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....@ctakes.apache.org
[mailto:dev-return-2288-Masanz.James=mayo....@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.ja...@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....@ctakes.apache.org
[mailto:dev-return-2286-Masanz.James=mayo....@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....@ctakes.apache.org
[mailto:dev-return-2270-Masanz.James=mayo....@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:w...@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.c...@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
