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" <[email protected]> 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:
