Izx33vJrQxf37pZxy4Ha128D0yl2ak1hSbm4Jp9kX5E&s=jkiqjWJUTs0H_ntVqssGJ2R6yWWYlNTVbWR6snNFxAM&e= ). However, the -res jars that I get through maven are completely empty, except for their META-INF folders. For other components, their -res jars do contain their resources as expected. Could something have gone wrong while publishing recent versions of these two?
These are my relevant maven imports:
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup</artifactId>
<version>3.2.2</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup-res</artifactId>
<version>3.2.2</version>
</dependency> <dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup-fast</artifactId>
<version>3.2.2</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup-fast-res</artifactId>
<version>3.2.2</version>
</dependency>
Jar content:
https://urldefense.proofpoint.com/v2/url?u=http-3A__grepcode.com_snapshot_repo1.maven.org_maven2_org.apache.ctakes_ctakes-2Ddictionary-2Dlookup-2Dres_3.2.1_&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Izx33vJrQxf37pZxy4Ha128D0yl2ak1hSbm4Jp9kX5E&s=eQsXb82VZXQ5MK1KABI7mJVs-E0Plpn1vhujzs0OJUU&e= https://urldefense.proofpoint.com/v2/url?u=http-3A__grepcode.com_snapshot_repo1.maven.org_maven2_org.apache.ctakes_ctakes-2Ddictionary-2Dlookup-2Dfast-2Dres_3.2.1_&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Izx33vJrQxf37pZxy4Ha128D0yl2ak1hSbm4Jp9kX5E&s=LbTzcUINCxbwdk3A7ssDgs9MMavHuXKEOQN35OuBd0E&e=
Jakob
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: den 9 juli 2015 19:54
To: dev@ctakes.apache.org
Subject: RE: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi Jakob,
Where those files exist really depends upon how you are trying to run. They start in src/main/resources/ directories in their respective -res projects.
If you are running from an IDE, make sure that the -res modules have been added to your project, and that the src/main/resources/ directories have been tagged as resource directories. I'm not an Eclipse expert either (I don't use it), but if it imports via maven it should be doing that automatically, or maybe tagging them as source directories.
If you are running from a full build of the application, there should be a resources/ directory in your root. If that directory exists and contains the .xml files, either run the app from the root directory or set $CTAKES_HOME to point to that root.
If you run with today's build you should see a listing of your classpath upon that error - which may or may not help you find the problem.
Sean
-----Original Message-----
From: Jakob Rogstadius [mailto:Jakob.Rogstadius@who-umc.org]
Sent: Thursday, July 09, 2015 8:43 AM
To: dev@ctakes.apache.org
Subject: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi cTakes devs,
I am trying to use cTakes' UMLS Dictionary Lookup annotator (either the older one or the newer fast one) through uimaFIT, and I am running into problems with resources that can't be found. Please bear with me if my problem description omits any relevant details, as I don't have much experience neither with cTakes, UIMA, Java, Maven nor Eclipse.
cTakes is imported into my Eclipse project through Maven, and I have a very basic pipeline running with a few annotators from UIMA and cTakes, along with a few custom ones. I have specified the UMLS login details in the arguments of the Eclipse runtime configuration, which works. However, when I add either a UmlsDictionaryLookupAnnotator or its fast version, they fail to resolve their respective lookup descriptor files. I have included a stack trace for the first method, while the second method throws a null pointer exception on AbstractJCasTermAnnotator.initialize() (line 129), due to the fileResource variable being null.
I have noticed that since cTakes version 3.1.1, the lookup descriptor file referenced in UmlsDictionaryLookupAnnotator.createAnnotatorDescription() is no longer included in ctakes-dictionary-lookup-res-3.x.x.jar. I don't know if the same change took place for the fast dictionary, but I can see that the xml file referenced in DictionaryLookupFactory.createUmlsDictionaryLookupDescription() is not present in the ctakes-dictionary-lookup-fast-res-3.2.2.jar that I get through Maven. Have these files moved, so that I now need to include something else? Am I doing something else wrong?
