RE: build tool suggestion

2015-05-06 Thread Finan, Sean 
Your IDE should have settings that allow custom warnings.  Also check out 
findbugs -- http://en.wikipedia.org/wiki/FindBugs

There might be a configurable maven plugin.  

It is a process ...

-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] 
Sent: Tuesday, May 05, 2015 8:01 PM
To: dev@ctakes.apache.org
Subject: build tool suggestion


Do you know offhand, would it be easy to have something run at build time that 
flags uses of FileReader?

Related - do we have anything at build time that produces warnings that are 
looked at?  When I check in a change, I just check whether the next build is 
successful or not.  I don't look for warnings other than what I see when I try 
a compile of my own on my own system.  Ideally I think it would be good to have 
the use of FileReader cause a meaningful warning.  But if there's no relatively 
easy way to do that, might we consider having it cause a build failure?  I 
think the benefits would outweigh the drawbacks.

-- James


From: Chen, Pei [pei.c...@childrens.harvard.edu]
Sent: Tuesday, May 05, 2015 5:55 PM
To: dev@ctakes.apache.org
Subject: RE: svn commit: r1677903 - in 
/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2:
 concept/BsvConceptFactory.java dictionary/BsvRareWordDictionary.java 
util/JdbcConnectionFactory.java

Can we use InputStreamReader instead of FileReader?
That way the resource can also be read from within a jar (potentially from 
maven central, etc.) and doesn't have to be fixed to a physical file...

i.e.
Instead of new BufferedReader(new FileReader(path)) new BufferedReader(new 
InputStreamReader(FileLocator.getAsStream(path)))

--Pei

-Original Message-
From: seanfi...@apache.org [mailto:seanfi...@apache.org]
Sent: Tuesday, May 05, 2015 6:42 PM
To: comm...@ctakes.apache.org
Subject: svn commit: r1677903 - in 
/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2:
 concept/BsvConceptFactory.java dictionary/BsvRareWordDictionary.java 
util/JdbcConnectionFactory.java

Author: seanfinan
Date: Tue May  5 22:41:26 2015
New Revision: 1677903

URL: 
https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_r1677903d=BQICaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WYm=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIags=wuwFl1DxU-yGWdGewROupvowHfYFay_u5LYKJUJF2VAe=
Log:
Use FileLocator to find BSV dictionaries

Modified:

ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java

ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java

ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java

Modified: 
ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java
URL: 
https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Ddictionary-2Dlookup-2Dfast_src_main_java_org_apache_ctakes_dictionary_lookup2_concept_BsvConceptFactory.java-3Frev-3D1677903-26r1-3D1677902-26r2-3D1677903-26view-3Ddiffd=BQICaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WYm=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIags=N_IOanbEYnXUTZ4ZO3vIjOeYun186kZGjXPKWp-Wi7ke=
==
--- 
ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java
 (original)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/
+++ ctakes/dictionary/lookup2/concept/BsvConceptFactory.java Tue May  5
+++ 22:41:26 2015
@@ -1,5 +1,6 @@
 package org.apache.ctakes.dictionary.lookup2.concept;

+import org.apache.ctakes.core.resource.FileLocator;
 import org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil;
 import org.apache.ctakes.dictionary.lookup2.util.LookupUtil;
 import org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil;
@@ -34,11 +35,12 @@ final public class BsvConceptFactory imp
}

public BsvConceptFactory( final String name, final String bsvFilePath ) {
-  this( name, new File( bsvFilePath ) );
-   }
-
-   public BsvConceptFactory( final String name, final File bsvFile ) {
-  final CollectionCuiTuiTerm cuiTuiTerms = parseBsvFile( bsvFile );
+//  this( name, new File( bsvFilePath ) );
+//   }
+//
+//   public BsvConceptFactory( final String name, final File bsvFile ) {
+//  final CollectionCuiTuiTerm cuiTuiTerms = parseBsvFile( bsvFile );
+  final CollectionCuiTuiTerm cuiTuiTerms = parseBsvFile( 
+bsvFilePath );
   final MapLong, Concept conceptMap = new HashMap( cuiTuiTerms.size() 
);
   for ( CuiTuiTerm cuiTuiTerm : cuiTuiTerms ) {

cTAKES - Smoking Status

2015-05-06 Thread Bohne, Jacqueline R 
We are trying to implement the Smoking Status pipeline at our site.  We have it 
up and running, but we're finding that TOBACCO: NONE is being incorrectly 
classified as a CURRENT_SMOKER.  I looked at the documentation and it appears 
that the SentenceAdjuster should be handling this situation?  I ran the 
pipeline in the CVD and when I remove the : the smoking status is correctly 
classified.

