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From james-mas...@apache.org
Subject svn commit: r1403908 [1/2] - in /incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root: BUILDING build_step1.properties build_step1.xml build_step2.properties build_step2.xml build_step3.xml
Date Tue, 30 Oct 2012 22:47:40 GMT
Author: james-masanz
Date: Tue Oct 30 22:47:40 2012
New Revision: 1403908

URL: http://svn.apache.org/viewvc?rev=1403908&view=rev
Log: (empty)

Added:
    incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/BUILDING
    incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step1.properties   (with props)
    incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step1.xml   (with props)
    incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step2.properties   (with props)
    incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step2.xml   (with props)
    incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step3.xml   (with props)

Added: incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/BUILDING
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/files%20for%20pipeline%20root/BUILDING?rev=1403908&view=auto
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/BUILDING (added)
+++ incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/BUILDING Tue Oct 30 22:47:40 2012
@@ -0,0 +1,35 @@
+
+This information relates to building ctakes-2.6-incubating
+
+First, check out all projects from SVN.
+For example, assertion and chunker are separate projects.
+
+There are three ant scripts used to build cTAKES. The ant scripts
+can be found in project 'files for pipeline root'.
+
+The ant scripts rely on ant-contrib.jar and on xmltask.jar,
+which are separate downloads. 
+They also depend on UIMA, which is a separate download available 
+from http://uima.apache.org/
+
+The three ant scripts are:
+
+ build_step1.xml: Generate type system (jcasgen) and compile code.
+ 
+ build_step2.xml: Reorganize directories so there is a single bin
+                  directory, so all descriptors are within a single
+                  subtree (under cTAKESdesc), and so all resources 
+                  are within a single subtree (under resources).
+              
+ build_step3.xml: Create a single jar file with all .class files
+                  from bin and from all dependent jars.
+
+Script build_step1 relies on values within build_step1.properties
+Script build_step2 relies on values within build_step2.properties
+
+Update those properties files for your environment.
+
+Script build_step3 relies on the basedir value within build_script3.xml
+
+Update the basedir value for your environment
+ 
\ No newline at end of file

Added: incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step1.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/files%20for%20pipeline%20root/build_step1.properties?rev=1403908&view=auto
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step1.properties (added)
+++ incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step1.properties Tue Oct 30 22:47:40 2012
@@ -0,0 +1,18 @@
+# Please do not comment or remove the following line.
+RELEASE_VERSION=2.6-incubating
+
+# UIMA_HOME is the same as your environment variable
+#           when you installed Apache UIMA.
+#           No trailing slash/backslash.
+#           This is optional, if not set, build.xml
+#           will read from your environment variable.
+UIMA_HOME=C:/Apps/ApacheSoftwareFoundation/uima/uimaj-2.4.0-bin
+
+
+# ECLIPSE_HOME is where you installed Eclipse IDE.
+#              No trailing slash/backslash.
+#              This is optional, if not set, build.xml
+#              will read from your environment variable.
+#              This is only useful if you are going to
+#              use Eclipse as your IDE after compiling.
+ECLIPSE_HOME=C:/Apps/eclipse-java-helios-win32/eclipse

Propchange: incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step1.properties
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step1.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/files%20for%20pipeline%20root/build_step1.xml?rev=1403908&view=auto
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step1.xml (added)
+++ incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step1.xml Tue Oct 30 22:47:40 2012
@@ -0,0 +1,917 @@
+<?xml version="1.0"?>
+
+<project name="cTAKES" default="generate_types" basedir=".">
+  <description>
+    Generate types and optionally compile cTAKES. 
+    Default target is generate_types.
+    The target named all generates type system, compiles all projects, and generates javadoc.
+  </description>
+
+
+<!-- ==================================================================================== -->
+<!--                DECLARATIONS                                                          -->
+<!-- ==================================================================================== -->
+
+    <!-- Use environmental variables -->
+    <property environment="env" />
+    <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
+    <!-- Set the following properties in build_step1.properties.                         -->
+    <!-- No trailing slashes please.                                                     -->
+    <!--     UIMA_HOME        UIMA installation directory                                -->
+    <!--     ECLIPSE_HOME     Eclipse installation directory                             -->
+    <!-- Values in this file will override environmental variables.                      -->
+    <!-- Be careful setting environmental variables as they may have surprising values,  -->
+    <!--    which can trigger unexpected behavior.                                       -->
+    <!-- NOTE TO WINDOWS USERS: Please use forward slashes or escaped backslashes        -->
+    <!--                        in directory names.                                      -->
+    <!--      For example: C:\\path\\to\\home\\of\\uima\\directory                       -->
+    <!--      or:          C:/path/to/home/of/uima/directory                             -->
+    <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
+    <property file="build_step1.properties" prefix="pf" />
+
+
+    <!-- - - - - - - - - - - - - - - - - -->
+    <!-- Set uima.home and eclipse.home  -->
+    <!-- - - - - - - - - - - - - - - - - -->
+    <condition property="uima.home" value="${pf.UIMA_HOME}">
+        <isset property="pf.UIMA_HOME" />
+    </condition>
+    <condition property="uima.home" value="${env.UIMA_HOME}">
+        <isset property="env.UIMA_HOME" />
+    </condition>
+    <condition property="eclipse.home" value="${pf.ECLIPSE_HOME}">
+        <isset property="pf.ECLIPSE_HOME" />
+    </condition>
+    <condition property="eclipse.home" value="${env.ECLIPSE_HOME}">
+        <isset property="env.ECLIPSE_HOME" />
+    </condition>
+    <!-- Use jcasgen_merge if Eclipse is found, otherwise, use jcasgen -->
+    <!-- CAVEAT: An environment variable is considered set             -->
+    <!--         even if its value is empty.                           -->
+    <condition property="jcasgener" value="jcasgen_merge" else="jcasgen">
+        <isset property="eclipse.home" />
+    </condition>
+    <condition property="jext" value="bat" else="sh">
+        <os family="windows" />
+    </condition>
+    <condition property="pipeline.version" value="${pf.RELEASE_VERSION}" else="version">
+        <isset property="pf.RELEASE_VERSION" />
+    </condition>
+
+    <!-- - - - - - - - - -->
+    <!-- Project folders -->
+    <!-- - - - - - - - - -->
+    <property name="_common_type_system.dir" value="../common-type-system" />
+    <property name="_assertion.dir" value="../assertion" />
+    <property name="_chunker.dir" value="../chunker" />
+    <property name="_clinical_documents_pipeline.dir" value="../clinical documents pipeline" />
+    <property name="_context_dependent_tokenizer.dir" value="../context dependent tokenizer" />
+    <property name="_core.dir" value="../core" />
+    <property name="_dictionary_lookup.dir" value="../dictionary lookup" />
+    <property name="_document_preprocessor.dir" value="../document preprocessor" />
+    <property name="_LVG.dir" value="../LVG" />
+    <property name="_NE_contexts.dir" value="../NE contexts" />
+    <property name="_POS_tagger.dir" value="../POS tagger" />
+    <property name="_dependency_parser.dir" value="../dependency parser" />
+    <property name="_pad_termspotter.dir" value="../PAD term spotter" />
+    <property name="_drug_ner.dir" value="../Drug NER" />
+    <property name="_smoking_status.dir" value="../smoking status" />
+    <property name="_side_effects.dir" value="../SideEffect" />
+    <property name="_constituency_parser.dir" value="../Constituency Parser" />
