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From chen...@apache.org
Subject svn commit: r1624031 - in /ctakes/trunk: ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/ ctakes-ytex-uima/desc/analysis_engine/ ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/ ctakes-ytex-uima/src/main/java/org/ap...
Date Wed, 10 Sep 2014 15:27:13 GMT
Author: chenpei
Date: Wed Sep 10 15:27:12 2014
New Revision: 1624031

URL: http://svn.apache.org/r1624031
Log:
CTAKES-311 - Search and replace legacy edu.mayo.bmi* to org.apache.ctakes type system references.
Removed old descriptors that still had those reference (obviously, they no longer work).

Removed:
    ctakes/trunk/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotatorOld.xml
    ctakes/trunk/ctakes-ytex-uima/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml
    ctakes/trunk/ctakes-ytex-uima/desc/analysis_engine/DrugNerDictionaryLookupAnnotator.xml
Modified:
    ctakes/trunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-mapper.xml
    ctakes/trunk/ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml
    ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotator.java
    ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/DocumentMapperServiceImpl.java
    ctakes/trunk/ctakes-ytex-web/.settings/org.eclipse.core.resources.prefs
    ctakes/trunk/ctakes-ytex-web/.settings/org.eclipse.wst.common.component
    ctakes/trunk/ctakes-ytex/scripts/data/hsql/uima/create_view.sql
    ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_livermass.sql
    ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_radiology.sql
    ctakes/trunk/ctakes-ytex/scripts/data/mssql/uima/create_view.sql
    ctakes/trunk/ctakes-ytex/scripts/data/mysql/uima/create_view.sql
    ctakes/trunk/ctakes-ytex/scripts/data/orcl/uima/create_view.sql

Modified: ctakes/trunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-mapper.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-mapper.xml?rev=1624031&r1=1624030&r2=1624031&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-mapper.xml
(original)
+++ ctakes/trunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-mapper.xml
Wed Sep 10 15:27:12 2014
@@ -80,7 +80,7 @@ http://www.springframework.org/schema/ao
 				</bean>
 				<bean class="org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo">
 					<property name="annoClassName"
-						value="edu.mayo.bmi.uima.coref.type.MarkablePairSet" />
+						value="org.apache.ctakes.coreference.type.MarkablePairSet" />
 					<property name="tableName" value="anno_link" />
 					<property name="columnMappingInfos">
 						<set>
@@ -99,7 +99,7 @@ http://www.springframework.org/schema/ao
 				</bean>
 				<bean class="org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo">
 					<property name="annoClassName"
-						value="edu.mayo.bmi.uima.core.type.textsem.MedicationEventMention" />
+						value="org.apache.ctakes.typesystem.type.textsem.MedicationEventMention" />
 					<property name="tableName" value="anno_med_event" />
 					<property name="columnMappingInfos">
 						<set>

Modified: ctakes/trunk/ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml?rev=1624031&r1=1624030&r2=1624031&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml (original)
+++ ctakes/trunk/ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml Wed Sep
10 15:27:12 2014
@@ -60,10 +60,10 @@
 					</type>
 				</inputs>
 				<outputs>
-					<type>edu.mayo.bmi.uima.core.type.textsem.EntityMention</type>
-					<type>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation
+					<type>org.apache.ctakes.typesystem.type.textsem.EntityMention</type>
+					<type>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
 					</type>
-					<type>edu.mayo.bmi.uima.core.type.textsem.MedicationEventMention
+					<type>org.apache.ctakes.typesystem.type.textsem.MedicationEventMention
 					</type>
 				</outputs>
 				<languagesSupported />

Modified: ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotator.java?rev=1624031&r1=1624030&r2=1624031&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotator.java
(original)
+++ ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotator.java
Wed Sep 10 15:27:12 2014
@@ -41,7 +41,7 @@ import com.mdimension.jchronic.utils.Spa
 /**
  * The cTAKES date doesn't actually parse the date. Parse the date with Chronic,
  * store a new annotation with the real date. Takes as initialization parameter
- * a type name; defaults to "edu.mayo.bmi.uima.cdt.ae.type.DateAnnotation"
+ * a type name; defaults to "org.apache.ctakes.typesystem.type.textsem.DateAnnotation"
  * Iterate through all annotations of this type, and use chronic to parse the
  * covered text.
  */
@@ -64,7 +64,7 @@ public class DateAnnotator extends JCasA
 		super.initialize(aContext);
 		dateType = (String) aContext.getConfigParameterValue("dateType");
 		if (dateType == null) {
-			dateType = "edu.mayo.bmi.uima.core.type.textsem.DateAnnotation";
+			dateType = "org.apache.ctakes.typesystem.type.textsem.DateAnnotation";
 		}
 	}
 