Also, I have downloaded the UMLS dictionary resources from https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.apache.org_downloads.cgi&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=HSSKy6iWmdl_k4qE22gY7Kb6oTqcfm2ZxVdjOzcjPyc&s=JO8tKCrrsRQMpvAb1evFEHf21pc1SFE7AjXaQGZEyIg&e= , but where do I place them for cTakes to be able to find them?
Stack trace for UmlsDictionaryLookupAnnotator.createAnnotatorDescription():
java.io.FileNotFoundException: No File exists at org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:118)
at org.umc.research.social_media_adr_detection.pipelines.ExtractDrugAndAEMentions.main(ExtractDrugAndAEMentions.java:128)
Exception in thread "main" org.apache.uima.resource.ResourceInitializationException
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:156)
at org.umc.research.social_media_adr_detection.pipelines.ExtractDrugAndAEMentions.main(ExtractDrugAndAEMentions.java:128)
Caused by: java.io.FileNotFoundException: No File exists at org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:118)
... 1 more
Any pointers would be greatly appreciated.
Best regards,
Jakob Rogstadius
Research Engineer
Uppsala Monitoring Centre
WHO Collaborating Centre for International Drug Monitoring
RE: Cannot resolve lookup descriptor files for
UmlsDictionaryLookupAnnotator
Posted by Jakob Rogstadius <Ja...@who-umc.org>.
Hi Sean,
Thanks for your response. I had to work on something else for a couple of days, but now I'm back at it.
As you say, I get UmlsDictionaryLookupAnnotator to work when I manually copy the files from the subversion repository to my local project. What I have now looks like this:
project-name
project-name/src/main/java/...
project-name/data/...
project-name/resources/...
project-name/org/apache/ctakes/dictionary/lookup/... (this folder was copied from cTakes svn and is where LookupDesc.xml and the others files are located)
However, this doesn't seem like the right approach at all. The other cTakes components that I have tried using have all imported neatly as jars from Maven central, together with their -res jars which contain the descriptor files and other resources that they reference. At no point have I previously downloaded the source project from the SVN server, and everything except the UMLS dictionary lookups have worked this way.
I am confused. You say that the -res jars are not supposed to contain these files, but then what are they supposed to contain? As I mentioned below, the current -res jar for UmlsDictionaryLookupAnnotator has no content, except for META-INF. And is this really the only way I can get the components to work? What am I missing?
In case it matters, I instantiate the annotator as follows using uimaFit:
AggregateBuilder aggregate = new AggregateBuilder();
...
aggregate.add(UmlsDictionaryLookupAnnotator.createAnnotatorDescription());
...
AnalysisEngine aggregateEngine = aggregate.createAggregate();
...
SimplePipeline.runPipeline(reader, aggregateEngine, writer, evaluator);
Best regards,
Jakob
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: den 10 juli 2015 18:29
To: dev@ctakes.apache.org
Subject: RE: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi Jakob,
The -res jars aren't supposed to contain those files. The files should be placed in the resources/ directory under the ctakes root parallel to lib/.
Can you take me through your checkout / installation and build / run steps? A list of your svn and maven commands might help me figure out what step is failing you.
Sean
-----Original Message-----
From: Jakob Rogstadius [mailto:Jakob.Rogstadius@who-umc.org]
Sent: Friday, July 10, 2015 3:04 AM
To: dev@ctakes.apache.org
Subject: RE: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi Sean,
Many thanks for your reply. Like you say, I see both the lookup descriptors and all other resources in the projects on the svn server (https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_trunk_&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Izx33vJrQxf37pZxy4Ha128D0yl2ak1hSbm4Jp9kX5E&s=jkiqjWJUTs0H_ntVqssGJ2R6yWWYlNTVbWR6snNFxAM&e= ). However, the -res jars that I get through maven are completely empty, except for their META-INF folders. For other components, their -res jars do contain their resources as expected. Could something have gone wrong while publishing recent versions of these two?
