You are viewing a plain text version of this content. The canonical link for it is here.
Posted to dev@ctakes.apache.org by "Coarr, Matt" <mc...@mitre.org> on 2013/01/18 19:32:10 UTC
Re: Failure on unpack-dependencies? [ctakes-dictionary-lookup
problem with rxnorm_index]
Tim, did you ever manage to get this working? Does anyone else have any ideas on this problem?
I'm trying to run the full pipeline on the ctakes trunk and I'm running into the same issue — rxnorm_index isn't found when initializing the dictionary lookup AE.
I also tried Pei's suggestion of cleaning and rebuilding. I tried both in eclipse (Project menu -> "clean…", then choose to clean all the project, and let eclipse automatically rebuild), and on the command-line ("mvn clean compile" from the root project).
I'll comment on my attempt from the command-line here…
I can see that it's trying to extract the dependency for "ctakes-resources-umls2011ab-3.1.0.jar". This jar file does have the rxnorm_index in the appropriate location, but the ctakes-dictionary-lookup/target/classes directory does not have any rxnorm_index directory. Again, this is true from a clean-then-build either from eclipse or the command-line.
Here's a fragment from the maven output (note the line that starts with "Unpacking…").
Here's the maven output:
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES dictionary lookup 3.1.0-incubating-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-dictionary-lookup ---
[INFO] Deleting /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target
[INFO]
[INFO] --- maven-remote-resources-plugin:1.3:process (default) @ ctakes-dictionary-lookup ---
[INFO]
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-dictionary-lookup ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 80 resources
[INFO] Copying 3 resources
[INFO]
[INFO] --- maven-dependency-plugin:2.6:unpack-dependencies (unpack-dependencies) @ ctakes-dictionary-lookup ---
[INFO] Unpacking /Users/mcoarr/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-umls2011ab/3.1.0/ctakes-resources-umls2011ab-3.1.0.jar to /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target/classes with includes "" and excludes ""
[INFO]
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-dictionary-lookup ---
[INFO] Compiling 58 source files to /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target/classes
Thanks!
Matt
From: Tim Miller <ti...@childrens.harvard.edu>>
Reply-To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
Date: Thursday, January 10, 2013 17:42
To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
Subject: Re: Failure on unpack-dependencies?
I'm having some trouble with this issue on trunk using eclipse. When I
try to run the default pipeline in the cvd it can't find the rxnorm_index:
Re: Failure on unpack-dependencies? [ctakes-dictionary-lookup
problem with rxnorm_index]
Posted by "Coarr, Matt" <mc...@mitre.org>.
Thanks Tim, Sean, and Pei!
After a few full builds of ctakes from the command-line, it actually did the extraction.
If it happens again, I'll just manually extract it until the issue is resolved.
Thanks for the quick help!!
Matt
From: Tim Miller <ti...@childrens.harvard.edu>>
Reply-To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
Date: Friday, January 18, 2013 13:55
To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
Subject: Re: Failure on unpack-dependencies? [ctakes-dictionary-lookup problem with rxnorm_index]
I can get it working with Pei's suggestion of doing mvn clean compile
from the command line. It is usually ok then even as I make other
changes to other projects, and then eventually at some point blows it
away (maybe when I do a project-wide maven update?).
Tim
Re: Failure on unpack-dependencies? [ctakes-dictionary-lookup problem
with rxnorm_index]
Posted by Tim Miller <ti...@childrens.harvard.edu>.
I can get it working with Pei's suggestion of doing mvn clean compile
from the command line. It is usually ok then even as I make other
changes to other projects, and then eventually at some point blows it
away (maybe when I do a project-wide maven update?).
Tim
On 01/18/2013 01:32 PM, Coarr, Matt wrote:
> Tim, did you ever manage to get this working? Does anyone else have any ideas on this problem?
>
> I'm trying to run the full pipeline on the ctakes trunk and I'm running into the same issue — rxnorm_index isn't found when initializing the dictionary lookup AE.
>
> I also tried Pei's suggestion of cleaning and rebuilding. I tried both in eclipse (Project menu -> "clean…", then choose to clean all the project, and let eclipse automatically rebuild), and on the command-line ("mvn clean compile" from the root project).
>
> I'll comment on my attempt from the command-line here…
>
> I can see that it's trying to extract the dependency for "ctakes-resources-umls2011ab-3.1.0.jar". This jar file does have the rxnorm_index in the appropriate location, but the ctakes-dictionary-lookup/target/classes directory does not have any rxnorm_index directory. Again, this is true from a clean-then-build either from eclipse or the command-line.