I am running the SimulatedProdAggregateTAE and the only customization I made 
was to change the TypeSystem file to have a lowercase s in the file name.

Is there a piece I am missing somewhere?  Any ideas?

Thank you!

Thank you,
Jacquie Bohne
Software Development Team Lead
BIRC - Research Analytics
bohne.jacquel...@mcrf.mfldclin.edumailto:bohne.jacquel...@mcrf.mfldclin.edu
715-221-6436 or 1-6436


__
The contents of this message may contain private, protected and/or privileged 
information.  If you received this message in error, you should destroy the 
e-mail message and any attachments or copies, and you are prohibited from 
retaining, distributing, disclosing or using any information contained within.  
Please contact the sender and advise of the erroneous delivery by return e-mail 
or telephone.  Thank you for your cooperation.

RE: build tool suggestion

2015-05-06 Thread Finan, Sean 
I understood that.  I check warnings before checkin.  You can do a search for 
something like https://wiki.jenkins-ci.org/display/JENKINS/Warnings+Plugin

-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] 
Sent: Wednesday, May 06, 2015 10:58 AM
To: 'dev@ctakes.apache.org'
Subject: RE: build tool suggestion


Sorry, I wasn't clear, when I said at build time, I meant the Jenkins 
automated build. 


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] 
Sent: Wednesday, May 06, 2015 9:52 AM
To: dev@ctakes.apache.org
Subject: RE: build tool suggestion

Your IDE should have settings that allow custom warnings.  Also check out 
findbugs -- 
https://urldefense.proofpoint.com/v2/url?u=http-3A__en.wikipedia.org_wiki_FindBugsd=BQIFAgc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=lQlT1hCegc_WtmY10BMmAxiwIIHNxqohrwW7CfGCFq8s=OQDh6ra47IQjNVh7WZteWKCf_xeSae36jIo_qcjxfS8e=
 

There might be a configurable maven plugin.  

It is a process ...

-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] 
Sent: Tuesday, May 05, 2015 8:01 PM
To: dev@ctakes.apache.org
Subject: build tool suggestion


Do you know offhand, would it be easy to have something run at build time that 
flags uses of FileReader?

Related - do we have anything at build time that produces warnings that are 
looked at?  When I check in a change, I just check whether the next build is 
successful or not.  I don't look for warnings other than what I see when I try 
a compile of my own on my own system.  Ideally I think it would be good to have 
the use of FileReader cause a meaningful warning.  But if there's no relatively 
easy way to do that, might we consider having it cause a build failure?  I 
think the benefits would outweigh the drawbacks.

-- James


From: Chen, Pei [pei.c...@childrens.harvard.edu]
Sent: Tuesday, May 05, 2015 5:55 PM
To: dev@ctakes.apache.org
Subject: RE: svn commit: r1677903 - in 
/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2:
 concept/BsvConceptFactory.java dictionary/BsvRareWordDictionary.java 
util/JdbcConnectionFactory.java

Can we use InputStreamReader instead of FileReader?
That way the resource can also be read from within a jar (potentially from 
maven central, etc.) and doesn't have to be fixed to a physical file...

i.e.
Instead of new BufferedReader(new FileReader(path)) new BufferedReader(new 
InputStreamReader(FileLocator.getAsStream(path)))

--Pei

-Original Message-
From: seanfi...@apache.org [mailto:seanfi...@apache.org]
Sent: Tuesday, May 05, 2015 6:42 PM
To: comm...@ctakes.apache.org
Subject: svn commit: r1677903 - in 
/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2:
 concept/BsvConceptFactory.java dictionary/BsvRareWordDictionary.java 
util/JdbcConnectionFactory.java

Author: seanfinan
Date: Tue May  5 22:41:26 2015
New Revision: 1677903

URL: 
https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_r1677903d=BQICaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WYm=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIags=wuwFl1DxU-yGWdGewROupvowHfYFay_u5LYKJUJF2VAe=
Log:
Use FileLocator to find BSV dictionaries

Modified:

ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java

ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java

ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java

Modified: 
ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java
URL: 
https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Ddictionary-2Dlookup-2Dfast_src_main_java_org_apache_ctakes_dictionary_lookup2_concept_BsvConceptFactory.java-3Frev-3D1677903-26r1-3D1677902-26r2-3D1677903-26view-3Ddiffd=BQICaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WYm=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIags=N_IOanbEYnXUTZ4ZO3vIjOeYun186kZGjXPKWp-Wi7ke=
==
--- 
ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java
 (original)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/
+++ ctakes/dictionary/lookup2/concept/BsvConceptFactory.java Tue May  5
+++ 22:41:26 2015
@@ -1,5 +1,6 @@
 package org.apache.ctakes.dictionary.lookup2.concept;

+import org.apache.ctakes.core.resource.FileLocator;
 import org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil;
 import

Re: build tool suggestion

2015-05-06 Thread Kim Ebert 
Would this only be for the Jenkins build?

I would prefer not to have this as part of the regular Maven build.

On Tue, May 5, 2015 at 6:00 PM, Masanz, James J. masanz.ja...@mayo.edu
wrote:


 Do you know offhand, would it be easy to have something run at build time
 that flags uses of FileReader?

 Related - do we have anything at build time that produces warnings that
 are looked at?  When I check in a change, I just check whether the next
 build is successful or not.  I don't look for warnings other than what I
 see when I try a compile of my own on my own system.  Ideally I think it
 would be good to have the use of FileReader cause a meaningful warning.
 But if there's no relatively easy way to do that, might we consider having
 it cause a build failure?  I think the benefits would outweigh the
 drawbacks.

 -- James

 
 From: Chen, Pei [pei.c...@childrens.harvard.edu]
 Sent: Tuesday, May 05, 2015 5:55 PM
 To: dev@ctakes.apache.org
 Subject: RE: svn commit: r1677903 - in
 /ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2:
 concept/BsvConceptFactory.java dictionary/BsvRareWordDictionary.java
 util/JdbcConnectionFactory.java

 Can we use InputStreamReader instead of FileReader?
 That way the resource can also be read from within a jar (potentially from
 maven central, etc.) and doesn't have to be fixed to a physical file...

 i.e.
 Instead of new BufferedReader(new FileReader(path))
 new BufferedReader(new InputStreamReader(FileLocator.getAsStream(path)))

 --Pei

 -Original Message-
 From: seanfi...@apache.org [mailto:seanfi...@apache.org]
 Sent: Tuesday, May 05, 2015 6:42 PM
 To: comm...@ctakes.apache.org
 Subject: svn commit: r1677903 - in
 /ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2:
 concept/BsvConceptFactory.java dictionary/BsvRareWordDictionary.java
 util/JdbcConnectionFactory.java

 Author: seanfinan
 Date: Tue May  5 22:41:26 2015
 New Revision: 1677903

 URL:
 https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_r1677903d=BQICaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WYm=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIags=wuwFl1DxU-yGWdGewROupvowHfYFay_u5LYKJUJF2VAe=
 Log:
 Use FileLocator to find BSV dictionaries

 Modified:

 ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java

 ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java

 ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java

 Modified:
 ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java
 URL:
 https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Ddictionary-2Dlookup-2Dfast_src_main_java_org_apache_ctakes_dictionary_lookup2_concept_BsvConceptFactory.java-3Frev-3D1677903-26r1-3D1677902-26r2-3D1677903-26view-3Ddiffd=BQICaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WYm=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIags=N_IOanbEYnXUTZ4ZO3vIjOeYun186kZGjXPKWp-Wi7ke=

 ==
 ---
 ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java
 (original)
 +++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/
 +++ ctakes/dictionary/lookup2/concept/BsvConceptFactory.java Tue May  5
 +++ 22:41:26 2015
 @@ -1,5 +1,6 @@
  package org.apache.ctakes.dictionary.lookup2.concept;

 +import org.apache.ctakes.core.resource.FileLocator;
  import org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil;
  import org.apache.ctakes.dictionary.lookup2.util.LookupUtil;
  import org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil;
 @@ -34,11 +35,12 @@ final public class BsvConceptFactory imp
 }

 public BsvConceptFactory( final String name, final String bsvFilePath
 ) {
 -  this( name, new File( bsvFilePath ) );
 -   }
 -
 -   public BsvConceptFactory( final String name, final File bsvFile ) {
 -  final CollectionCuiTuiTerm cuiTuiTerms = parseBsvFile( bsvFile );
 +//  this( name, new File( bsvFilePath ) );
 +//   }
 +//
 +//   public BsvConceptFactory( final String name, final File bsvFile ) {
 +//  final CollectionCuiTuiTerm cuiTuiTerms = parseBsvFile( bsvFile
 );
 +  final CollectionCuiTuiTerm cuiTuiTerms = parseBsvFile(
 +bsvFilePath );
final MapLong, Concept conceptMap = new HashMap(
 cuiTuiTerms.size() );
for ( CuiTuiTerm cuiTuiTerm : cuiTuiTerms ) {
   final CollectionMapConceptCode, String, ? extends
 CollectionString codes @@ -90,11 +92,21 @@ final public class

RE: build tool suggestion

2015-05-06 Thread Masanz, James J. 