These are my relevant maven imports:
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup</artifactId>
<version>3.2.2</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup-res</artifactId>
<version>3.2.2</version>
</dependency> <dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup-fast</artifactId>
<version>3.2.2</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup-fast-res</artifactId>
<version>3.2.2</version>
</dependency>
Jar content:
https://urldefense.proofpoint.com/v2/url?u=http-3A__grepcode.com_snapshot_repo1.maven.org_maven2_org.apache.ctakes_ctakes-2Ddictionary-2Dlookup-2Dres_3.2.1_&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Izx33vJrQxf37pZxy4Ha128D0yl2ak1hSbm4Jp9kX5E&s=eQsXb82VZXQ5MK1KABI7mJVs-E0Plpn1vhujzs0OJUU&e= https://urldefense.proofpoint.com/v2/url?u=http-3A__grepcode.com_snapshot_repo1.maven.org_maven2_org.apache.ctakes_ctakes-2Ddictionary-2Dlookup-2Dfast-2Dres_3.2.1_&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Izx33vJrQxf37pZxy4Ha128D0yl2ak1hSbm4Jp9kX5E&s=LbTzcUINCxbwdk3A7ssDgs9MMavHuXKEOQN35OuBd0E&e=
Jakob
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: den 9 juli 2015 19:54
To: dev@ctakes.apache.org
Subject: RE: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi Jakob,
Where those files exist really depends upon how you are trying to run. They start in src/main/resources/ directories in their respective -res projects.
If you are running from an IDE, make sure that the -res modules have been added to your project, and that the src/main/resources/ directories have been tagged as resource directories. I'm not an Eclipse expert either (I don't use it), but if it imports via maven it should be doing that automatically, or maybe tagging them as source directories.
If you are running from a full build of the application, there should be a resources/ directory in your root. If that directory exists and contains the .xml files, either run the app from the root directory or set $CTAKES_HOME to point to that root.
If you run with today's build you should see a listing of your classpath upon that error - which may or may not help you find the problem.
Sean
-----Original Message-----
From: Jakob Rogstadius [mailto:Jakob.Rogstadius@who-umc.org]
Sent: Thursday, July 09, 2015 8:43 AM
To: dev@ctakes.apache.org
Subject: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi cTakes devs,
I am trying to use cTakes' UMLS Dictionary Lookup annotator (either the older one or the newer fast one) through uimaFIT, and I am running into problems with resources that can't be found. Please bear with me if my problem description omits any relevant details, as I don't have much experience neither with cTakes, UIMA, Java, Maven nor Eclipse.
cTakes is imported into my Eclipse project through Maven, and I have a very basic pipeline running with a few annotators from UIMA and cTakes, along with a few custom ones. I have specified the UMLS login details in the arguments of the Eclipse runtime configuration, which works. However, when I add either a UmlsDictionaryLookupAnnotator or its fast version, they fail to resolve their respective lookup descriptor files. I have included a stack trace for the first method, while the second method throws a null pointer exception on AbstractJCasTermAnnotator.initialize() (line 129), due to the fileResource variable being null.
I have noticed that since cTakes version 3.1.1, the lookup descriptor file referenced in UmlsDictionaryLookupAnnotator.createAnnotatorDescription() is no longer included in ctakes-dictionary-lookup-res-3.x.x.jar. I don't know if the same change took place for the fast dictionary, but I can see that the xml file referenced in DictionaryLookupFactory.createUmlsDictionaryLookupDescription() is not present in the ctakes-dictionary-lookup-fast-res-3.2.2.jar that I get through Maven. Have these files moved, so that I now need to include something else? Am I doing something else wrong?
