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
<[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:
