Author: seanfinan
Date: Tue May 5 22:41:26 2015
New Revision: 1677903
URL: http://svn.apache.org/r1677903
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:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java?rev=1677903&r1=1677902&r2=1677903&view=diff
==============================================================================
---
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:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java?rev=1677903&r1=1677902&r2=1677903&view=diff
==============================================================================
---
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:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java?rev=1677903&r1=1677902&r2=1677903&view=diff
==============================================================================
---
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" );