+    <property name="_coref_resolver.dir" value="../coref-resolver" />
+    <property name="_relation_extractor.dir" value="../relation-extractor" />
+    	
+    <property name="_utils_project.dir" value="../utils" />
+
+	<property name="docs.dir" value="../docs" />
+	<!-- If change these above, also check below for utils -->
+
+    <!-- - - - - - - - - - - -->
+    <!-- Project subfolders  -->
+    <!-- - - - - - - - - - - -->
+    <property name="src.dir" value="src" />
+    <property name="bin.dir" value="bin" />
+    <property name="lib.dir" value="lib" />
+    <property name="desc.dir" value="desc" />
+    <property name="res.dir" value="resources" />
+	
+    <property name="compile.debug" value="true" />
+
+    <!-- - - - - - - - - - - - - - -->
+    <!-- Project build classpaths  -->
+    <!-- - - - - - - - - - - - - - -->
+    <property name="_uima.lib" value="${uima.home}/lib/uima-core.jar:${uima.home}/lib/uima-document-annotation.jar:${uima.home}/lib/uima-tools.jar:${uima.home}/lib/uima-cpe.jar" />
+    <property name="_junit.lib" value="${_core.dir}/${lib.dir}/junit.jar" />
+    <path id="_assertion.cp">
+        <pathelement path="${_assertion.dir}/${src.dir}" />
+        <pathelement path="${_assertion.dir}/conf" />
+        <pathelement path="${_assertion.dir}/${res.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement path="${_dependency_parser.dir}/${bin.dir}" />
+        <pathelement location="${_assertion.dir}/${lib.dir}/commons-cli-1.2.jar"/>
+        <pathelement location="${_assertion.dir}/${lib.dir}/commons-lang-2.6.jar"/>
+        <pathelement location="${_assertion.dir}/${lib.dir}/jackson-core-asl-1.5.0.jar"/>
+        <pathelement location="${_assertion.dir}/${lib.dir}/jackson-mapper-asl-1.5.0.jar"/>
+        <pathelement location="${_assertion.dir}/${lib.dir}/jcarafe-core_2.9.1-0.9.8.3.RC4.jar"/>
+        <pathelement location="${_assertion.dir}/${lib.dir}/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar"/>
+        <pathelement location="${_assertion.dir}/${lib.dir}/med-facts-i2b2-1.2-SNAPSHOT.jar"/>
+        <pathelement location="${_assertion.dir}/${lib.dir}/med-facts-zoner-1.1.jar"/>
+        <pathelement location="${_assertion.dir}/${lib.dir}/sbinary_2.9.0-0.4.0.jar"/>
+        <pathelement location="${_assertion.dir}/${lib.dir}/scala-library-2.9.0.jar"/>
+        <pathelement location="${_core.dir}/${lib.dir}/opennlp-tools-1.5.2-incubating.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/opennlp-maxent-3.0.2-incubating.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/uimafit-1.2.0.jar" />
+    	<pathelement location="${_assertion.dir}/${lib.dir}/cleartk-eval-0.8.1.jar"/>
+    	<pathelement location="${_assertion.dir}/${lib.dir}/cleartk-examples-0.6.0.jar"/>
+    	<pathelement location="${_assertion.dir}/${lib.dir}/cleartk-ml-1.0.1.jar"/>
+    	<pathelement location="${_assertion.dir}/${lib.dir}/cleartk-ml-opennlp-maxent-1.0.2.jar"/>
+    	<pathelement location="${_assertion.dir}/${lib.dir}/cleartk-test-util-1.0.1.jar"/>
+    	<pathelement location="${_assertion.dir}/${lib.dir}/cleartk-type-system-1.0.0.jar"/>
+    	<pathelement location="${_assertion.dir}/${lib.dir}/cleartk-util-0.8.1.jar"/>
+        <pathelement path="${_uima.lib}" />
+        <pathelement path="${_junit.lib}" />
+    </path>
+    <path id="_chunker.cp">
+        <pathelement path="${_chunker.dir}/${src.dir}" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement path="${_POS_tagger.dir}/${bin.dir}" />
+        <pathelement location="${_core.dir}/${lib.dir}/opennlp-tools-1.5.2-incubating.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/opennlp-maxent-3.0.2-incubating.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement path="${_uima.lib}" />
+        <pathelement path="${_junit.lib}" />
+    </path>
+    <path id="_clinical_documents_pipeline.cp">
+        <pathelement path="${_clinical_documents_pipeline.dir}/${src.dir}" />
+        <pathelement path="${_chunker.dir}/${bin.dir}" />
+        <pathelement path="${_context_dependent_tokenizer.dir}/${bin.dir}" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />    	
