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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject Re: cTAKES Groovy...
Date Fri, 06 Dec 2013 18:53:40 GMT
I originally had it had pure java buffered file writer...
But this should work for win7 (tested)

Sent from my iPhone

> On Dec 6, 2013, at 12:09 PM, "Masanz, James J." <Masanz.James@mayo.edu> wrote:
> 
> 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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