Modified: ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/DocumentMapperServiceImpl.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/DocumentMapperServiceImpl.java?rev=1624031&r1=1624030&r2=1624031&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/DocumentMapperServiceImpl.java
(original)
+++ ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/DocumentMapperServiceImpl.java
Wed Sep 10 15:27:12 2014
@@ -383,7 +383,7 @@ public class DocumentMapperServiceImpl i
 				: analysisBatch);
 		// look for the ctakes DocumentID anno
 		if (setUimaDocId(jcas, doc,
-				"edu.mayo.bmi.uima.core.type.structured.DocumentID",
+				"org.apache.ctakes.typesystem.type.structured.DocumentID",
 				"documentID") == null) {
 			// look for the uima SourceDocumentInformation anno
 			setUimaDocId(jcas, doc,

Modified: ctakes/trunk/ctakes-ytex-web/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-web/.settings/org.eclipse.core.resources.prefs?rev=1624031&r1=1624030&r2=1624031&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-web/.settings/org.eclipse.core.resources.prefs (original)
+++ ctakes/trunk/ctakes-ytex-web/.settings/org.eclipse.core.resources.prefs Wed Sep 10 15:27:12
2014
@@ -1,3 +1,4 @@
 eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
 encoding//src/main/resources=UTF-8
 encoding/<project>=UTF-8

Modified: ctakes/trunk/ctakes-ytex-web/.settings/org.eclipse.wst.common.component
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-web/.settings/org.eclipse.wst.common.component?rev=1624031&r1=1624030&r2=1624031&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-web/.settings/org.eclipse.wst.common.component (original)
+++ ctakes/trunk/ctakes-ytex-web/.settings/org.eclipse.wst.common.component Wed Sep 10 15:27:12
2014
@@ -4,10 +4,10 @@
         <wb-resource deploy-path="/" source-path="/src/main/webapp" tag="defaultRootSource"/>
         <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
         <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/resources"/>
-        <dependent-module archiveName="ctakes-ytex-3.1.2-SNAPSHOT.jar" deploy-path="/WEB-INF/lib"
handle="module:/resource/ctakes-ytex/ctakes-ytex">
+        <dependent-module archiveName="ctakes-ytex-3.2.1-SNAPSHOT.jar" deploy-path="/WEB-INF/lib"
handle="module:/resource/ctakes-ytex/ctakes-ytex">
             <dependency-type>uses</dependency-type>
         </dependent-module>
-        <dependent-module archiveName="ctakes-ytex-res-3.1.2-SNAPSHOT.jar" deploy-path="/WEB-INF/lib"
handle="module:/resource/ctakes-ytex-res/ctakes-ytex-res">
+        <dependent-module archiveName="ctakes-ytex-res-3.2.1-SNAPSHOT.jar" deploy-path="/WEB-INF/lib"
handle="module:/resource/ctakes-ytex-res/ctakes-ytex-res">
             <dependency-type>uses</dependency-type>
         </dependent-module>
         <property name="context-root" value="ctakes-ytex-web"/>

Modified: ctakes/trunk/ctakes-ytex/scripts/data/hsql/uima/create_view.sql
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/scripts/data/hsql/uima/create_view.sql?rev=1624031&r1=1624030&r2=1624031&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/scripts/data/hsql/uima/create_view.sql (original)
+++ ctakes/trunk/ctakes-ytex/scripts/data/hsql/uima/create_view.sql Wed Sep 10 15:27:12 2014
@@ -57,7 +57,7 @@ INNER JOIN anno_ontology_concept  o ON o
 inner join anno_contain ac on da.anno_base_id = ac.child_anno_base_id
 INNER join anno_base s
   on ac.parent_anno_base_id = s.anno_base_id
-  and s.uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name = 'edu.mayo.bmi.uima.core.type.textspan.Sentence')
+  and s.uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name = 'org.apache.ctakes.typesystem.type.textspan.Sentence')
 INNER JOIN document d on da.document_id = d.document_id
 ;
 

Modified: ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_livermass.sql
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_livermass.sql?rev=1624031&r1=1624030&r2=1624031&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_livermass.sql
(original)
+++ ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_livermass.sql
Wed Sep 10 15:27:12 2014
@@ -119,7 +119,7 @@ from
 				where s.uima_type_id in 
 					(select uima_type_id 
 					from esld.ref_uima_type 
-					where uima_type_name = 'edu.mayo.bmi.uima.core.sentence.type.Sentence')
+					where uima_type_name = 'org.apache.ctakes.typesystem.type.textspan.Sentence')
 				and liv.code in ('C1278929', 'C0023884', 'C0205054' /* hepatic */, 'C0227486' /* left
lobe */, 'C0227481' /* right lobe */)
 				and mass.code in ('C0221198', 'C0577559', 'ESLD_MASS')
 				and mass.span_begin >= sda.span_begin