+        <pathelement path="${_dictionary_lookup.dir}/${bin.dir}" />
+        <pathelement path="${_document_preprocessor.dir}/${bin.dir}" />
+        <pathelement path="${_LVG.dir}/${bin.dir}" />
+        <pathelement path="${_NE_contexts.dir}/${bin.dir}" />
+        <pathelement path="${_POS_tagger.dir}/${bin.dir}" />
+	<!--
+            <pathelement path="${_dependency_parser.dir}/${bin.dir}" />
+	-->
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement path="${_uima.lib}" />
+    </path>
+    <path id="_context_dependent_tokenizer.cp">
+        <pathelement path="${_context_dependent_tokenizer.dir}/${src.dir}" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement path="${_uima.lib}" />
+    </path>
+    <path id="_core.cp">
+        <pathelement path="${_core.dir}/${src.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement path="${_junit.lib}" />
+        <pathelement location="${_core.dir}/${lib.dir}/jdom.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/lucene-core-3.0.2.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/opennlp-maxent-3.0.2-incubating.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/OpenAI_FSM.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/opennlp-tools-1.5.2-incubating.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/SQLWrapper.jar" />    	
+        <pathelement location="${_core.dir}/${lib.dir}/FindStructAPI.jar" />    	
+        <pathelement location="${_core.dir}/${lib.dir}/struct_mult.jar" />    	
+        <!-- <pathelement location="${_core.dir}/${lib.dir}/uimafit-1.2.0.jar" /> -->    	
+        <pathelement path="${_uima.lib}" />
+    </path>
+    <path id="_common_type_system.cp">
+        <pathelement path="${_core.dir}/${src.dir}" />
+    	<!-- <pathelement location="${_core.dir}/${lib.dir}/jdom.jar" /> --> 
+        <!-- <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" /> -->
+        <!-- <pathelement location="${_core.dir}/${lib.dir}/lucene-core-3.0.2.jar" /> --> 
+        <pathelement location="${_common_type_system.dir}/${lib.dir}/libsvm-2.91.jar" />
+        <pathelement path="${_uima.lib}" />
+        <pathelement path="${_junit.lib}" />
+    </path>	
+    <path id="_dictionary_lookup.cp">
+        <pathelement path="${_dictionary_lookup.dir}/${src.dir}" />
+        <pathelement path="${_dictionary_lookup.dir}/scripts/java" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement location="${_core.dir}/${lib.dir}/jdom.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/lucene-core-3.0.2.jar" />
+        <pathelement path="${_uima.lib}" />
+    </path>
+    <path id="_document_preprocessor.cp">
+        <pathelement path="${_document_preprocessor.dir}/${src.dir}" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement location="${_document_preprocessor.dir}/${lib.dir}/xercesImpl.jar" />
+        <pathelement location="${_document_preprocessor.dir}/${lib.dir}/xml-apis.jar" />
+        <pathelement location="${_document_preprocessor.dir}/${lib.dir}/xmlParserAPIs.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement path="${_uima.lib}" />
+        <pathelement path="${_junit.lib}" />
+    </path>
+    <path id="_LVG.cp">
+        <pathelement path="${_LVG.dir}/${src.dir}" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement location="${_LVG.dir}/${lib.dir}/lvg2010dist.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement path="${_uima.lib}" />
+    </path>
+    <path id="_NE_contexts.cp">
+        <pathelement path="${_NE_contexts.dir}/${src.dir}" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement path="${_uima.lib}" />
+        <pathelement path="${_junit.lib}" />
+    </path>
+    <path id="_POS_tagger.cp">
+        <pathelement path="${_POS_tagger.dir}/{$src.dir}" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement location="${_core.dir}/${lib.dir}/jdom.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/opennlp-maxent-3.0.2-incubating.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/opennlp-tools-1.5.2-incubating.jar" />
+        <pathelement path="${_uima.lib}" />
+        <pathelement path="${_junit.lib}" />
+    </path>
+    <path id="_dependency_parser.cp">
