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From seanfi...@apache.org
Subject svn commit: r1571821 - in /ctakes/sandbox/ctakes-dictionary-lookup2-res: ./ src/ src/main/ src/main/resources/ src/main/resources/org/ src/main/resources/org/apache/ src/main/resources/org/apache/ctakes/ src/main/resources/org/apache/ctakes/dictionary/...
Date Tue, 25 Feb 2014 20:54:56 GMT
Author: seanfinan
Date: Tue Feb 25 20:54:55 2014
New Revision: 1571821

URL: http://svn.apache.org/r1571821
Log:
First commit of new dictionary lookup module.  No jira

Added:
    ctakes/sandbox/ctakes-dictionary-lookup2-res/
    ctakes/sandbox/ctakes-dictionary-lookup2-res/LICENSE   (with props)
    ctakes/sandbox/ctakes-dictionary-lookup2-res/pom.xml   (with props)
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/cTakesSnomed.xml
  (with props)
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv/
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv/CustomBsvDictionary.bsv
  (with props)
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv/RareWord_BSV.xml
  (with props)
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/CustomBsvDictionary.bsv
  (with props)
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/RareWord_SNOMED_BSV.xml
  (with props)
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multitable/
    ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multitable/RareWordTermsUMLS.xml
  (with props)

Added: ctakes/sandbox/ctakes-dictionary-lookup2-res/LICENSE
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-dictionary-lookup2-res/LICENSE?rev=1571821&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-dictionary-lookup2-res/LICENSE (added)
+++ ctakes/sandbox/ctakes-dictionary-lookup2-res/LICENSE Tue Feb 25 20:54:55 2014
@@ -0,0 +1,202 @@
+
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+      agreed to in writing, Licensor provides the Work (and each
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Propchange: ctakes/sandbox/ctakes-dictionary-lookup2-res/LICENSE
------------------------------------------------------------------------------
    svn:eol-style = native

Added: ctakes/sandbox/ctakes-dictionary-lookup2-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-dictionary-lookup2-res/pom.xml?rev=1571821&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-dictionary-lookup2-res/pom.xml (added)
+++ ctakes/sandbox/ctakes-dictionary-lookup2-res/pom.xml Tue Feb 25 20:54:55 2014
@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <parent>
+    <groupId>org.apache.ctakes</groupId>
+    <artifactId>ctakes</artifactId>
+    <version>3.1.2-SNAPSHOT</version>
+  </parent>
+  <artifactId>ctakes-dictionary-lookup2-res</artifactId>
+  <name>Apache cTAKES Resources dictionary-lookup2</name>
+  <description>Resources Project for ctakes-dictionary-lookup2</description>
+</project>

Propchange: ctakes/sandbox/ctakes-dictionary-lookup2-res/pom.xml
------------------------------------------------------------------------------
    svn:eol-style = native

Added: ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/cTakesSnomed.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/cTakesSnomed.xml?rev=1571821&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/cTakesSnomed.xml
(added)
+++ ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/cTakesSnomed.xml
Tue Feb 25 20:54:55 2014
@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<lookupSpecification>
+   <!--  Defines what dictionaries will be used  -->
+   <rareWordDictionaries>
+      <!-- typeId 0 is the cTakes constant for unknown - let the consumer take care of
typing  -->
+      <dictionary id="cTakes" externalResourceKey="cTakesSnomed" caseSensitive="false"
typeId="0">
+         <implementation>
+            <rareWordUmls tableName="cTakes_umls"/>
+         </implementation>
+      </dictionary>
+   </rareWordDictionaries>
+
+   <!-- PrecisionTermConsumer will only persist only the longest overlapping span of any
semantic group -->
+   <rareWordConsumer className="org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer">
+      <properties>
+         <property key="codingScheme" value="cTakes"/>
+      </properties>
+   </rareWordConsumer>
+
+   <!-- DefaultTermConsumer will persist all spans  -->
+<!--   <rareWordConsumer className="org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer
<properties>
+         <property key="codingScheme" value="cTakes"/>
+      </properties>
+   </rareWordConsumer>  -->
+</lookupSpecification>

Propchange: ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/cTakesSnomed.xml
------------------------------------------------------------------------------
    svn:eol-style = native

Added: ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv/CustomBsvDictionary.bsv
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv/CustomBsvDictionary.bsv?rev=1571821&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv/CustomBsvDictionary.bsv
(added)
+++ ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv/CustomBsvDictionary.bsv
Tue Feb 25 20:54:55 2014
@@ -0,0 +1,7 @@
+CUSTOM1|ctakes
+CUSTOM1|ctakes application
+CUSTOM2|new dictionary lookup
+CUSTOM2|dictionary lookup, new
+CUSTOM3|faster and stronger
+CUSTOM3|stronger and faster
+

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------------------------------------------------------------------------------
    svn:eol-style = native

Added: ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv/RareWord_BSV.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv/RareWord_BSV.xml?rev=1571821&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv/RareWord_BSV.xml
(added)
+++ ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv/RareWord_BSV.xml
Tue Feb 25 20:54:55 2014
@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<lookupSpecification>
+   <!--  Defines what dictionaries will be used  -->
+   <rareWordDictionaries>
+      <!-- typeId 0 is the cTakes constant for unknown - let the consumer take care of
typing  -->
+      <dictionary id="customBsv" externalResourceKey="CustomBsvDictionary" caseSensitive="false"
typeId="0">
+         <implementation>
+            <rareWordBsv/>
+         </implementation>
+      </dictionary>
+   </rareWordDictionaries>
+
+   <!-- PrecisionTermConsumer will only persist only the longest overlapping span of any
semantic group -->
+   <rareWordConsumer className="org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer">
+      <properties>
+         <property key="codingScheme" value="cTakes"/>
+      </properties>
+   </rareWordConsumer>
+
+   <!-- DefaultTermConsumer will persist all spans  -->
+   <!--   <rareWordConsumer className="org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer
   <properties>
+            <property key="codingScheme" value="cTakes"/>
+         </properties>
+      </rareWordConsumer>  -->
+</lookupSpecification>

