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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...
Thread-Index: Ac7q9KBJFv2IYr9mQtyV356nZun8sQALbdTwAByH4OABaCbogABbxd+gAACEj7A=
Date: Fri, 6 Dec 2013 17:12:46 +0000
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FYI, the groovy error I was getting was a typo on my part

I had this:
out >> new URL(url).openStream()
instead of=20
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=3Dmayo.edu@ctakes.apache.org [mailto:dev=
-return-2286-Masanz.James=3Dmayo.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 resour=
ces, or post it somewhere temporarily.=20

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/s=
rc/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.n=
et.www.protocol.http.HttpURLConnection$HttpInputStream) values: [sun.net.ww=
w.protocol.http.HttpURLConnection$HttpInputStream@74be95bf]
Possible solutions: leftShift(java.lang.Object), leftShift(java.io.InputStr=
eam), leftShift([B)
groovy.lang.MissingMethodException: No signature of method: java.io.Buffere=
dOutputStream.rightShift() is applicable for argument types: (sun.net.www.p=
rotocol.http.HttpURLConnection$HttpInputStream) values: [sun.net.www.protoc=
ol.http.HttpURLConnection$HttpInputStream@74be95bf]
Possible solutions: leftShift(java.lang.Object), leftShift(java.io.InputStr=
eam), 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 Wi=
n7?

-- James


-----Original Message-----
From: dev-return-2270-Masanz.James=3Dmayo.edu@ctakes.apache.org [mailto:dev=
-return-2270-Masanz.James=3Dmayo.edu@ctakes.apache.org] On Behalf Of Tim Mi=
ller
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-p=
ipeline 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 belon=
g 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=20
> (IN of) (NP (NP (NN aspirin)) (PP (IN for) (NP (NP (NN pain)) (PP-LOC=20
> (IN in) (NP (NN knee)))))))))(. .)))
>
> Maybe we could create one that will output UMLS CUI/Codes... and then oth=
ers 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=20
>> fantastic build/deployment/dependency management tool that is in many=20
>> ways much nicer to work with than Maven, though it plays nicely with=20
>> Maven (for example, it can use Maven repositories). Gradle is also prove=
n 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=20
>> 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=20
>> 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