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From chen...@apache.org
Subject svn commit: r1727698 [1/3] - in /ctakes/sandbox/ctakes-clinical-deid: ./ src/main/resources/META-INF/org.apache.uima.fit/ src/main/resources/wordlists/ src/main/ruta/org/apache/ctakes/deid/ src/test/java/org/apache/ctakes/deid/
Date Sat, 30 Jan 2016 14:08:08 GMT
Author: chenpei
Date: Sat Jan 30 14:08:08 2016
New Revision: 1727698

URL: http://svn.apache.org/viewvc?rev=1727698&view=rev
Log:
CTAKES-384 Applying patch.Thanks Peter Klugl.

Modified:
    ctakes/sandbox/ctakes-clinical-deid/pom.xml
    ctakes/sandbox/ctakes-clinical-deid/pom.xml.orig
    ctakes/sandbox/ctakes-clinical-deid/pom.xml.rej
    ctakes/sandbox/ctakes-clinical-deid/src/main/resources/META-INF/org.apache.uima.fit/types.txt
    ctakes/sandbox/ctakes-clinical-deid/src/main/resources/wordlists/profession.txt
    ctakes/sandbox/ctakes-clinical-deid/src/main/resources/wordlists/street_full_ind.txt
    ctakes/sandbox/ctakes-clinical-deid/src/main/resources/wordlists/street_ind.txt
    ctakes/sandbox/ctakes-clinical-deid/src/main/resources/wordlists/us_state.txt
    ctakes/sandbox/ctakes-clinical-deid/src/main/resources/wordlists/us_state_acronym_abbreviation.txt
    ctakes/sandbox/ctakes-clinical-deid/src/main/ruta/org/apache/ctakes/deid/Deid.ruta
    ctakes/sandbox/ctakes-clinical-deid/src/main/ruta/org/apache/ctakes/deid/Deid.ruta.orig
    ctakes/sandbox/ctakes-clinical-deid/src/main/ruta/org/apache/ctakes/deid/Dictionaries.ruta
    ctakes/sandbox/ctakes-clinical-deid/src/main/ruta/org/apache/ctakes/deid/Street.ruta
    ctakes/sandbox/ctakes-clinical-deid/src/main/ruta/org/apache/ctakes/deid/ZipState.ruta
    ctakes/sandbox/ctakes-clinical-deid/src/test/java/org/apache/ctakes/deid/DeidPipelineTest.java

Modified: ctakes/sandbox/ctakes-clinical-deid/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/pom.xml?rev=1727698&r1=1727697&r2=1727698&view=diff
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/pom.xml (original)
+++ ctakes/sandbox/ctakes-clinical-deid/pom.xml Sat Jan 30 14:08:08 2016
@@ -141,7 +141,7 @@
 
               <!-- Type of type system imports. false = import by location. -->
               <!-- default value: false -->
-              <importByName>false</importByName>
+              <importByName>true</importByName>
 
               <!-- Option to resolve imports while building. -->
               <!-- default value: false -->

Modified: ctakes/sandbox/ctakes-clinical-deid/pom.xml.orig
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/pom.xml.orig?rev=1727698&r1=1727697&r2=1727698&view=diff
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/pom.xml.orig (original)
+++ ctakes/sandbox/ctakes-clinical-deid/pom.xml.orig Sat Jan 30 14:08:08 2016
@@ -1,211 +0,0 @@
-<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>
-
-  <artifactId>ctakes-clinical-deid</artifactId>
-
-  <parent>
-    <groupId>org.apache.ctakes</groupId>
-    <artifactId>ctakes</artifactId>
-    <version>3.2.3-SNAPSHOT</version>
-  </parent>
-
-  <properties>
-    <ruta-version>2.4.0</ruta-version>
-<!--     <ruta-version>2.3.1</ruta-version> -->
-  </properties>
-
-  <!--  use ruta-2.4.0-rc2 for now until its released -->
-  <repositories>
-    <repository>
-      <id>staged-release</id>
-      <url>https://repository.apache.org/content/repositories/orgapacheuima-1081/</url>
-    </repository>
-  </repositories>
-  <pluginRepositories>
-    <pluginRepository>
-      <id>staged-release</id>
-      <url>https://repository.apache.org/content/repositories/orgapacheuima-1081/</url>
-    </pluginRepository>
-  </pluginRepositories>
-
-  <dependencies>
-    <dependency>
-      <groupId>org.apache.ctakes</groupId>
-      <artifactId>ctakes-clinical-pipeline</artifactId>
-    </dependency>
-    <dependency>
-      <groupId>org.apache.uima</groupId>
-      <artifactId>ruta-core</artifactId>
-      <version>${ruta-version}</version>
-    </dependency>
-    <dependency>
-      <groupId>org.apache.uima</groupId>
-      <artifactId>ruta-core-ext</artifactId>
-      <version>${ruta-version}</version>
-    </dependency>
-  </dependencies>
-  
-  
-  
-  <build>
-    <resources>
-      <resource>
-        <directory>src/main/ruta</directory>
-      </resource>
-      <resource>
-        <directory>src/main/resources</directory>
-      </resource>
-      <resource>
-        <directory>target/generated-sources/ruta/descriptor</directory>
-      </resource>
-    </resources>
-  
-    <plugins>
-      <plugin>
-        <groupId>org.apache.uima</groupId>
-        <artifactId>ruta-maven-plugin</artifactId>
-        <version>${ruta-version}</version>
-        <executions>
-          <execution>
-            <id>descriptors</id>
-            <!-- use this phase so that the ruta script files are already 
-              copied to target/classes -->
-            <!-- no need to specify the included script directories with 
-              <scriptFiles> -->
-            <phase>generate-resources</phase>
-            <goals>
-              <goal>generate</goal>
-            </goals>
-            <configuration>
-
-              <!-- This is a exemplary configuration, which explicitly specifies 
-                the default configuration values if not mentioned otherwise. -->
-               <scriptFiles>
-                <directory>${basedir}/src/main/ruta</directory>
-                <includes>
-                  <include>**/*.ruta</include>
-                </includes>
-               </scriptFiles>
-
-              <!-- The directory where the generated type system descriptors 
-                will be written stored. -->
-              <!-- default value: ${project.build.directory}/generated-sources/ruta/descriptor
-->
-              <typeSystemOutputDirectory>${project.build.directory}/generated-sources/ruta/descriptor</typeSystemOutputDirectory>
-
-              <!-- The directory where the generated analysis engine descriptors 
-                will be stored. -->
-              <!-- default value: ${project.build.directory}/generated-sources/ruta/descriptor
-->
-              <analysisEngineOutputDirectory>${project.build.directory}/generated-sources/ruta/descriptor</analysisEngineOutputDirectory>
-
-              <!-- The template descriptor for the generated type system. 
-                By default the descriptor of the maven dependency is loaded. -->
-              <!-- default value: none -->
-              <!-- not used in this example <typeSystemTemplate>...</typeSystemTemplate>
-->
-
-              <!-- The template descriptor for the generated analysis engine. 
-                By default the descriptor of the maven dependency is loaded. -->
-              <!-- default value: none -->
-              <!-- not used in this example <analysisEngineTemplate>...</analysisEngineTemplate>
-->
-
-              <!-- Script paths of the generated analysis engine descriptor. -->
-              <!-- default value: none -->
-              <scriptPaths>
-                <scriptPath>${basedir}/src/main/ruta/</scriptPath>
-              </scriptPaths>
-
-              <!-- Descriptor paths of the generated analysis engine descriptor. -->
-              <!-- default value: none -->
-              <descriptorPaths>
-                <descriptorPath>${project.build.directory}/generated-sources/ruta/descriptor</descriptorPath>
-              </descriptorPaths>
-
-              <!-- Resource paths of the generated analysis engine descriptor. -->
-              <!-- default value: none -->
-              <resourcePaths>
-                <resourcePath>${basedir}/src/main/resources/</resourcePath>
-                <resourcePath>${project.build.directory}/generated-sources/ruta/resources/</resourcePath>
-              </resourcePaths>
-
-              <!-- Suffix used for the generated type system descriptors. -->
-              <!-- default value: Engine -->
-              <analysisEngineSuffix>RutaAnnotator</analysisEngineSuffix>
-
-              <!-- Suffix used for the generated analysis engine descriptors. -->
-              <!-- default value: TypeSystem -->
-              <typeSystemSuffix>RutaTypeSystem</typeSystemSuffix>
-
-              <!-- Source file encoding. -->
-              <!-- default value: ${project.build.sourceEncoding} -->
-              <encoding>UTF-8</encoding>
-
-              <!-- Type of type system imports. false = import by location. -->
-              <!-- default value: false -->
-              <importByName>false</importByName>
-
-              <!-- Option to resolve imports while building. -->
-              <!-- default value: false -->
-              <resolveImports>false</resolveImports>
-
-              <!-- Amount of retries for building dependent descriptors. 
-                Default value -1 leads to three retires for each script. -->
-              <!-- default value: -1 -->
-              <maxBuildRetries>-1</maxBuildRetries>
-
-              <!-- List of packages with language extensions -->
-              <!-- default value: none -->
-              <extensionPackages>
-                <extensionPackage>org.apache.uima.ruta</extensionPackage>
-              </extensionPackages>
-
-              <!-- Add UIMA Ruta nature to .project -->
-              <!-- default value: false -->
-              <addRutaNature>true</addRutaNature>
-
-              <!-- Buildpath of the UIMA Ruta Workbench (IDE) for this project -->
-              <!-- default value: none -->
-              <buildPaths>
-                <buildPath>script:src/main/ruta/</buildPath>
-<!--                 <buildPath>descriptor:target/generated-sources/ruta/descriptor/</buildPath>
-->
-<!--                 <buildPath>resources:src/main/resources/wordlists</buildPath>
-->
-              </buildPaths>
-
-            </configuration>
-          </execution>
-          <execution>
-            <id>mtwl</id>
-            <phase>generate-resources</phase>
-            <goals>
-              <goal>mtwl</goal>
-            </goals>
-            <configuration>
-              <compress>false</compress>
-              <inputFiles>
-                <directory>${basedir}/src/main/resources/wordlists</directory>
-                <includes>
-                  <include>*.txt</include>
-                </includes>
-              </inputFiles>
-              <outputFile>${project.build.directory}/generated-sources/ruta/resources/generated.mtwl</outputFile>
-              <encoding>UTF-8</encoding>
-            </configuration>
-          </execution>
-        </executions>
-      </plugin>
-    </plugins>
-  </build>
-  <dependencyManagement>
-    <dependencies>
-      <dependency>
-        <groupId>org.apache.uima</groupId>
-        <artifactId>uimaj-core</artifactId>
-        <version>2.8.1</version>
-      </dependency>
-      <dependency>
-         <groupId>xml-apis</groupId>
-         <artifactId>xml-apis</artifactId>
-        <version>1.4.01</version>
-      </dependency>
-    </dependencies>
-  </dependencyManagement>
-</project>
\ No newline at end of file

Modified: ctakes/sandbox/ctakes-clinical-deid/pom.xml.rej
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/pom.xml.rej?rev=1727698&r1=1727697&r2=1727698&view=diff
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/pom.xml.rej (original)
+++ ctakes/sandbox/ctakes-clinical-deid/pom.xml.rej Sat Jan 30 14:08:08 2016
@@ -1,94 +0,0 @@
-***************
-*** 11,20 ****
-    </parent>
-  
-    <properties>
-- <!--     <ruta-version>2.4.0-SNAPSHOT</ruta-version> -->
--     <ruta-version>2.3.1</ruta-version>
-    </properties>
-  
-  
-    <dependencies>
-      <dependency>
---- 11,33 ----
-    </parent>
-  
-    <properties>
-+     <ruta-version>2.4.0</ruta-version>
-+ <!--     <ruta-version>2.3.1</ruta-version> -->
-    </properties>
-  
-+   <!--  use ruta-2.4.0-rc1 for now until its released -->
-+   <repositories>
-+     <repository>
-+       <id>staged-release</id>
-+       <url>https://repository.apache.org/content/repositories/orgapacheuima-1080/</url>
-+     </repository>
-+   </repositories>
-+   <pluginRepositories>
-+     <pluginRepository>
-+       <id>staged-release</id>
-+       <url>https://repository.apache.org/content/repositories/orgapacheuima-1080/</url>
-+     </pluginRepository>
-+   </pluginRepositories>
-  
-    <dependencies>
-      <dependency>
-***************
-*** 172,202 ****
-  
-              </configuration>
-            </execution>
-- <!--           <execution> -->
-- <!--             <id>mtwl</id> -->
-- <!--             <phase>generate-resources</phase> -->
-- <!--             <goals> -->
-- <!--               <goal>mtwl</goal> -->
-- <!--             </goals> -->
-- <!--             <configuration> -->
-- <!--               Compress resulting tree word list. -->
-- <!--               default value: true -->
-- <!--               <compress>true</compress> -->
-- <!--               The source files for the multi tree word list. -->
-- <!--               default value: none -->
-- <!--               <inputFiles> -->
-- <!--                 <directory>${basedir}/src/main/resources/wordlists</directory>
-->
-- <!--                 <includes> -->
-- <!--                   <include>*.txt</include> -->
-- <!--                 </includes> -->
-- <!--               </inputFiles> -->
-- <!--               default value: ${project.build.directory}/generated-sources/ruta/resources/generated.mtwl
-->
-- <!--               <outputFile>${project.build.directory}/generated-sources/ruta/resources/generated.mtwl</outputFile>
-->
-- <!--               Source file encoding. -->
-- <!--               default value: ${project.build.sourceEncoding} -->
-- <!--               <encoding>UTF-8</encoding> -->
-- <!--             </configuration> -->
-- <!--           </execution> -->
-          </executions>
-        </plugin>
-      </plugins>
---- 190,213 ----
-  
-              </configuration>
-            </execution>
-+           <execution>
-+             <id>mtwl</id>
-+             <phase>generate-resources</phase>
-+             <goals>
-+               <goal>mtwl</goal>
-+             </goals>
-+             <configuration>
-+               <compress>false</compress>
-+               <inputFiles>
-+                 <directory>${basedir}/src/main/resources/wordlists</directory>
-+                 <includes>
-+                   <include>*.txt</include>
-+                 </includes>
-+               </inputFiles>
-+               <outputFile>${project.build.directory}/generated-sources/ruta/resources/generated.mtwl</outputFile>
-+               <encoding>UTF-8</encoding>
-+             </configuration>
-+           </execution>
-          </executions>
-        </plugin>
-      </plugins>

Modified: ctakes/sandbox/ctakes-clinical-deid/src/main/resources/META-INF/org.apache.uima.fit/types.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/src/main/resources/META-INF/org.apache.uima.fit/types.txt?rev=1727698&r1=1727697&r2=1727698&view=diff
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/src/main/resources/META-INF/org.apache.uima.fit/types.txt
(original)
+++ ctakes/sandbox/ctakes-clinical-deid/src/main/resources/META-INF/org.apache.uima.fit/types.txt
Sat Jan 30 14:08:08 2016
@@ -7,12 +7,4 @@ classpath*:org/apache/ctakes/drugner/typ
 classpath*:org/apache/ctakes/padtermspotter/types/TypeSystem.xml
 classpath*:org/apache/ctakes/smokingstatus/types/TypeSystem.xml
 classpath*:org/apache/ctakes/sideeffect/types/TypeSystem.xml
-classpath*:org/apache/ctakes/typesystem/types/TypeSystem.xml
-classpath*:org/apache/ctakes/assertion/types/TypeSystem.xml
-classpath*:org/apache/ctakes/assertion/zoner/types/TypeSystem.xml
-classpath*:org/apache/ctakes/constituency/parser/types/LabeledTree.xml
-classpath*:org/apache/ctakes/coreference/types/TypeSystem.xml
-classpath*:org/apache/ctakes/drugner/types/TypeSystem.xml
-classpath*:org/apache/ctakes/padtermspotter/types/TypeSystem.xml
-classpath*:org/apache/ctakes/smokingstatus/types/TypeSystem.xml
-classpath*:org/apache/ctakes/sideeffect/types/TypeSystem.xml
\ No newline at end of file
+classpath*:org/apache/ctakes/deid/DeidRutaTypeSystem.xml
\ No newline at end of file



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