Also, I have downloaded the UMLS dictionary resources from https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.apache.org_downloads.cgi&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=HSSKy6iWmdl_k4qE22gY7Kb6oTqcfm2ZxVdjOzcjPyc&s=JO8tKCrrsRQMpvAb1evFEHf21pc1SFE7AjXaQGZEyIg&e= , but where do I place them for cTakes to be able to find them?
Stack trace for UmlsDictionaryLookupAnnotator.createAnnotatorDescription():
java.io.FileNotFoundException: No File exists at org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:118)
at org.umc.research.social_media_adr_detection.pipelines.ExtractDrugAndAEMentions.main(ExtractDrugAndAEMentions.java:128)
Exception in thread "main" org.apache.uima.resource.ResourceInitializationException
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:156)
at org.umc.research.social_media_adr_detection.pipelines.ExtractDrugAndAEMentions.main(ExtractDrugAndAEMentions.java:128)
Caused by: java.io.FileNotFoundException: No File exists at org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:118)
... 1 more
Any pointers would be greatly appreciated.
Best regards,
Jakob Rogstadius
Research Engineer
Uppsala Monitoring Centre
WHO Collaborating Centre for International Drug Monitoring
RE: Cannot resolve lookup descriptor files for
UmlsDictionaryLookupAnnotator
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Jakob,
The -res jars aren't supposed to contain those files. The files should be placed in the resources/ directory under the ctakes root parallel to lib/.
Can you take me through your checkout / installation and build / run steps? A list of your svn and maven commands might help me figure out what step is failing you.
Sean
-----Original Message-----
From: Jakob Rogstadius [mailto:Jakob.Rogstadius@who-umc.org]
Sent: Friday, July 10, 2015 3:04 AM
To: dev@ctakes.apache.org
Subject: RE: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi Sean,
Many thanks for your reply. Like you say, I see both the lookup descriptors and all other resources in the projects on the svn server (https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_trunk_&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Izx33vJrQxf37pZxy4Ha128D0yl2ak1hSbm4Jp9kX5E&s=jkiqjWJUTs0H_ntVqssGJ2R6yWWYlNTVbWR6snNFxAM&e= ). However, the -res jars that I get through maven are completely empty, except for their META-INF folders. For other components, their -res jars do contain their resources as expected. Could something have gone wrong while publishing recent versions of these two?
These are my relevant maven imports:
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup</artifactId>
<version>3.2.2</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup-res</artifactId>
<version>3.2.2</version>
</dependency> <dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup-fast</artifactId>
<version>3.2.2</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup-fast-res</artifactId>
<version>3.2.2</version>
</dependency>
Jar content:
https://urldefense.proofpoint.com/v2/url?u=http-3A__grepcode.com_snapshot_repo1.maven.org_maven2_org.apache.ctakes_ctakes-2Ddictionary-2Dlookup-2Dres_3.2.1_&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Izx33vJrQxf37pZxy4Ha128D0yl2ak1hSbm4Jp9kX5E&s=eQsXb82VZXQ5MK1KABI7mJVs-E0Plpn1vhujzs0OJUU&e= https://urldefense.proofpoint.com/v2/url?u=http-3A__grepcode.com_snapshot_repo1.maven.org_maven2_org.apache.ctakes_ctakes-2Ddictionary-2Dlookup-2Dfast-2Dres_3.2.1_&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Izx33vJrQxf37pZxy4Ha128D0yl2ak1hSbm4Jp9kX5E&s=LbTzcUINCxbwdk3A7ssDgs9MMavHuXKEOQN35OuBd0E&e=
Jakob
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: den 9 juli 2015 19:54
To: dev@ctakes.apache.org
Subject: RE: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi Jakob,
Where those files exist really depends upon how you are trying to run. They start in src/main/resources/ directories in their respective -res projects.
If you are running from an IDE, make sure that the -res modules have been added to your project, and that the src/main/resources/ directories have been tagged as resource directories. I'm not an Eclipse expert either (I don't use it), but if it imports via maven it should be doing that automatically, or maybe tagging them as source directories.
If you are running from a full build of the application, there should be a resources/ directory in your root. If that directory exists and contains the .xml files, either run the app from the root directory or set $CTAKES_HOME to point to that root.
If you run with today's build you should see a listing of your classpath upon that error - which may or may not help you find the problem.
Sean
-----Original Message-----
From: Jakob Rogstadius [mailto:Jakob.Rogstadius@who-umc.org]
Sent: Thursday, July 09, 2015 8:43 AM
To: dev@ctakes.apache.org
Subject: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi cTakes devs,
I am trying to use cTakes' UMLS Dictionary Lookup annotator (either the older one or the newer fast one) through uimaFIT, and I am running into problems with resources that can't be found. Please bear with me if my problem description omits any relevant details, as I don't have much experience neither with cTakes, UIMA, Java, Maven nor Eclipse.
cTakes is imported into my Eclipse project through Maven, and I have a very basic pipeline running with a few annotators from UIMA and cTakes, along with a few custom ones. I have specified the UMLS login details in the arguments of the Eclipse runtime configuration, which works. However, when I add either a UmlsDictionaryLookupAnnotator or its fast version, they fail to resolve their respective lookup descriptor files. I have included a stack trace for the first method, while the second method throws a null pointer exception on AbstractJCasTermAnnotator.initialize() (line 129), due to the fileResource variable being null.
I have noticed that since cTakes version 3.1.1, the lookup descriptor file referenced in UmlsDictionaryLookupAnnotator.createAnnotatorDescription() is no longer included in ctakes-dictionary-lookup-res-3.x.x.jar. I don't know if the same change took place for the fast dictionary, but I can see that the xml file referenced in DictionaryLookupFactory.createUmlsDictionaryLookupDescription() is not present in the ctakes-dictionary-lookup-fast-res-3.2.2.jar that I get through Maven. Have these files moved, so that I now need to include something else? Am I doing something else wrong?
Also, I have downloaded the UMLS dictionary resources from https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.apache.org_downloads.cgi&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=HSSKy6iWmdl_k4qE22gY7Kb6oTqcfm2ZxVdjOzcjPyc&s=JO8tKCrrsRQMpvAb1evFEHf21pc1SFE7AjXaQGZEyIg&e= , but where do I place them for cTakes to be able to find them?
Stack trace for UmlsDictionaryLookupAnnotator.createAnnotatorDescription():
java.io.FileNotFoundException: No File exists at org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:118)
at org.umc.research.social_media_adr_detection.pipelines.ExtractDrugAndAEMentions.main(ExtractDrugAndAEMentions.java:128)
Exception in thread "main" org.apache.uima.resource.ResourceInitializationException
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:156)
at org.umc.research.social_media_adr_detection.pipelines.ExtractDrugAndAEMentions.main(ExtractDrugAndAEMentions.java:128)
Caused by: java.io.FileNotFoundException: No File exists at org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:118)
... 1 more
Any pointers would be greatly appreciated.
Best regards,
Jakob Rogstadius
Research Engineer
Uppsala Monitoring Centre
WHO Collaborating Centre for International Drug Monitoring
RE: Cannot resolve lookup descriptor files for
UmlsDictionaryLookupAnnotator
Posted by Jakob Rogstadius <Ja...@who-umc.org>.
Hi Sean,
Many thanks for your reply. Like you say, I see both the lookup descriptors and all other resources in the projects on the svn server (https://svn.apache.org/repos/asf/ctakes/trunk/). However, the -res jars that I get through maven are completely empty, except for their META-INF folders. For other components, their -res jars do contain their resources as expected. Could something have gone wrong while publishing recent versions of these two?
