+1 for that. We should also address the TODO comment in there before release...
> On Dec 6, 2013, at 3:01 PM, "Masanz, James J." <masanz.ja...@mayo.edu> wrote: > > > Sounds like before publicizing any groovy scripts we need to have some > testing on clean Win and clean *nix systems. > > FYI, after I fixed the typo I had in the script on my Windows 7 machine where > I do cTAKES development (and hence has jwnl under my .m2) and set JAVA_OPTS > to have enough heap space, I have the groovy script running fine there. > > I have not solved my issues on my ubuntu server yet where > "Error grabbing Grapes -- [unresolved dependency: jwnl#jwnl;1.3.3: not found]" > > I'll try to get back to that another day. > > Thanks all for the help. > > -----Original Message----- > From: dev-return-2295-Masanz.James=mayo....@ctakes.apache.org > [mailto:dev-return-2295-Masanz.James=mayo....@ctakes.apache.org] On Behalf Of > Finan, Sean > Sent: Friday, December 06, 2013 1:46 PM > To: dev@ctakes.apache.org > Subject: RE: cTAKES Groovy... > > 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 >