+        <pathelement path="${_dependency_parser.dir}/{$src.dir}" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement path="${_LVG.dir}/${bin.dir}" />
+        <pathelement path="${_POS_tagger.dir}/${bin.dir}" />
+        <pathelement path="${_chunker.dir}/${bin.dir}" />
+        <pathelement path="${_context_dependent_tokenizer.dir}/${bin.dir}" />
+        <pathelement path="${_dependency_parser.dir}/{$resources.dir}" />
+        <!-- <pathelement location="${_dependency_parser.dir}/${lib.dir}/liblinear-1.51.jar" /> -->
+    	<pathelement location="${_dependency_parser.dir}/${lib.dir}/cleartk-util-0.8.1.jar"/>
+    	<pathelement location="${_dependency_parser.dir}/${lib.dir}/args4j-2.0.16.jar"/>
+    	<pathelement location="${_dependency_parser.dir}/${lib.dir}/hppc-0.3.1.jar"/>
+    	<pathelement location="${_dependency_parser.dir}/${lib.dir}/clearparser-0.33.jar"/>
+    	<pathelement location="${_dependency_parser.dir}/${lib.dir}/commons-io-2.0.1.jar"/>
+    	<pathelement location="${_dependency_parser.dir}/${lib.dir}/commons-lang-2.4.jar"/>
+    	<pathelement location="${_dependency_parser.dir}/${lib.dir}/commons-logging-1.1.1.jar"/>
+    	<pathelement location="${_core.dir}/${lib.dir}/uimafit-1.2.0.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement path="${_junit.lib}" />
+        <pathelement path="${_uima.lib}" />
+    </path>
+
+    <path id="_pad_termspotter.cp">
+        <pathelement path="${_pad_termspotter.dir}/${src.dir}" />
+        <pathelement path="${_clinical_documents_pipeline.dir}/${bin.dir}" />
+        <pathelement path="${_chunker.dir}/${bin.dir}" />
+        <pathelement path="${_context_dependent_tokenizer.dir}/${bin.dir}" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/OpenAI_FSM.jar" />
+        <pathelement path="${_dictionary_lookup.dir}/${bin.dir}" />
+        <pathelement path="${_NE_contexts.dir}/${bin.dir}" />
+        <pathelement path="${_POS_tagger.dir}/${bin.dir}" />
+        <pathelement path="${_uima.lib}" />
+    </path>
+
+    <path id="_drug_ner.cp">
+        <pathelement path="${_drug_ner.dir}/${src.dir}" />
+        <pathelement path="${_clinical_documents_pipeline.dir}/${bin.dir}" />
+        <pathelement path="${_context_dependent_tokenizer.dir}/${bin.dir}" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement location="${_core.dir}/${lib.dir}/jdom.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/lucene-core-3.0.2.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/opennlp-maxent-3.0.2-incubating.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/OpenAI_FSM.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/opennlp-tools-1.5.2-incubating.jar" />
+        <pathelement path="${_dictionary_lookup.dir}/${bin.dir}" />
+        <pathelement path="${_NE_contexts.dir}/${bin.dir}" />
+        <pathelement path="${_POS_tagger.dir}/${bin.dir}" />
+        <pathelement path="${_uima.lib}" />
+	</path>
+
+    <path id="_smoking_status.cp">
+        <pathelement path="${_smoking_status.dir}/${src.dir}" />
+        <pathelement path="${_clinical_documents_pipeline.dir}/${bin.dir}" />
+        <pathelement location="${_core.dir}/${lib.dir}/jdom.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement path="${_chunker.dir}/${bin.dir}" />
+        <pathelement path="${_context_dependent_tokenizer.dir}/${bin.dir}" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement path="${_dictionary_lookup.dir}/${bin.dir}" />
+        <pathelement path="${_document_preprocessor.dir}/${bin.dir}" />
+        <pathelement location="${_core.dir}/${lib.dir}/OpenAI_FSM.jar" />
+        <pathelement path="${_LVG.dir}/${bin.dir}" />
+        <pathelement path="${_NE_contexts.dir}/${bin.dir}" />
+        <pathelement path="${_POS_tagger.dir}/${bin.dir}" />
+        <pathelement location="${_smoking_status.dir}/${lib.dir}/libsvm-2.91.jar" />
+        <pathelement location="${_smoking_status.dir}/${lib.dir}/lucene-core-3.0.2.jar" />
+        <pathelement path="${_uima.lib}" />
+    </path>
+
+    <path id="_side_effects.cp">
+        <pathelement path="${_side_effects.dir}/${src.dir}" />
