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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: cTAKES Groovy...
Date Fri, 06 Dec 2013 17:12:46 GMT
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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