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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: cTAKES Groovy...
Date Fri, 06 Dec 2013 20:01:22 GMT

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.edu@ctakes.apache.org [mailto:dev-return-2295-Masanz.James=mayo.edu@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.miller@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.edu@ctakes.apache.org 
> [mailto:dev-return-2288-Masanz.James=mayo.edu@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.James@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.edu@ctakes.apache.org [mailto:dev-return-2286-Masanz.James=mayo.edu@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.edu@ctakes.apache.org 
> [mailto:dev-return-2270-Masanz.James=mayo.edu@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:wkt@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.Chen@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


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