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    svn:eol-style = native

Added: ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/CustomBsvDictionary.bsv
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/CustomBsvDictionary.bsv?rev=1571821&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/CustomBsvDictionary.bsv
(added)
+++ ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/CustomBsvDictionary.bsv
Tue Feb 25 20:54:55 2014
@@ -0,0 +1,7 @@
+CUSTOM1|ctakes
+CUSTOM1|ctakes application
+CUSTOM2|new dictionary lookup
+CUSTOM2|dictionary lookup, new
+CUSTOM3|faster and stronger
+CUSTOM3|stronger and faster
+

Propchange: ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/CustomBsvDictionary.bsv
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Added: ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/RareWord_SNOMED_BSV.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/RareWord_SNOMED_BSV.xml?rev=1571821&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/RareWord_SNOMED_BSV.xml
(added)
+++ ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/RareWord_SNOMED_BSV.xml
Tue Feb 25 20:54:55 2014
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<lookupSpecification>
+   <!--  Defines what dictionaries will be used  -->
+   <rareWordDictionaries>
+      <!-- typeId 0 is the cTakes constant for unknown - let the consumer take care of
typing  -->
+      <dictionary id="cTakes" externalResourceKey="cTakesSnomed" caseSensitive="false"
typeId="0">
+         <implementation>
+            <rareWordUmls tableName="cTakes_umls"/>
+         </implementation>
+      </dictionary>
+
+      <!-- typeId 0 is the cTakes constant for unknown - let the consumer take care of
typing  -->
+      <dictionary id="customBsv" externalResourceKey="CustomBsvDictionary" caseSensitive="false"
typeId="0">
+         <implementation>
+            <rareWordBsv/>
+         </implementation>
+      </dictionary>
+   </rareWordDictionaries>
+
+   <!-- PrecisionTermConsumer will only persist only the longest overlapping span of any
semantic group -->
+   <rareWordConsumer className="org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer">
+      <properties>
+         <property key="codingScheme" value="cTakes"/>
+      </properties>
+   </rareWordConsumer>
+
+   <!-- DefaultTermConsumer will persist all spans  -->
+<!--   <rareWordConsumer className="org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer
<properties>
+         <property key="codingScheme" value="cTakes"/>
+      </properties>
+   </rareWordConsumer>  -->
+</lookupSpecification>

Propchange: ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/RareWord_SNOMED_BSV.xml
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    svn:eol-style = native

Added: ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multitable/RareWordTermsUMLS.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multitable/RareWordTermsUMLS.xml?rev=1571821&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multitable/RareWordTermsUMLS.xml
(added)
+++ ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multitable/RareWordTermsUMLS.xml
Tue Feb 25 20:54:55 2014
@@ -0,0 +1,61 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<lookupSpecification>
+   <!--  Defines what dictionaries will be used  -->
+   <rareWordDictionaries>
+      <!-- typeId 6 is the cTakes constant for anatomical sites  -->
+      <dictionary id="cTakesAnat" externalResourceKey="cTakesUmls" caseSensitive="false"
typeId="6">
+         <implementation>
+            <rareWordUmls tableName="cTakesAnat"/>
+         </implementation>
+      </dictionary>
+      <!-- typeId 2 is the cTakes constant for diseases and disorders  -->
+      <dictionary id="cTakesDiso" externalResourceKey="cTakesUmls" caseSensitive="false"
typeId="2">
+         <implementation>
+            <rareWordUmls tableName="cTakesDiso"/>
+         </implementation>
+      </dictionary>
+      <!-- typeId 3 is the cTakes constant for the invented semantic group "finding",
aka signs and symptoms  -->
+      <dictionary id="cTakesFind" externalResourceKey="cTakesUmls" caseSensitive="false"
typeId="3">
+         <implementation>
+            <rareWordUmls tableName="cTakesFind"/>
+         </implementation>
+      </dictionary>
+      <!-- typeId 5 is the cTakes constant for procedures  -->
+      <dictionary id="cTakesProc" externalResourceKey="cTakesUmls" caseSensitive="false"
typeId="5">
+         <implementation>
+            <rareWordUmls tableName="cTakesProc"/>
+         </implementation>
+      </dictionary>
+      <!-- typeId 1 is the cTakes constant for drugs  -->
+      <dictionary id="cTakesDrug" externalResourceKey="cTakesUmls" caseSensitive="false"
typeId="1">
+         <implementation>
+            <rareWordUmls tableName="cTakesDrug"/>
+         </implementation>
+      </dictionary>
+   </rareWordDictionaries>
+   <rareWordConsumer className="org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer">
+      <properties>
+         <property key="codingScheme" value="Umls"/>
+      </properties>
+   </rareWordConsumer>
+</lookupSpecification>

Propchange: ctakes/sandbox/ctakes-dictionary-lookup2-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multitable/RareWordTermsUMLS.xml
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    svn:eol-style = native



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