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From brittfi...@apache.org
Subject svn commit: r1500517 - in /ctakes/sandbox/ctakes-scrubber-deid: pom.xml release.properties scrubber.properties.sh
Date Sun, 07 Jul 2013 19:28:27 GMT
Author: brittfitch
Date: Sun Jul  7 19:28:27 2013
New Revision: 1500517

URL: http://svn.apache.org/r1500517
Log:
add project files. 

Added:
    ctakes/sandbox/ctakes-scrubber-deid/pom.xml   (with props)
    ctakes/sandbox/ctakes-scrubber-deid/release.properties   (with props)
    ctakes/sandbox/ctakes-scrubber-deid/scrubber.properties.sh

Added: ctakes/sandbox/ctakes-scrubber-deid/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-scrubber-deid/pom.xml?rev=1500517&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-scrubber-deid/pom.xml (added)
+++ ctakes/sandbox/ctakes-scrubber-deid/pom.xml Sun Jul  7 19:28:27 2013
@@ -0,0 +1,105 @@
+<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>3.1.0-SNAPSHOT</version>
+  </parent>
+  <artifactId>ctakes-scrubber-deid</artifactId>
+  <version>3.1-SNAPSHOT</version>
+  <name>cTAKES Scrubber De-Identification</name>
+  <description>cTAKES Scrubber De-Identification module</description>
+  
+  <dependencies>
+        <dependency>
+            <groupId>mysql</groupId>
+            <artifactId>mysql-connector-java</artifactId>
+            <version>5.0.5</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.uima</groupId>
+            <artifactId>uimaj-core</artifactId>
+            <version>2.3.1</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.uima</groupId>
+            <artifactId>uimaj-cpe</artifactId>
+            <version>2.3.1</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.uima</groupId>
+            <artifactId>uimaj-examples</artifactId>
+            <version>2.3.1</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.uima</groupId>
+            <artifactId>uimaj-tools</artifactId>
+            <version>2.3.1</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.uima</groupId>
+            <artifactId>uimaj-bootstrap</artifactId>
+            <version>2.3.1</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.uima</groupId>
+            <artifactId>jVinci</artifactId>
+            <version>2.3.1</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.uima</groupId>
+            <artifactId>uimaj-adapter-soap</artifactId>
+            <version>2.3.1</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.uima</groupId>
+            <artifactId>uimaj-adapter-vinci</artifactId>
+            <version>2.3.1</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.uima</groupId>
+            <artifactId>uimaj-document-annotation</artifactId>
+            <version>2.3.1</version>
+        </dependency>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.9</version>
+        </dependency>
+        <dependency>
+            <groupId>log4j</groupId>
+            <artifactId>log4j</artifactId>
+            <version>1.2.11</version>
+        </dependency>
+        <dependency>
+            <groupId>com.thoughtworks.xstream</groupId>
+            <artifactId>xstream</artifactId>
+            <version>1.4.2</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.ctakes</groupId>
+            <artifactId>ctakes-type-system</artifactId>
+        </dependency>
+
+        <!-- THIRD PARTY COMPONENTS, NOT FOR REDISTRIBUTION -->
+        <dependency>
+			<groupId>nz.ac.waikato.cms.weka</groupId>
+			<artifactId>weka-stable</artifactId>
+			<version>3.6.6</version>
+		</dependency>
+		            
+        <!-- <dependency>
+            <groupId>weka</groupId>
+            <artifactId>weka</artifactId>
+            <version>3.6.3</version>
+            <scope>provided</scope>
+        </dependency> -->
+<!--         <dependency>
+            <groupId>weka</groupId>
+            <artifactId>weka</artifactId>
+            <version>3.6.3</version>
+            <classifier>sources</classifier>
+            <scope>provided</scope>
+        </dependency> -->
+    </dependencies>
+</project>
\ No newline at end of file

Propchange: ctakes/sandbox/ctakes-scrubber-deid/pom.xml
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-scrubber-deid/release.properties
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-scrubber-deid/release.properties?rev=1500517&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-scrubber-deid/release.properties (added)
+++ ctakes/sandbox/ctakes-scrubber-deid/release.properties Sun Jul  7 19:28:27 2013
@@ -0,0 +1,4 @@
+# For non-interactive (--batch-mode) release builds
+scm.tag=3.0
+releaseVersion=3.0
+developmentVersion=3.1-SNAPSHOT

Propchange: ctakes/sandbox/ctakes-scrubber-deid/release.properties
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-scrubber-deid/scrubber.properties.sh
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-scrubber-deid/scrubber.properties.sh?rev=1500517&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-scrubber-deid/scrubber.properties.sh (added)
+++ ctakes/sandbox/ctakes-scrubber-deid/scrubber.properties.sh Sun Jul  7 19:28:27 2013
@@ -0,0 +1,27 @@
+export SCRUBBER_DB_DRIVER=com.mysql.jdbc.Driver
+export SCRUBBER_DB_NAME=scrubber
+export SCRUBBER_DB_USER=scrubber
+export SCRUBBER_DB_PWD=scrubber
+export SCRUBBER_DB_URI=jdbc:mysql://localhost:3306/scrubber
+export SCRUBBER_DIR_DB_TEMP=/tmp
+export SCRUBBER_DIR_INPUT_HUMAN_ANNOTATIONS_TRAIN=data/input/phi/train
+export SCRUBBER_DIR_INPUT_HUMAN_ANNOTATIONS_TEST=data/input/phi/test
+export SCRUBBER_HUMAN_ANNOTATIONS_IMPLEMENTATION=org.spin.scrubber.classification.HumanAnnotationsExtractorProtege
+export SCRUBBER_DIR_INPUT_PUBS_XML=data/input/pubs/xml
+export SCRUBBER_DIR_INPUT_PUBS_TXT=data/input/pubs/txt
+export SCRUBBER_DIR_INPUT_PUBS_PROCESSED=data/input/pubs/processed
+export SCRUBBER_DIR_INPUT_TRAIN=data/input/cases/train
+export SCRUBBER_DIR_INPUT_TEST=data/input/cases/test
+export SCRUBBER_DIR_OUTPUT_TEST=data/scrubbed/test
+export SCRUBBER_DIR_MODELS=data/models
+export SCRUBBER_FILE_MODEL_TRAIN=train.arff
+export SCRUBBER_FILE_MODEL_TEST=test.arff
+export SCRUBBER_UIMA_READER_FILE_TRAIN=reader_files_train.xml
+export SCRUBBER_UIMA_READER_FILE_TEST=reader_files_test.xml
+export SCRUBBER_UIMA_READER_FILE_PUBS=reader_files_pubs.xml
+export SCRUBBER_UIMA_READER_IMPL_TRAIN=org.spin.scrubber.uima.reader.FileSystemCollectionReaderXML
+export SCRUBBER_UIMA_READER_IMPL_TEST=org.spin.scrubber.uima.reader.FileSystemCollectionReaderXML
+export SCRUBBER_UIMA_READER_IMPL_PUBS=org.spin.scrubber.uima.reader.FileSystemCollectionReader
+export SCRUBBER_CLASSIFICATION_COST_MATRIX="[0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0; 100.0 0.0
1.0 1.0 1.0 1.0 1.0 1.0 1.0; 100.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 1.0; 100.0 1.0 1.0 0.0 1.0
1.0 1.0 1.0 1.0; 100.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0; 100.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0
1.0; 100.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0; 100.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0; 100.0 1.0
1.0 1.0 1.0 1.0 1.0 1.0 0.0]"
+export SCRUBBER_LOCALHOST_NUM_THREADS=2
+export SCRUBBER_TEST_DB_AVAILABLE=false



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