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
<[email protected]<mailto:[email protected]>>
Reply-To:
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Date: Thursday, January 10, 2013 17:42
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
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:
