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From: "Masanz, James J." <Masanz.James@mayo.edu>
To: "'dev@ctakes.apache.org'" <dev@ctakes.apache.org>
Subject: RE: cTAKES Groovy...
Thread-Topic: cTAKES Groovy...
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Date: Fri, 6 Dec 2013 17:37:27 +0000
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Sounds good to me. Thanks!

-----Original Message-----
From: dev-return-2289-Masanz.James=3Dmayo.edu@ctakes.apache.org [mailto:dev=
-return-2289-Masanz.James=3Dmayo.edu@ctakes.apache.org] On Behalf Of Tim Mi=
ller
Sent: Friday, December 06, 2013 11:36 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES Groovy...

Sure, I checked it in under=20
ctakes-constituency-parser/scripts/groovy/parser.groovy per my=20
understanding of the thread from a few days go about where to put these=20
things.
Tim

On 12/06/2013 12:03 PM, Masanz, James J. wrote:
> Tim, could you check that change in you made to not download the big reso=
urces, or post it somewhere temporarily.
>
> I'm having this issue when trying to run the  groovy script (I'm on Windo=
ws 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.InputS=
tream), leftShift([B)
> groovy.lang.MissingMethodException: No signature of method: java.io.Buffe=
redOutputStream.rightShift() is applicable for argument types: (sun.net.www=
.protocol.http.HttpURLConnection$HttpInputStream) values: [sun.net.www.prot=
ocol.http.HttpURLConnection$HttpInputStream@74be95bf]
> Possible solutions: leftShift(java.lang.Object), leftShift(java.io.InputS=
tream), 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=3Dmayo.edu@ctakes.apache.org [mailto:d=
ev-return-2270-Masanz.James=3Dmayo.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 whic=
h 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 referenc=
e 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 o=
r can we maybe put groovy scripts somewhere alongside the projects they bel=
ong to? Maybe in the scripts/ directory or scripts/groovy, scripts/perl, et=
c.? 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 ot=
hers 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 prov=
en 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