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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
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
Date Wed, 06 May 2015 14:45:31 GMT
We could, but GetAsStream does not do as  complete a search as locateFile.  GetAsStream would
not be able to find the resource that was being used at the time (deepphe custom bsv).  getAsStream
can be improved - maybe a jira?

-----Original Message-----
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu] 
Sent: Tuesday, May 05, 2015 6:58 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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