Hi James, As Tim states > I have it in my .m2 directory And I think that is why it is working for Tim. You may -not- have the same version (if any) in your .m2 directory. I have had problems maintaining multiple dev versions of cTakes on a single machine because of maven's utilization of the .m2 cache directory. It is possible, but a pain. That was an aside ...
If you do end up having a library in your .m2, then it is possible that grape is not using it by default on your machine (though I don't know why). You can try the following from http://groovy.codehaus.org/Grape : If you find yourself wanting to reuse artifacts that you already have locally in your Maven2 repository, then you can add this line to your ~/.groovy/grapeConfig.xml: <ibiblio name="local" root="file:${user.home}/.m2/repository/" m2compatible="true"/> Anyway, it sounds like the script is not quite as standalone as it could be. -----Original Message----- From: Tim Miller [mailto:timothy.mil...@childrens.harvard.edu] Sent: Friday, December 06, 2013 2:19 PM To: dev@ctakes.apache.org Subject: Re: cTAKES Groovy... I have it in my .m2 directory timestamped October 2012. I believe the most recent versions of grape will look in m2 and grab from there if it exists. Tim On 12/06/2013 02:14 PM, Masanz, James J. wrote: > Thanks Sean. > > Something doesn't seem to be working for me related to getting dependencies. > > I did a wget of the parser.groovy that Tim just checked in today. > > Then trying to run that groovy script I get this error: > > $ groovy parser.groovy test-data-for-groovy/ > org.codehaus.groovy.control.MultipleCompilationErrorsException: startup > failed: > General error during conversion: Error grabbing Grapes -- [unresolved > dependency: jwnl#jwnl;1.3.3: not found] > java.lang.RuntimeException: Error grabbing Grapes -- [unresolved > dependency: jwnl#jwnl;1.3.3: not found] > > So I tried this (I'm no grape expert but a google search led to this > suggestion) but it fails: > $ grape -V resolve jwnl jwnl 1.3.3 > > I see the following issue was created by opennlp that looks related > https://issues.apache.org/jira/browse/OPENNLP-510 > saying that jwnl:jwnl 1.3.3 is no longer available (!) > > What I don't get is why no one else is seeing this error. > Maybe everyone else already had that in their local maven repos? Hard to > believe though given OPENNLP-510 is from May 2012. > > Fyi: > > $groovy --version > Groovy Version: 1.8.6 JVM: 1.6.0_27 Vendor: Sun Microsystems Inc. OS: > Linux > > > -----Original Message----- > From: dev-return-2288-Masanz.James=mayo....@ctakes.apache.org > [mailto:dev-return-2288-Masanz.James=mayo....@ctakes.apache.org] On > Behalf Of Finan, Sean > Sent: Friday, December 06, 2013 11:19 AM > To: dev@ctakes.apache.org > Subject: RE: cTAKES Groovy... > > Aside from a crash course almost 10 years ago, I haven't touched groovy very > much. However, if you are having issues with" shifts" and files, you can > look here: > > http://blog.retep.org/category/development/java/groovy/ > > He defines what he calls shift operators for the file operations. > > For all I know this is where Pei got his code, but it might be worth checking > if anybody runs into errors. > > -----Original Message----- > From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] > Sent: Friday, December 06, 2013 12:13 PM > To: 'dev@ctakes.apache.org' > Subject: RE: cTAKES Groovy... > > FYI, the groovy error I was getting was a typo on my part > > I had this: > out >> new URL(url).openStream() > instead of > out << new URL(url).openStream() > > so it was trying to do a shift operation of some sort > > -----Original Message----- > From: dev-return-2286-Masanz.James=mayo....@ctakes.apache.org > [mailto:dev-return-2286-Masanz.James=mayo....