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From chen...@apache.org
Subject svn commit: r1603912 - in /ctakes/trunk: ctakes-clinical-pipeline/desc/analysis_engine/auto/ ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/ ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup...
Date Thu, 19 Jun 2014 15:06:58 GMT
Author: chenpei
Date: Thu Jun 19 15:06:57 2014
New Revision: 1603912

URL: http://svn.apache.org/r1603912
Log:
CTAKES-297 - Updated paths. 
-removed hardcoded personal paths in autogenerated desc.
-updated temporal pipelines to use the new factory methods for dictionary lookup.

Removed:
    ctakes/trunk/ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db_hsql.xml
Modified:
    ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/auto/defaultPipeline.xml
    ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java

Modified: ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/auto/defaultPipeline.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/auto/defaultPipeline.xml?rev=1603912&r1=1603911&r2=1603912&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/auto/defaultPipeline.xml (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/auto/defaultPipeline.xml Thu
Jun 19 15:06:57 2014
@@ -30669,7 +30669,7 @@ Equivalent to cTAKES: edu.mayo.bmi.uima.
                                         <nameValuePair>
                                             <name>URL</name>
                                             <value>
-                                                <string>jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/rx_norm_hsqldb/umls</string>
+                                                <string>jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/rxnorm-hsqldb/umls</string>
                                             </value>
                                         </nameValuePair>
                                     </configurationParameterSettings>
@@ -30720,7 +30720,7 @@ Equivalent to cTAKES: edu.mayo.bmi.uima.
                             <name>org.apache.ctakes.core.resource.FileResourceImpl-1</name>
                             <description/>
                             <configurableDataResourceSpecifier>
-                                <url>file:/home/tmill/Projects/apache-ctakes/maven.1348675223521/ctakes-dictionary-lookup-res/target/classes/org/apache/ctakes/dictionary/lookup/LookupDesc_Db_hsql.xml</url>
+                                <url>file:org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml</url>
                                 <resourceMetaData>
                                     <name/>
                                     <configurationParameters/>

Modified: ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java?rev=1603912&r1=1603911&r2=1603912&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
(original)
+++ ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
Thu Jun 19 15:06:57 2014
@@ -141,7 +141,7 @@ public class UmlsDictionaryLookupAnnotat
               JdbcConnectionResourceImpl.PARAM_DRIVER_CLASS,
               "org.hsqldb.jdbcDriver",
               JdbcConnectionResourceImpl.PARAM_URL,
-              "jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/rx_norm_hsqldb/umls"),
+              "jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/rxnorm-hsqldb/umls"),
           "OrangeBookIndexReader",
           ExternalResourceFactory.createExternalResourceDescription(
               JdbcConnectionResourceImpl.class,

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java?rev=1603912&r1=1603911&r2=1603912&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
Thu Jun 19 15:06:57 2014
@@ -421,42 +421,9 @@ public abstract class Evaluation_ImplBas
         "DeleteAction",
         new String[] { "selector=B" }));
     // add UMLS on top of lookup windows
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
-        UmlsDictionaryLookupAnnotator.class,
-        "ctakes.umlsaddr",
-        "https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser",
-        "ctakes.umlsvendor",
-        "NLM-6515182895",
-        "LookupDescriptor",
-        ExternalResourceFactory.createExternalResourceDescription(
-            FileResourceImpl.class,
-            FileLocator.locateFile("org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml")),
-        "DbConnection",
-        ExternalResourceFactory.createExternalResourceDescription(
-            JdbcConnectionResourceImpl.class,
-            "",
-            JdbcConnectionResourceImpl.PARAM_DRIVER_CLASS,
-            "org.hsqldb.jdbcDriver",
-            JdbcConnectionResourceImpl.PARAM_URL,
-            // 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,
-            "",
-            "UseMemoryIndex",
-            true,
-            "IndexDirectory",
-            new File("target/unpacked/org/apache/ctakes/dictionary/lookup/rxnorm_index").getAbsoluteFile()),
-        "OrangeBookIndexReader",
-        ExternalResourceFactory.createExternalResourceDescription(
-            LuceneIndexReaderResourceImpl.class,
-            "",
-            "UseMemoryIndex",
-            true,
-            "IndexDirectory",
-            FileLocator.locateFile("org/apache/ctakes/dictionary/lookup/OrangeBook"))));
+    aggregateBuilder.add(
+    		UmlsDictionaryLookupAnnotator.createAnnotatorDescription()
+    		);
 
     // add lvg annotator
     String[] XeroxTreebankMap = {

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?rev=1603912&r1=1603911&r2=1603912&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
Thu Jun 19 15:06:57 2014
@@ -130,42 +130,7 @@ public abstract class TemporalExtraction
     // maximize lookup windows
     aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
     // add UMLS on top of lookup windows
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
-        UmlsDictionaryLookupAnnotator.class,
-        "ctakes.umlsaddr",
-        "https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser",
-        "ctakes.umlsvendor",
-        "NLM-6515182895",
-        "LookupDescriptor",
-        ExternalResourceFactory.createExternalResourceDescription(
-            FileResourceImpl.class,
-            FileLocator.locateFile("org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml")),
-        "DbConnection",
-        ExternalResourceFactory.createExternalResourceDescription(
-            JdbcConnectionResourceImpl.class,
-            "",
-            JdbcConnectionResourceImpl.PARAM_DRIVER_CLASS,
-            "org.hsqldb.jdbcDriver",
-            JdbcConnectionResourceImpl.PARAM_URL,
-            // 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,
-            "",
-            "UseMemoryIndex",
-            true,
-            "IndexDirectory",
-            new File("target/unpacked/org/apache/ctakes/dictionary/lookup/rxnorm_index").getAbsoluteFile()),
-        "OrangeBookIndexReader",
-        ExternalResourceFactory.createExternalResourceDescription(
-            LuceneIndexReaderResourceImpl.class,
-            "",
-            "UseMemoryIndex",
-            true,
-            "IndexDirectory",
-            "org/apache/ctakes/dictionary/lookup/OrangeBook")));
+    aggregateBuilder.add(UmlsDictionaryLookupAnnotator.createAnnotatorDescription());
 
     // add lvg annotator
     String[] XeroxTreebankMap = {



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