These are my relevant maven imports:
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup</artifactId>
<version>3.2.2</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup-res</artifactId>
<version>3.2.2</version>
</dependency> <dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup-fast</artifactId>
<version>3.2.2</version>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup-fast-res</artifactId>
<version>3.2.2</version>
</dependency>
Jar content:
http://grepcode.com/snapshot/repo1.maven.org/maven2/org.apache.ctakes/ctakes-dictionary-lookup-res/3.2.1/ http://grepcode.com/snapshot/repo1.maven.org/maven2/org.apache.ctakes/ctakes-dictionary-lookup-fast-res/3.2.1/
Jakob
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: den 9 juli 2015 19:54
To: dev@ctakes.apache.org
Subject: RE: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi Jakob,
Where those files exist really depends upon how you are trying to run. They start in src/main/resources/ directories in their respective -res projects.
If you are running from an IDE, make sure that the -res modules have been added to your project, and that the src/main/resources/ directories have been tagged as resource directories. I'm not an Eclipse expert either (I don't use it), but if it imports via maven it should be doing that automatically, or maybe tagging them as source directories.
If you are running from a full build of the application, there should be a resources/ directory in your root. If that directory exists and contains the .xml files, either run the app from the root directory or set $CTAKES_HOME to point to that root.
If you run with today's build you should see a listing of your classpath upon that error - which may or may not help you find the problem.
Sean
-----Original Message-----
From: Jakob Rogstadius [mailto:Jakob.Rogstadius@who-umc.org]
Sent: Thursday, July 09, 2015 8:43 AM
To: dev@ctakes.apache.org
Subject: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi cTakes devs,
I am trying to use cTakes' UMLS Dictionary Lookup annotator (either the older one or the newer fast one) through uimaFIT, and I am running into problems with resources that can't be found. Please bear with me if my problem description omits any relevant details, as I don't have much experience neither with cTakes, UIMA, Java, Maven nor Eclipse.
cTakes is imported into my Eclipse project through Maven, and I have a very basic pipeline running with a few annotators from UIMA and cTakes, along with a few custom ones. I have specified the UMLS login details in the arguments of the Eclipse runtime configuration, which works. However, when I add either a UmlsDictionaryLookupAnnotator or its fast version, they fail to resolve their respective lookup descriptor files. I have included a stack trace for the first method, while the second method throws a null pointer exception on AbstractJCasTermAnnotator.initialize() (line 129), due to the fileResource variable being null.
I have noticed that since cTakes version 3.1.1, the lookup descriptor file referenced in UmlsDictionaryLookupAnnotator.createAnnotatorDescription() is no longer included in ctakes-dictionary-lookup-res-3.x.x.jar. I don't know if the same change took place for the fast dictionary, but I can see that the xml file referenced in DictionaryLookupFactory.createUmlsDictionaryLookupDescription() is not present in the ctakes-dictionary-lookup-fast-res-3.2.2.jar that I get through Maven. Have these files moved, so that I now need to include something else? Am I doing something else wrong?
Also, I have downloaded the UMLS dictionary resources from https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.apache.org_downloads.cgi&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=HSSKy6iWmdl_k4qE22gY7Kb6oTqcfm2ZxVdjOzcjPyc&s=JO8tKCrrsRQMpvAb1evFEHf21pc1SFE7AjXaQGZEyIg&e= , but where do I place them for cTakes to be able to find them?
Stack trace for UmlsDictionaryLookupAnnotator.createAnnotatorDescription():
java.io.FileNotFoundException: No File exists at org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:118)
at org.umc.research.social_media_adr_detection.pipelines.ExtractDrugAndAEMentions.main(ExtractDrugAndAEMentions.java:128)
Exception in thread "main" org.apache.uima.resource.ResourceInitializationException
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:156)
at org.umc.research.social_media_adr_detection.pipelines.ExtractDrugAndAEMentions.main(ExtractDrugAndAEMentions.java:128)
Caused by: java.io.FileNotFoundException: No File exists at org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:118)
... 1 more
Any pointers would be greatly appreciated.