@ctakes.apache.org] On Behalf Of > Masanz, James J. > Sent: Friday, December 06, 2013 11:03 AM > To: 'dev@ctakes.apache.org' > Subject: RE: cTAKES Groovy... > > Tim, could you check that change in you made to not download the big > resources, or post it somewhere temporarily. > > I'm having this issue when trying to run the groovy script (I'm on Windows > 7, if that makes a difference) and having it faster might help debug. > > C:\using-groovy> groovy parser.groovy test-data-for-groovy > Reading from directory: test-data-for-groovy > Downloading: > http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-core-res/src/main/ > resources/org/apache/ctakes/core/sentdetect/sd-med-model.zip > Caught: groovy.lang.MissingMethodException: No signature of method: > java.io.BufferedOutputStream.rightShift() is applicable for argument > types: (sun.net.www.protocol.http.HttpURLConnection$HttpInputStream) > values: > [sun.net.www.protocol.http.HttpURLConnection$HttpInputStream@74be95bf] > Possible solutions: leftShift(java.lang.Object), > leftShift(java.io.InputStream), leftShift([B) > groovy.lang.MissingMethodException: No signature of method: > java.io.BufferedOutputStream.rightShift() is applicable for argument > types: (sun.net.www.protocol.http.HttpURLConnection$HttpInputStream) > values: > [sun.net.www.protocol.http.HttpURLConnection$HttpInputStream@74be95bf] > Possible solutions: leftShift(java.lang.Object), > leftShift(java.io.InputStream), leftShift([B) > at parser.downloadFile(parser.groovy:99) > at parser.run(parser.groovy:64) > > Anyone run into such an error from groovy? Anyone else running groovy on Win7? > > -- James > > > -----Original Message----- > From: dev-return-2270-Masanz.James=mayo....@ctakes.apache.org > [mailto:dev-return-2270-Masanz.James=mayo....@ctakes.apache.org] On > Behalf Of Tim Miller > Sent: Wednesday, December 04, 2013 9:09 AM > To: dev@ctakes.apache.org > Subject: Re: cTAKES Groovy... > > Very cool. I was noticing that it was downloading the umls resources which > the parser itself doesn't need -- so I made a change to not grab > clinical-pipeline and grab directly the things it was getting through that > reference and now it runs even faster with only a 35M initial download. > > I'd like to check in my change -- should we keep working out of sandbox or > can we maybe put groovy scripts somewhere alongside the projects they belong > to? Maybe in the scripts/ directory or scripts/groovy, scripts/perl, etc.? > Any opinions on this? > > Tim > > > On 11/27/2013 12:19 PM, Chen, Pei wrote: >> The sample constituency parser printer should be working now... >> Just copy and paste the text to parser.groovy and make it executable. >> All you should need is groovy installed on your machine. >> http://svn.apache.org/repos/asf/ctakes/sandbox/groovy/parser.groovy >> $ parser.groovy input >> Reading from directory: input >> (TOP (S (NP-SBJ (NN patient)) (VP (VBD took) (NP (NP (NNS 50mg)) >> (PP (IN of) (NP (NP (NN aspirin)) (PP (IN for) (NP (NP (NN pain)) >> (PP-LOC (IN in) (NP (NN knee)))))))))(. .))) >> >> Maybe we could create one that will output UMLS CUI/Codes... and then others >> could easily modify to their needs. >> >> --Pei >>> -----Original Message----- >>> From: William Karl Thompson [mailto:w...@northwestern.edu] >>> Sent: Tuesday, November 26, 2013 10:46 PM >>> To: dev@ctakes.apache.org >>> Subject: RE: cTAKES Groovy... >>> >>> That is very cool! >>> >>> Since we're talking Groovy, I'd just like make a plug for Gradle, a >>> fantastic build/deployment/dependency management tool that is in >>> many ways much nicer to work with than Maven, though it plays nicely >>> with Maven (for example, it can use Maven repositories). Gradle is also >>> proven technology: >>> it's the build tool for the Android operating system. >>> ________________________________________ >>> From: Chen, Pei [pei.c...@childrens.harvard.edu] >>> Sent: Tuesday, November 26, 2013 4:13 PM >>> To: dev@ctakes.apache.org >>> Subject: cTAKES Groovy... >>> >>> Tim had a good end user use case: >>> I just want to use the ctakes constituency parser and output the >>> tree text to console. >>> So I was inspired by Richard example of groovy... >>> Check out: >>> http://svn.apache.org/repos/asf/ctakes/sandbox/groovy/parser.groovy >>> >>> The groovy script will "Automagically" download the required >>> classes,jars,resources and automatically runs. >>> No longer requires the user to have any knowledge of UIMA, cTAKES, etc. >>> Sample: >>> $ parser.groovy input >>> Reading from directory: input >>> patient took 50mg of aspirin for pain in knee. >>> begin:0 end:48 >>> >>> Pretty cool, 'eh... >>> --Pei