+        <pathelement location="${_core.dir}/${lib.dir}/jdom.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement location="${_side_effects.dir}/${lib.dir}/libsvm-2.91.jar" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement location="${_drug_ner.dir}/${bin.dir}" />
+        <pathelement path="${_dictionary_lookup.dir}/${bin.dir}" />
+        <pathelement path="${_uima.lib}" />
+    </path>
+
+    <path id="_constituency_parser.cp" >
+    <pathelement path="${_constituency_parser.dir}/${src.dir}" />
+    <pathelement path="${_clinical_documents_pipeline.dir}/${bin.dir}" />
+    <pathelement location="${_core.dir}/${lib.dir}/jdom.jar" />
+    <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+    <pathelement path="${_core.dir}/${bin.dir}" />
+    <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+    <pathelement location="${_core.dir}/${lib.dir}/opennlp-tools-1.5.2-incubating.jar" />
+    <pathelement path="${_uima.lib}" />
+    </path>
+
+    <path id="_coref_resolver.cp" >
+        <pathelement path="${_coref_resolver.dir}/${src.dir}" />
+        <pathelement location="${_coref_resolver.dir}/${lib.dir}/Jama-1.0.2.jar" />
+        <pathelement location="${_coref_resolver.dir}/${lib.dir}/libsvm.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/jdom.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement location="${_side_effects.dir}/${lib.dir}/libsvm-2.91.jar" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />    	
+        <pathelement path="${_constituency_parser.dir}/${bin.dir}" />
+        <pathelement path="${_dependency_parser.dir}/${bin.dir}" />
+        <pathelement path="${_dictionary_lookup.dir}/${bin.dir}" />
+        <pathelement location="${_core.dir}/${lib.dir}/opennlp-tools-1.5.2-incubating.jar" />
+        <pathelement path="${_uima.lib}" />
+    </path>
+
+    <path id="_relation_extractor.cp">
+        <pathelement path="${_relation_extractor.dir}/{$src.dir}" />
+        <pathelement path="${_relation_extractor.dir}/test/{$src.dir}" />
+        <pathelement path="${_common_type_system.dir}/${bin.dir}" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+    	
+        <pathelement path="${_uima.lib}" />
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/cleartk-chunker-1.0.1.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/cleartk-eval-0.8.1.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/cleartk-ml-1.0.1.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/cleartk-ml-libsvm-1.0.1.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/cleartk-ml-opennlp-maxent-1.0.2.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/cleartk-ml-svmlight-1.0.2.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/cleartk-test-util-1.0.1.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/cleartk-util-0.8.1.jar"/>
+
+    	<pathelement location="${_core.dir}/${lib.dir}/uimafit-1.2.0.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/args4j-2.0.16.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/commons-io-2.0.1.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/commons-lang-2.4.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/commons-logging-1.1.1.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/guava-10.0.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/hppc-0.4.1.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/spring-core-3.0.3.RELEASE.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/jdom.jar"/>
+    	<pathelement location="${_relation_extractor.dir}/${lib.dir}/libsvm-3.1.jar"/>
+
+        <pathelement path="${_clinical_documents_pipeline.dir}/${bin.dir}" />
+        <pathelement path="${_dependency_parser.dir}/${bin.dir}" />
+        <pathelement path="${_context_dependent_tokenizer.dir}/${bin.dir}" />
+        <pathelement path="${_constituency_parser.dir}/${bin.dir}" />
+        <pathelement path="${_NE_contexts.dir}/${bin.dir}" />
+        <pathelement path="${_chunker.dir}/${bin.dir}" />
+
+        <pathelement path="${_junit.lib}" />
+    </path>
+
+
+	
+	
+	<!-- - - - - - - - - - -->
+    <!-- Runtime classpath -->
+    <!-- - - - - - - - - - -->
+    <path id="testrun.cp">
+        <pathelement path="${_uima.lib}" />