Best regards,
Jakob Rogstadius
Research Engineer
Uppsala Monitoring Centre
WHO Collaborating Centre for International Drug Monitoring
RE: Cannot resolve lookup descriptor files for
UmlsDictionaryLookupAnnotator
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Jakob,
Where those files exist really depends upon how you are trying to run. They start in src/main/resources/ directories in their respective -res projects.
If you are running from an IDE, make sure that the -res modules have been added to your project, and that the src/main/resources/ directories have been tagged as resource directories. I'm not an Eclipse expert either (I don't use it), but if it imports via maven it should be doing that automatically, or maybe tagging them as source directories.
If you are running from a full build of the application, there should be a resources/ directory in your root. If that directory exists and contains the .xml files, either run the app from the root directory or set $CTAKES_HOME to point to that root.
If you run with today's build you should see a listing of your classpath upon that error - which may or may not help you find the problem.
Sean
-----Original Message-----
From: Jakob Rogstadius [mailto:Jakob.Rogstadius@who-umc.org]
Sent: Thursday, July 09, 2015 8:43 AM
To: dev@ctakes.apache.org
Subject: Cannot resolve lookup descriptor files for UmlsDictionaryLookupAnnotator
Hi cTakes devs,
I am trying to use cTakes' UMLS Dictionary Lookup annotator (either the older one or the newer fast one) through uimaFIT, and I am running into problems with resources that can't be found. Please bear with me if my problem description omits any relevant details, as I don't have much experience neither with cTakes, UIMA, Java, Maven nor Eclipse.
cTakes is imported into my Eclipse project through Maven, and I have a very basic pipeline running with a few annotators from UIMA and cTakes, along with a few custom ones. I have specified the UMLS login details in the arguments of the Eclipse runtime configuration, which works. However, when I add either a UmlsDictionaryLookupAnnotator or its fast version, they fail to resolve their respective lookup descriptor files. I have included a stack trace for the first method, while the second method throws a null pointer exception on AbstractJCasTermAnnotator.initialize() (line 129), due to the fileResource variable being null.
I have noticed that since cTakes version 3.1.1, the lookup descriptor file referenced in UmlsDictionaryLookupAnnotator.createAnnotatorDescription() is no longer included in ctakes-dictionary-lookup-res-3.x.x.jar. I don't know if the same change took place for the fast dictionary, but I can see that the xml file referenced in DictionaryLookupFactory.createUmlsDictionaryLookupDescription() is not present in the ctakes-dictionary-lookup-fast-res-3.2.2.jar that I get through Maven. Have these files moved, so that I now need to include something else? Am I doing something else wrong?
Also, I have downloaded the UMLS dictionary resources from https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.apache.org_downloads.cgi&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=HSSKy6iWmdl_k4qE22gY7Kb6oTqcfm2ZxVdjOzcjPyc&s=JO8tKCrrsRQMpvAb1evFEHf21pc1SFE7AjXaQGZEyIg&e= , but where do I place them for cTakes to be able to find them?
Stack trace for UmlsDictionaryLookupAnnotator.createAnnotatorDescription():
java.io.FileNotFoundException: No File exists at org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:118)
at org.umc.research.social_media_adr_detection.pipelines.ExtractDrugAndAEMentions.main(ExtractDrugAndAEMentions.java:128)
Exception in thread "main" org.apache.uima.resource.ResourceInitializationException
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:156)
at org.umc.research.social_media_adr_detection.pipelines.ExtractDrugAndAEMentions.main(ExtractDrugAndAEMentions.java:128)
Caused by: java.io.FileNotFoundException: No File exists at org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.createAnnotatorDescription(UmlsDictionaryLookupAnnotator.java:118)
... 1 more
Any pointers would be greatly appreciated.
Best regards,
Jakob Rogstadius
Research Engineer
Uppsala Monitoring Centre
WHO Collaborating Centre for International Drug Monitoring