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From stevenbeth...@apache.org
Subject svn commit: r1431154 - in /incubator/ctakes/trunk/ctakes-temporal: pom.xml src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
Date Wed, 09 Jan 2013 23:51:41 GMT
Author: stevenbethard
Date: Wed Jan  9 23:51:41 2013
New Revision: 1431154

URL: http://svn.apache.org/viewvc?rev=1431154&view=rev
Log:
Adds UMLS entity chunk features back to the EventAnnotator evalution

Modified:
    incubator/ctakes/trunk/ctakes-temporal/pom.xml
    incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java
    incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java

Modified: incubator/ctakes/trunk/ctakes-temporal/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/pom.xml?rev=1431154&r1=1431153&r2=1431154&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/pom.xml (original)
+++ incubator/ctakes/trunk/ctakes-temporal/pom.xml Wed Jan  9 23:51:41 2013
@@ -95,5 +95,67 @@
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-dependency-parser</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>net.sourceforge.ctakesresources</groupId>
+			<artifactId>ctakes-resources-umls2011ab</artifactId>
+			<version>3.1.0</version>
+		</dependency>
 	</dependencies>
+	<!-- The below is all necessary to unpack the UMLS resources since they 
+		can't be used from the classpath -->
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-dependency-plugin</artifactId>
+				<executions>
+					<execution>
+						<id>unpack</id>
+						<phase>initialize</phase>
+						<goals>
+							<goal>unpack</goal>
+						</goals>
+						<configuration>
+							<artifactItems>
+								<artifactItem>
+									<groupId>net.sourceforge.ctakesresources</groupId>
+									<artifactId>ctakes-resources-umls2011ab</artifactId>
+									<version>3.1.0</version>
+								</artifactItem>
+							</artifactItems>
+							<outputDirectory>${project.build.directory}/unpacked</outputDirectory>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+		</plugins>
+		<pluginManagement>
+			<plugins>
+				<plugin>
+					<groupId>org.eclipse.m2e</groupId>
+					<artifactId>lifecycle-mapping</artifactId>
+					<version>1.0.0</version>
+					<configuration>
+						<lifecycleMappingMetadata>
+							<pluginExecutions>
+								<pluginExecution>
+									<pluginExecutionFilter>
+										<groupId>org.apache.maven.plugins</groupId>
+										<artifactId>maven-dependency-plugin</artifactId>
+										<versionRange>[2.0,)</versionRange>
+										<goals>
+											<goal>unpack</goal>
+										</goals>
+									</pluginExecutionFilter>
+									<action>
+										<execute />
+									</action>
+								</pluginExecution>
+							</pluginExecutions>
+						</lifecycleMappingMetadata>
+					</configuration>
+				</plugin>
+			</plugins>
+		</pluginManagement>
+	</build>
 </project>
\ No newline at end of file

Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java?rev=1431154&r1=1431153&r2=1431154&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java
(original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java
Wed Jan  9 23:51:41 2013
@@ -93,12 +93,10 @@ public class EvaluationOfEventSpans exte
     super(baseDirectory, rawTextDirectory, knowtatorXMLDirectory, EnumSet.of(
         AnnotatorType.PART_OF_SPEECH_TAGS,
         AnnotatorType.CHUNKS,
+        AnnotatorType.UMLS_NAMED_ENTITIES,
         AnnotatorType.DEPENDENCIES,
         AnnotatorType.SEMANTIC_ROLES));
-        //AnnotatorType.UMLS_NAMED_ENTITIES,
         //AnnotatorType.LEXICAL_VARIANTS,
-        //AnnotatorType.DEPENDENCIES,
-        //AnnotatorType.SEMANTIC_ROLES));
     this.probabilityOfKeepingANegativeExample = probabilityOfKeepingANegativeExample;
     this.featureSelectionThreshold = featureSelectionThreshold;
     this.smoteNeighborNumber = numOfSmoteNeighbors;

Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java?rev=1431154&r1=1431153&r2=1431154&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
(original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
Wed Jan  9 23:51:41 2013
@@ -19,7 +19,6 @@
 package org.apache.ctakes.temporal.eval;
 
 import java.io.File;
-import java.net.URISyntaxException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
@@ -232,28 +231,16 @@ public abstract class Evaluation_ImplBas
           "DeleteAction",
           new String[] { "selector=B" }));
       // add UMLS on top of lookup windows
-      String umlsUser = System.getProperty("umls.user");
-      String umlsPassword = System.getProperty("umls.password");
-      if (umlsUser == null || umlsPassword == null) {
-        throw new IllegalArgumentException(
-            "The properties umls.user and umls.password must be set to use the "
-                + "UmlsDictionaryLookupAnnotator. You can set them by provding java with
the "
-                + "arguments -Dumls.user=... and -Dumls.password=...");
-      }
       aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
           UmlsDictionaryLookupAnnotator.class,
-          "UMLSAddr",
+          "ctakes.umlsaddr",
           "https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser",
-          "UMLSVendor",
+          "ctakes.umlsvendor",
           "NLM-6515182895",
-          "UMLSUser",
-          umlsUser,
-          "UMLSPW",
-          umlsPassword,
           "LookupDescriptor",
           ExternalResourceFactory.createExternalResourceDescription(
               FileResourceImpl.class,
-              getResourceAsFile(UmlsDictionaryLookupAnnotator.class, "../LookupDesc_Db.xml")),
+              new File("target/unpacked/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml").getAbsoluteFile()),
           "DbConnection",
           ExternalResourceFactory.createExternalResourceDescription(
               JdbcConnectionResourceImpl.class,
@@ -261,7 +248,9 @@ public abstract class Evaluation_ImplBas
               JdbcConnectionResourceImpl.PARAM_DRIVER_CLASS,
               "org.hsqldb.jdbcDriver",
               JdbcConnectionResourceImpl.PARAM_URL,
-              "jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/umls"),
+              // Should be the following but it's WAY too slow
+              //"jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/umls"),
+              "jdbc:hsqldb:file:target/unpacked/org/apache/ctakes/dictionary/lookup/umls2011ab/umls"),
           "RxnormIndexReader",
           ExternalResourceFactory.createExternalResourceDescription(
               LuceneIndexReaderResourceImpl.class,
@@ -269,7 +258,7 @@ public abstract class Evaluation_ImplBas
               "UseMemoryIndex",
               true,
               "IndexDirectory",
-              getResourceAsFile(UmlsDictionaryLookupAnnotator.class, "../rxnorm_index")),
+              new File("target/unpacked/org/apache/ctakes/dictionary/lookup/rxnorm_index").getAbsoluteFile()),
           "OrangeBookIndexReader",
           ExternalResourceFactory.createExternalResourceDescription(
               LuceneIndexReaderResourceImpl.class,
@@ -277,7 +266,7 @@ public abstract class Evaluation_ImplBas
               "UseMemoryIndex",
               true,
               "IndexDirectory",
-              getResourceAsFile(UmlsDictionaryLookupAnnotator.class, "../OrangeBook"))));
+              new File("target/unpacked/org/apache/ctakes/dictionary/lookup/OrangeBook").getAbsoluteFile())));
     }
 
     // add lvg annotator
@@ -340,7 +329,7 @@ public abstract class Evaluation_ImplBas
           "LvgCmdApi",
           ExternalResourceFactory.createExternalResourceDescription(
               LvgCmdApiResourceImpl.class,
-              getResourceAsFile(LvgAnnotator.class, "../data/config/lvg.properties")));
+              "org/apache/ctakes/lvg/data/config/lvg.properties"));
       aggregateBuilder.add(lvgAnnotator);
     }
 
@@ -356,14 +345,6 @@ public abstract class Evaluation_ImplBas
     return aggregateBuilder.createAggregateDescription();
   }
 
-  /**
-   * This is hack to deal with classes that don't handle resources correctly
-   */
-  private static File getResourceAsFile(Class<?> cls, String path) throws URISyntaxException
{
-    // this will fail if the resource is not a real File, but the UMLS code assumes that
-    return new File(cls.getResource(path).toURI());
-  }
-
   public static class CopyNPChunksToLookupWindowAnnotations extends JCasAnnotator_ImplBase
{
 
     @Override



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