Sorry, I wasn't clear, when I said at build time, I meant the Jenkins 
automated build. 


-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] 
Sent: Wednesday, May 06, 2015 9:52 AM
To: dev@ctakes.apache.org
Subject: RE: build tool suggestion

Your IDE should have settings that allow custom warnings.  Also check out 
findbugs -- http://en.wikipedia.org/wiki/FindBugs

There might be a configurable maven plugin.  

It is a process ...

-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] 
Sent: Tuesday, May 05, 2015 8:01 PM
To: dev@ctakes.apache.org
Subject: build tool suggestion


Do you know offhand, would it be easy to have something run at build time that 
flags uses of FileReader?

Related - do we have anything at build time that produces warnings that are 
looked at?  When I check in a change, I just check whether the next build is 
successful or not.  I don't look for warnings other than what I see when I try 
a compile of my own on my own system.  Ideally I think it would be good to have 
the use of FileReader cause a meaningful warning.  But if there's no relatively 
easy way to do that, might we consider having it cause a build failure?  I 
think the benefits would outweigh the drawbacks.

-- James


From: Chen, Pei [pei.c...@childrens.harvard.edu]
Sent: Tuesday, May 05, 2015 5:55 PM
To: dev@ctakes.apache.org
Subject: RE: svn commit: r1677903 - in 
/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2:
 concept/BsvConceptFactory.java dictionary/BsvRareWordDictionary.java 
util/JdbcConnectionFactory.java

Can we use InputStreamReader instead of FileReader?
That way the resource can also be read from within a jar (potentially from 
maven central, etc.) and doesn't have to be fixed to a physical file...

i.e.
Instead of new BufferedReader(new FileReader(path)) new BufferedReader(new 
InputStreamReader(FileLocator.getAsStream(path)))

--Pei

-Original Message-
From: seanfi...@apache.org [mailto:seanfi...@apache.org]
Sent: Tuesday, May 05, 2015 6:42 PM
To: comm...@ctakes.apache.org
Subject: svn commit: r1677903 - in 
/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2:
 concept/BsvConceptFactory.java dictionary/BsvRareWordDictionary.java 
util/JdbcConnectionFactory.java

Author: seanfinan
Date: Tue May  5 22:41:26 2015
New Revision: 1677903

URL: 
https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_r1677903d=BQICaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WYm=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIags=wuwFl1DxU-yGWdGewROupvowHfYFay_u5LYKJUJF2VAe=
Log:
Use FileLocator to find BSV dictionaries

Modified:

ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java

ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java

ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java

Modified: 
ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java
URL: 
https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Ddictionary-2Dlookup-2Dfast_src_main_java_org_apache_ctakes_dictionary_lookup2_concept_BsvConceptFactory.java-3Frev-3D1677903-26r1-3D1677902-26r2-3D1677903-26view-3Ddiffd=BQICaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WYm=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIags=N_IOanbEYnXUTZ4ZO3vIjOeYun186kZGjXPKWp-Wi7ke=
==
--- 
ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java
 (original)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/
+++ ctakes/dictionary/lookup2/concept/BsvConceptFactory.java Tue May  5
+++ 22:41:26 2015
@@ -1,5 +1,6 @@
 package org.apache.ctakes.dictionary.lookup2.concept;

+import org.apache.ctakes.core.resource.FileLocator;
 import org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil;
 import org.apache.ctakes.dictionary.lookup2.util.LookupUtil;
 import org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil;
@@ -34,11 +35,12 @@ final public class BsvConceptFactory imp
}

public BsvConceptFactory( final String name, final String bsvFilePath ) {
-  this( name, new File( bsvFilePath ) );
-   }
-
-   public BsvConceptFactory( final String name, final File bsvFile ) {
-  final CollectionCuiTuiTerm cuiTuiTerms = parseBsvFile( bsvFile );
+//  this( name, new File( bsvFilePath ) );
+//   }
+//
+//   public BsvConceptFactory( final String name, final File bsvFile ) {
+//  final

RE: build tool suggestion

2015-05-06 Thread Masanz, James J. 

I was suggesting it only for the Jenkins build, so that people who might not 
want it as part of their own builds won't see it. But to catch people who might 
not have their own warning individually defined or who miss it in the warnings 
of their own build. 

-Original Message-
From: Kim Ebert [mailto:kim.eb...@perfectsearchcorp.com] 
Sent: Wednesday, May 06, 2015 10:13 AM
To: dev@ctakes.apache.org
Subject: Re: build tool suggestion

Would this only be for the Jenkins build?

I would prefer not to have this as part of the regular Maven build.

On Tue, May 5, 2015 at 6:00 PM, Masanz, James J. masanz.ja...@mayo.edu
wrote:


 Do you know offhand, would it be easy to have something run at build time
 that flags uses of FileReader?

 Related - do we have anything at build time that produces warnings that
 are looked at?  When I check in a change, I just check whether the next
 build is successful or not.  I don't look for warnings other than what I
 see when I try a compile of my own on my own system.  Ideally I think it
 would be good to have the use of FileReader cause a meaningful warning.
 But if there's no relatively easy way to do that, might we consider having
 it cause a build failure?  I think the benefits would outweigh the
 drawbacks.

 -- James

 
 From: Chen, Pei [pei.c...@childrens.harvard.edu]
 Sent: Tuesday, May 05, 2015 5:55 PM
 To: dev@ctakes.apache.org
 Subject: RE: svn commit: r1677903 - in
 /ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2:
 concept/BsvConceptFactory.java dictionary/BsvRareWordDictionary.java
 util/JdbcConnectionFactory.java

 Can we use InputStreamReader instead of FileReader?
 That way the resource can also be read from within a jar (potentially from
 maven central, etc.) and doesn't have to be fixed to a physical file...

 i.e.
 Instead of new BufferedReader(new FileReader(path))
 new BufferedReader(new InputStreamReader(FileLocator.getAsStream(path)))

 --Pei

 -Original Message-
 From: seanfi...@apache.org [mailto:seanfi...@apache.org]
 Sent: Tuesday, May 05, 2015 6:42 PM
 To: comm...@ctakes.apache.org
 Subject: svn commit: r1677903 - in
 /ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2:
 concept/BsvConceptFactory.java dictionary/BsvRareWordDictionary.java
 util/JdbcConnectionFactory.java

 Author: seanfinan
 Date: Tue May  5 22:41:26 2015
 New Revision: 1677903

 URL:
 https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_r1677903d=BQICaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WYm=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIags=wuwFl1DxU-yGWdGewROupvowHfYFay_u5LYKJUJF2VAe=
 Log:
 Use FileLocator to find BSV dictionaries

 Modified:

 ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java

 ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java

 ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java

 Modified:
 ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java
 URL:
 https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Ddictionary-2Dlookup-2Dfast_src_main_java_org_apache_ctakes_dictionary_lookup2_concept_BsvConceptFactory.java-3Frev-3D1677903-26r1-3D1677902-26r2-3D1677903-26view-3Ddiffd=BQICaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WYm=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIags=N_IOanbEYnXUTZ4ZO3vIjOeYun186kZGjXPKWp-Wi7ke=

 ==
 ---
 ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java
 (original)
 +++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/
 +++ ctakes/dictionary/lookup2/concept/BsvConceptFactory.java Tue May  5
 +++ 22:41:26 2015
 @@ -1,5 +1,6 @@
  package org.apache.ctakes.dictionary.lookup2.concept;

 +import org.apache.ctakes.core.resource.FileLocator;
  import org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil;
  import org.apache.ctakes.dictionary.lookup2.util.LookupUtil;
  import org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil;
 @@ -34,11 +35,12 @@ final public class BsvConceptFactory imp
 }

 public BsvConceptFactory( final String name, final String bsvFilePath
 ) {
 -  this( name, new File( bsvFilePath ) );
 -   }
 -
 -   public BsvConceptFactory( final String name, final File bsvFile ) {
 -  final CollectionCuiTuiTerm cuiTuiTerms = parseBsvFile( bsvFile );
 +//  this( name, new File( bsvFilePath ) );
 +//   }
 +//
 +//   public BsvConceptFactory( final String name, final