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From Kim Ebert <kim.eb...@perfectsearchcorp.com>
Subject Re: build tool suggestion
Date Wed, 06 May 2015 15:12:37 GMT
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.James@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.Chen@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: seanfinan@apache.org [mailto:seanfinan@apache.org]
> Sent: Tuesday, May 05, 2015 6:42 PM
> To: commits@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_r1677903&d=BQICaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIag&s=wuwFl1DxU-yGWdGewROupvowHfYFay_u5LYKJUJF2VA&e=
> 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-3Ddiff&d=BQICaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIag&s=N_IOanbEYnXUTZ4ZO3vIjOeYun186kZGjXPKWp-Wi7k&e=
>
> ==============================================================================
> ---
> 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 Collection<CuiTuiTerm> cuiTuiTerms = parseBsvFile( bsvFile );
> +//      this( name, new File( bsvFilePath ) );
> +//   }
> +//
> +//   public BsvConceptFactory( final String name, final File bsvFile ) {
> +//      final Collection<CuiTuiTerm> cuiTuiTerms = parseBsvFile( bsvFile
> );
> +      final Collection<CuiTuiTerm> cuiTuiTerms = parseBsvFile(
> +bsvFilePath );
>        final Map<Long, Concept> conceptMap = new HashMap<>(
> cuiTuiTerms.size() );
>        for ( CuiTuiTerm cuiTuiTerm : cuiTuiTerms ) {
>           final CollectionMap<ConceptCode, String, ? extends
> Collection<String>> codes @@ -90,11 +92,21 @@ final public class
> BsvConceptFactory imp
>      * CUI|TUI|Text|PreferredTerm
>      * </p>
>      * If the TUI column is omitted then the entityId for the dictionary
> is used as the TUI
> +    * <p/>
> +    * //    * @param bsvFile file containing term rows and bsv columns
>      *
> -    * @param bsvFile file containing term rows and bsv columns
> +    * @param bsvFilePath file containing term rows and bsv columns
>      * @return collection of all valid terms read from the bsv file
>      */
> -   static private Collection<CuiTuiTerm> parseBsvFile( final File bsvFile
> ) {
> +//   static private Collection<CuiTuiTerm> parseBsvFile( final File
> bsvFile ) {
> +   static private Collection<CuiTuiTerm> parseBsvFile( final String
> bsvFilePath ) {
> +      File bsvFile = null;
> +      try {
> +         bsvFile = FileLocator.locateFile( bsvFilePath );
> +      } catch ( IOException ioE ) {
> +         ioE.getMessage();
> +         return Collections.emptyList();
> +      }
>        final Collection<CuiTuiTerm> cuiTuiTerms = new ArrayList<>();
>        try ( final BufferedReader reader = new BufferedReader( new
> FileReader( bsvFile ) ) ) {
>           String line = reader.readLine();
>
> Modified:
> ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.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_dictionary_BsvRareWordDictionary.java-3Frev-3D1677903-26r1-3D1677902-26r2-3D1677903-26view-3Ddiff&d=BQICaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIag&s=2mhfaak7geaJl8hCTk1LX9lWoSX7h9cRaSwYmnf6w0k&e=
>
> ==============================================================================
> ---
> ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java
> (original)
> +++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/
> +++ ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java Tue
> +++ May  5 22:41:26 2015
> @@ -18,6 +18,7 @@
>   */
>  package org.apache.ctakes.dictionary.lookup2.dictionary;
>
> +import org.apache.ctakes.core.resource.FileLocator;
>  import org.apache.ctakes.dictionary.lookup2.term.RareWordTerm;
>  import org.apache.ctakes.dictionary.lookup2.util.FastLookupToken;
>  import org.apache.ctakes.dictionary.lookup2.util.LookupUtil;
> @@ -31,6 +32,7 @@ import java.io.FileReader;  import java.io.IOException;
> import java.util.ArrayList;  import java.util.Collection;
> +import java.util.Collections;
>  import java.util.Properties;
>
>  import static
> org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator.CuiTerm;
> @@ -59,11 +61,12 @@ final public class BsvRareWordDictionary
>
>
>     public BsvRareWordDictionary( final String name, final String
> bsvFilePath ) {
> -      this( name, new File( bsvFilePath ) );
> -   }
> -
> -   public BsvRareWordDictionary( final String name, final File bsvFile ) {
> -      final Collection<CuiTerm> cuiTerms = parseBsvFile( bsvFile );
> +//      this( name, new File( bsvFilePath ) );
> +//   }
> +//
> +//   public BsvRareWordDictionary( final String name, final File bsvFile
> ) {
> +//      final Collection<CuiTerm> cuiTerms = parseBsvFile( bsvFile );
> +      final Collection<CuiTerm> cuiTerms = parseBsvFile( bsvFilePath );
>        final CollectionMap<String, RareWordTerm, ? extends
> Collection<RareWordTerm>> rareWordTermMap
>              = RareWordTermMapCreator.createRareWordTermMap( cuiTerms );
>        _delegateDictionary = new MemRareWordDictionary( name,
> rareWordTermMap ); @@ -109,11 +112,21 @@ final public class
> BsvRareWordDictionary
>      * CUI|TUI|Text|PreferredTerm
>      * </p>
>      * If the TUI column is omitted then the entityId for the dictionary
> is used as the TUI
> +    * <p/>
> +    * //    * @param bsvFile file containing term rows and bsv columns
>      *
> -    * @param bsvFile file containing term rows and bsv columns
> +    * @param bsvFilePath path to file containing term rows and bsv
> + columns
>      * @return collection of all valid terms read from the bsv file
>      */
> -   static private Collection<CuiTerm> parseBsvFile( final File bsvFile ) {
> +//   static private Collection<CuiTerm> parseBsvFile( final File bsvFile
> ) {
> +   static private Collection<CuiTerm> parseBsvFile( final String
> bsvFilePath ) {
> +      File bsvFile = null;
> +      try {
> +         bsvFile = FileLocator.locateFile( bsvFilePath );
> +      } catch ( IOException ioE ) {
> +         ioE.getMessage();
> +         return Collections.emptyList();
> +      }
>        final Collection<CuiTerm> cuiTerms = new ArrayList<>();
>        try ( final BufferedReader reader = new BufferedReader( new
> FileReader( bsvFile ) ) ) {
>           String line = reader.readLine();
>
> Modified:
> ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.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_util_JdbcConnectionFactory.java-3Frev-3D1677903-26r1-3D1677902-26r2-3D1677903-26view-3Ddiff&d=BQICaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIag&s=Zojydr1XQ2pr1l6pOrj2iBFd-7iR3__MBP6GNOBDIlQ&e=
>
> ==============================================================================
> ---
> ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java
> (original)
> +++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/
> +++ ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java Tue May  5
> +++ 22:41:26 2015
> @@ -21,8 +21,6 @@ import java.util.*;
>  public enum JdbcConnectionFactory {
>     INSTANCE;
>
> -   static private final String CTAKES_HOME = "CTAKES_HOME";
> -
>     static final private Logger LOGGER = Logger.getLogger(
> "JdbcConnectionFactory" );
>     static final private Logger DOT_LOGGER = Logger.getLogger(
> "ProgressAppender" );
>     static final private Logger EOL_LOGGER = Logger.getLogger(
> "ProgressDone" );
>
>
>

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