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Posted to commits@ctakes.apache.org by ch...@apache.org on 2014/09/10 17:27:13 UTC
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...
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
;