>
> Here's a fragment from the maven output (note the line that starts with "Unpacking…").
>
> Here's the maven output:
>
> [INFO] ------------------------------------------------------------------------
> [INFO] Building Apache cTAKES dictionary lookup 3.1.0-incubating-SNAPSHOT
> [INFO] ------------------------------------------------------------------------
> [INFO]
> [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-dictionary-lookup ---
> [INFO] Deleting /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target
> [INFO]
> [INFO] --- maven-remote-resources-plugin:1.3:process (default) @ ctakes-dictionary-lookup ---
> [INFO]
> [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-dictionary-lookup ---
> [debug] execute contextualize
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] Copying 80 resources
> [INFO] Copying 3 resources
> [INFO]
> [INFO] --- maven-dependency-plugin:2.6:unpack-dependencies (unpack-dependencies) @ ctakes-dictionary-lookup ---
> [INFO] Unpacking /Users/mcoarr/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-umls2011ab/3.1.0/ctakes-resources-umls2011ab-3.1.0.jar to /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target/classes with includes "" and excludes ""
> [INFO]
> [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-dictionary-lookup ---
> [INFO] Compiling 58 source files to /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target/classes
>
> Thanks!
> Matt
>
> From: Tim Miller <ti...@childrens.harvard.edu>>
> Reply-To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
> Date: Thursday, January 10, 2013 17:42
> To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
> Subject: Re: Failure on unpack-dependencies?
>
> I'm having some trouble with this issue on trunk using eclipse. When I
> try to run the default pipeline in the cvd it can't find the rxnorm_index:
RE: Failure on unpack-dependencies? [ctakes-dictionary-lookup
problem with rxnorm_index]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Yes, it is the Lucene problem re: reading from a jar. Get rid of that jar from your lib/ and make certain that your dictionary/lookup/ looks good.
Btw, this is Jira CTAKES-121
-----Original Message-----
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: Friday, January 18, 2013 1:46 PM
To: <ct...@incubator.apache.org>
Cc: ctakes-dev@incubator.apache.org
Subject: Re: Failure on unpack-dependencies? [ctakes-dictionary-lookup problem with rxnorm_index]
I wonder if its worth it to update the instructions to just unzip it manually. Probably more complicated to try to do it automatically do it with the plugins...
Or remove the requirement to unpack jars (I think it was a Lucene limitation not be able to read from a jar file)
Sent from my iPhone
On Jan 18, 2013, at 1:32 PM, "Coarr, Matt" <mc...@mitre.org> wrote:
> Tim, did you ever manage to get this working? Does anyone else have any ideas on this problem?
>
> I'm trying to run the full pipeline on the ctakes trunk and I'm running into the same issue - rxnorm_index isn't found when initializing the dictionary lookup AE.
>
> I also tried Pei's suggestion of cleaning and rebuilding. I tried both in eclipse (Project menu -> "clean...", then choose to clean all the project, and let eclipse automatically rebuild), and on the command-line ("mvn clean compile" from the root project).
>
> I'll comment on my attempt from the command-line here...
>
> I can see that it's trying to extract the dependency for "ctakes-resources-umls2011ab-3.1.0.jar". This jar file does have the rxnorm_index in the appropriate location, but the ctakes-dictionary-lookup/target/classes directory does not have any rxnorm_index directory. Again, this is true from a clean-then-build either from eclipse or the command-line.
>
> Here's a fragment from the maven output (note the line that starts with "Unpacking...").
>
> Here's the maven output:
>
> [INFO]
> ----------------------------------------------------------------------
> -- [INFO] Building Apache cTAKES dictionary lookup
> 3.1.0-incubating-SNAPSHOT [INFO]
> ----------------------------------------------------------------------
> --
> [INFO]
> [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @
> ctakes-dictionary-lookup --- [INFO] Deleting
> /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target
> [INFO]
> [INFO] --- maven-remote-resources-plugin:1.3:process (default) @
> ctakes-dictionary-lookup --- [INFO] [INFO] ---
> maven-resources-plugin:2.5:resources (default-resources) @
> ctakes-dictionary-lookup --- [debug] execute contextualize [INFO]
> Using 'UTF-8' encoding to copy filtered resources.
> [INFO] Copying 80 resources
> [INFO] Copying 3 resources
> [INFO]
> [INFO] --- maven-dependency-plugin:2.6:unpack-dependencies
> (unpack-dependencies) @ ctakes-dictionary-lookup --- [INFO] Unpacking /Users/mcoarr/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-umls2011ab/3.1.0/ctakes-resources-umls2011ab-3.1.0.jar to /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target/classes with includes "" and excludes ""
> [INFO]
> [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @
> ctakes-dictionary-lookup --- [INFO] Compiling 58 source files to
> /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target
> /classes
>
> Thanks!
> Matt
>
> From: Tim Miller
> <timothy.miller@childrens.harvard.edu<mailto:timothy.miller@childrens.
> harvard.edu>>
> Reply-To:
> "ctakes-dev@incubator.apache.org<mailto:ctakes-dev@incubator.apache.or
> g>"
> <ctakes-dev@incubator.apache.org<mailto:ctakes-dev@incubator.apache.or
> g>>
> Date: Thursday, January 10, 2013 17:42
> To:
> "ctakes-dev@incubator.apache.org<mailto:ctakes-dev@incubator.apache.or
> g>"
> <ctakes-dev@incubator.apache.org<mailto:ctakes-dev@incubator.apache.or
> g>>
> Subject: Re: Failure on unpack-dependencies?
>
> I'm having some trouble with this issue on trunk using eclipse. When I
> try to run the default pipeline in the cvd it can't find the rxnorm_index:
Re: Failure on unpack-dependencies? [ctakes-dictionary-lookup
problem with rxnorm_index]
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
I wonder if its worth it to update the instructions to just unzip it manually. Probably more complicated to try to do it automatically do it with the plugins...
Or remove the requirement to unpack jars (I think it was a Lucene limitation not be able to read from a jar file)
Sent from my iPhone
On Jan 18, 2013, at 1:32 PM, "Coarr, Matt" <mc...@mitre.org> wrote:
> Tim, did you ever manage to get this working? Does anyone else have any ideas on this problem?
>
> I'm trying to run the full pipeline on the ctakes trunk and I'm running into the same issue — rxnorm_index isn't found when initializing the dictionary lookup AE.
>
> I also tried Pei's suggestion of cleaning and rebuilding. I tried both in eclipse (Project menu -> "clean…", then choose to clean all the project, and let eclipse automatically rebuild), and on the command-line ("mvn clean compile" from the root project).
>
> I'll comment on my attempt from the command-line here…
>
> I can see that it's trying to extract the dependency for "ctakes-resources-umls2011ab-3.1.0.jar". This jar file does have the rxnorm_index in the appropriate location, but the ctakes-dictionary-lookup/target/classes directory does not have any rxnorm_index directory. Again, this is true from a clean-then-build either from eclipse or the command-line.
>
> Here's a fragment from the maven output (note the line that starts with "Unpacking…").
>
> Here's the maven output:
>
> [INFO] ------------------------------------------------------------------------
> [INFO] Building Apache cTAKES dictionary lookup 3.1.0-incubating-SNAPSHOT
> [INFO] ------------------------------------------------------------------------
> [INFO]
> [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-dictionary-lookup ---
> [INFO] Deleting /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target
> [INFO]
> [INFO] --- maven-remote-resources-plugin:1.3:process (default) @ ctakes-dictionary-lookup ---
> [INFO]
> [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-dictionary-lookup ---
> [debug] execute contextualize
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] Copying 80 resources
> [INFO] Copying 3 resources
> [INFO]
> [INFO] --- maven-dependency-plugin:2.6:unpack-dependencies (unpack-dependencies) @ ctakes-dictionary-lookup ---
> [INFO] Unpacking /Users/mcoarr/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-umls2011ab/3.1.0/ctakes-resources-umls2011ab-3.1.0.jar to /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target/classes with includes "" and excludes ""
> [INFO]
> [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-dictionary-lookup ---
> [INFO] Compiling 58 source files to /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target/classes
>
> Thanks!
> Matt
>
> From: Tim Miller <ti...@childrens.harvard.edu>>
> Reply-To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
> Date: Thursday, January 10, 2013 17:42
> To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
> Subject: Re: Failure on unpack-dependencies?
>
> I'm having some trouble with this issue on trunk using eclipse. When I
> try to run the default pipeline in the cvd it can't find the rxnorm_index: