Issue #15: Add a CTAKES implementation

Update to CTAKES 4.0.0
phenotips · Aug 17, 2017 · 81770c7 · 81770c7
1 parent ef5bae8
commit 81770c7
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Showing 18 changed files with 28 additions and 1,903 deletions.
diff --git a/ctakes-service/pom.xml b/ctakes-service/pom.xml
@@ -45,7 +45,7 @@
   <properties>
     <coverage.instructionRatio>0.16</coverage.instructionRatio>
     <checkstyle.suppressions.location>${basedir}/src/checkstyle/checkstyle-suppressions.xml</checkstyle.suppressions.location>
-    <ctakes.version>3.2.2</ctakes.version>
+    <ctakes.version>4.0.0</ctakes.version>
   </properties>
 
   <dependencies>
@@ -115,6 +115,12 @@
       <groupId>org.apache.ctakes</groupId>
       <artifactId>ctakes-dictionary-lookup</artifactId>
       <version>${ctakes.version}</version>
+      <exclusions>
+        <exclusion>
+          <groupId>net.sourceforge.ctakesresources</groupId>
+          <artifactId>*</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
     <dependency>
       <groupId>org.apache.ctakes</groupId>
@@ -130,6 +136,12 @@
       <groupId>org.apache.ctakes</groupId>
       <artifactId>ctakes-lvg</artifactId>
       <version>${ctakes.version}</version>
+      <exclusions>
+        <exclusion>
+          <groupId>net.sourceforge.ctakesresources</groupId>
+          <artifactId>*</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
     <dependency>
       <groupId>commons-validator</groupId>
@@ -181,21 +193,24 @@
   <build>
     <plugins>
       <plugin>
-        <groupId>com.googlecode.maven-download-plugin</groupId>
-        <artifactId>download-maven-plugin</artifactId>
-        <version>1.3.0</version>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-dependency-plugin</artifactId>
         <executions>
           <execution>
-            <id>download-lvg</id>
-            <phase>compile</phase>
+            <id>unpack-lvg</id>
             <goals>
-              <goal>wget</goal>
+              <goal>unpack</goal>
             </goals>
             <configuration>
-              <url>https://lexsrv3.nlm.nih.gov/LexSysGroup/Projects/lvg/2008/release/lvg2008.tgz</url>
-              <outputDirectory>${project.build.directory}</outputDirectory>
-              <unpack>true</unpack>
-              <md5>6dde9ebffae96185820d914131a93dc1</md5>
+              <artifactItems>
+                <artifactItem>
+                  <groupId>net.sourceforge.ctakesresources</groupId>
+                  <artifactId>ctakes-resources-lvg2008</artifactId>
+                  <version>${ctakes.version}</version>
+                  <type>jar</type>
+                  <outputDirectory>${project.build.directory}/lvg2008</outputDirectory>
+                </artifactItem>
+              </artifactItems>
             </configuration>
           </execution>
         </executions>
@@ -211,10 +226,10 @@
               <goal>copy-resources</goal>
             </goals>
             <configuration>
-              <outputDirectory>${project.build.directory}/classes/data/HSqlDb</outputDirectory>
+              <outputDirectory>${project.build.directory}/classes/</outputDirectory>
               <resources>
                 <resource>
-                  <directory>${project.build.directory}/lvg2008/data/HSqlDb</directory>
+                  <directory>${project.build.directory}/lvg2008/org/apache/ctakes/lvg/</directory>
                 </resource>
               </resources>
             </configuration>

diff --git a/ctakes-service/src/main/resources/data/ReadMe.txt b/ctakes-service/src/main/resources/data/ReadMe.txt
diff --git a/ctakes-service/src/main/resources/data/Unicode/diacriticMap.data b/ctakes-service/src/main/resources/data/Unicode/diacriticMap.data
diff --git a/ctakes-service/src/main/resources/data/Unicode/ligatureMap.data b/ctakes-service/src/main/resources/data/Unicode/ligatureMap.data
diff --git a/ctakes-service/src/main/resources/data/Unicode/nonStripMap.data b/ctakes-service/src/main/resources/data/Unicode/nonStripMap.data
diff --git a/ctakes-service/src/main/resources/data/Unicode/symbolMap.data b/ctakes-service/src/main/resources/data/Unicode/symbolMap.data
diff --git a/ctakes-service/src/main/resources/data/Unicode/synonymMap.data b/ctakes-service/src/main/resources/data/Unicode/synonymMap.data