Modified: ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_radiology.sql
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_radiology.sql?rev=1624031&r1=1624030&r2=1624031&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_radiology.sql
(original)
+++ ctakes/trunk/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_radiology.sql
Wed Sep 10 15:27:12 2014
@@ -154,7 +154,7 @@ from
 				-- sentence annotation
 				inner join esld.anno_base s on oda.document_id = s.document_id
 				inner join esld.ref_uima_type ut on s.uima_type_id = ut.uima_type_id
-				where ut.uima_type_name = 'edu.mayo.bmi.uima.core.sentence.type.Sentence'
+				where ut.uima_type_name = 'org.apache.ctakes.typesystem.type.textspan.Sentence'
 				-- get the report section
 				and seg.segment_id = 'REPORT'
 				-- radiology & abdomen annotations in same sentence

Modified: ctakes/trunk/ctakes-ytex/scripts/data/mssql/uima/create_view.sql
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/scripts/data/mssql/uima/create_view.sql?rev=1624031&r1=1624030&r2=1624031&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/scripts/data/mssql/uima/create_view.sql (original)
+++ ctakes/trunk/ctakes-ytex/scripts/data/mssql/uima/create_view.sql Wed Sep 10 15:27:12 2014
@@ -59,8 +59,8 @@ left join 
   select ac.child_anno_base_id, s.span_begin, s.span_end
   from $(db_schema).anno_contain ac 
   INNER join $(db_schema).anno_base s on ac.parent_anno_base_id = s.anno_base_id
-  where s.uima_type_id in (select uima_type_id from $(db_schema).ref_uima_type where uima_type_name
= 'edu.mayo.bmi.uima.core.type.textspan.Sentence')
-  and ac.child_uima_type_id in (select uima_type_id from $(db_schema).ref_uima_type where
uima_type_name = 'edu.mayo.bmi.uima.core.type.textsem.EntityMention')
+  where s.uima_type_id in (select uima_type_id from $(db_schema).ref_uima_type where uima_type_name
= 'org.apache.ctakes.typesystem.type.textspan.Sentence')
+  and ac.child_uima_type_id in (select uima_type_id from $(db_schema).ref_uima_type where
uima_type_name = 'org.apache.ctakes.typesystem.type.textsem.EntityMention')
 ) s on da.anno_base_id = s.child_anno_base_id
 INNER JOIN $(db_schema).v_document d on da.document_id = d.document_id
 ;

Modified: ctakes/trunk/ctakes-ytex/scripts/data/mysql/uima/create_view.sql
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/scripts/data/mysql/uima/create_view.sql?rev=1624031&r1=1624030&r2=1624031&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/scripts/data/mysql/uima/create_view.sql (original)
+++ ctakes/trunk/ctakes-ytex/scripts/data/mysql/uima/create_view.sql Wed Sep 10 15:27:12 2014
@@ -57,7 +57,7 @@ INNER JOIN anno_ontology_concept  o ON o
 inner join anno_contain ac on da.anno_base_id = ac.child_anno_base_id
 INNER join anno_base s
   on ac.parent_anno_base_id = s.anno_base_id
-  and s.uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name = 'edu.mayo.bmi.uima.core.type.textspan.Sentence')
+  and s.uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name = 'org.apache.ctakes.typesystem.type.textspan.Sentence')
 INNER JOIN document d on da.document_id = d.document_id
 ;
 

Modified: ctakes/trunk/ctakes-ytex/scripts/data/orcl/uima/create_view.sql
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/scripts/data/orcl/uima/create_view.sql?rev=1624031&r1=1624030&r2=1624031&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/scripts/data/orcl/uima/create_view.sql (original)
+++ ctakes/trunk/ctakes-ytex/scripts/data/orcl/uima/create_view.sql Wed Sep 10 15:27:12 2014
@@ -58,8 +58,8 @@ left join 
   select ac.child_anno_base_id, s.span_begin, s.span_end
   from anno_contain ac 
   INNER join anno_base s on ac.parent_anno_base_id = s.anno_base_id
-  where s.uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name =
'edu.mayo.bmi.uima.core.type.textspan.Sentence')
-  and ac.child_uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name
= 'edu.mayo.bmi.uima.core.type.textsem.EntityMention')
+  where s.uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name =
'org.apache.ctakes.typesystem.type.textspan.Sentence')
+  and ac.child_uima_type_id in (select uima_type_id from ref_uima_type where uima_type_name
= 'org.apache.ctakes.typesystem.type.textsem.EntityMention')
 ) s on da.anno_base_id = s.child_anno_base_id
 INNER JOIN v_document d on da.document_id = d.document_id
 ;



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