+        <!-- binary (.class) directories -->
+        <pathelement path="${_chunker.dir}/${bin.dir}" />
+        <pathelement path="${_clinical_documents_pipeline.dir}/${bin.dir}" />
+        <pathelement path="${_constituency_parser.dir}/${bin.dir}" />
+        <pathelement path="${_context_dependent_tokenizer.dir}/${bin.dir}" />
+        <pathelement path="${_core.dir}/${bin.dir}" />
+    	<pathelement path="${_common_type_system.dir}/${bin.dir}" />    	
+        <pathelement path="${_dependency_parser.dir}/${bin.dir}" />
+        <pathelement path="${_dictionary_lookup.dir}/${bin.dir}" />
+        <pathelement path="${_document_preprocessor.dir}/${bin.dir}" />
+        <pathelement path="${_LVG.dir}/${bin.dir}" />
+        <pathelement path="${_NE_contexts.dir}/${bin.dir}" />
+        <pathelement path="${_POS_tagger.dir}/${bin.dir}" />
+    	
+        <!-- resource directories -->
+        <pathelement path="${_chunker.dir}/${res.dir}" />
+        <pathelement path="${_clinical_documents_pipeline.dir}/${res.dir}" />
+        <pathelement path="${_constituency_parser.dir}/${res.dir}" />
+        <pathelement path="${_context_dependent_tokenizer.dir}/${res.dir}" />
+        <pathelement path="${_core.dir}/${res.dir}" />
+        <pathelement path="${_dependency_parser.dir}/${res.dir}" />
+        <pathelement path="${_dictionary_lookup.dir}/${res.dir}" />
+        <pathelement path="${_document_preprocessor.dir}/${res.dir}" />
+        <pathelement path="${_LVG.dir}/${res.dir}" />
+        <pathelement path="${_NE_contexts.dir}/${res.dir}" />
+        <pathelement path="${_POS_tagger.dir}/${res.dir}" />
+    	
+        <!-- library jars directories -->
+        <pathelement location="${_core.dir}/${lib.dir}/log4j-1.2.15.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/jdom.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/lucene-core-3.0.2.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/opennlp-tools-1.5.2-incubating.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/opennlp-maxent-3.0.2-incubating.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/OpenAI_FSM.jar" />
+        <pathelement location="${_document_preprocessor.dir}/${lib.dir}/xercesImpl.jar" />
+        <pathelement location="${_document_preprocessor.dir}/${lib.dir}/xml-apis.jar" />
+        <pathelement location="${_document_preprocessor.dir}/${lib.dir}/xmlParserAPIs.jar" />
+        <pathelement location="${_LVG.dir}/${lib.dir}/lvg2010dist.jar" />
+        <pathelement location="${_core.dir}/${lib.dir}/SQLWrapper.jar" />    	
+        <pathelement location="${_dependency_parser.dir}/${lib.dir}/liblinear-1.51.jar" />
+ 
+
+	<!--
+            <pathelement path="${_dependency_parser.dir}/${bin.dir}" />
+            <pathelement path="${_dependency_parser.dir}/${res.dir}" />
+            <pathelement path="${_dependency_parser.dir}" />
+            <pathelement location="${_dependency_parser.dir}/{$lib.dir}/hppc-0.3.1.jar" />
+            <pathelement location="${_dependency_parser.dir}/{$lib.dir}/liblinear-1.51.jar" />
+            <pathelement location="${_dependency_parser.dir}/{$lib.dir}/args4j-2.0.12.jar" />
+	-->
+    </path>
+
+
+<!-- ==================================================================================== -->
+<!--                       TARGETS                                                        -->
+<!-- ==================================================================================== -->
+
+    <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
+    <!-- Clean up all binary java .class files & JCasGend types  -->
+    <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
+    <target name="clean" description="Remove compiled java files and type system files.">
+        <delete dir="${_chunker.dir}/${bin.dir}" />
+        <delete dir="${_clinical_documents_pipeline.dir}/${bin.dir}" />
+        <delete dir="${_context_dependent_tokenizer.dir}/${bin.dir}" />
+        <delete dir="${_core.dir}/${bin.dir}" />
+        <delete dir="${_common_type_system.dir}/${bin.dir}" />    	
+        <delete dir="${_dictionary_lookup.dir}/${bin.dir}" />
+        <delete dir="${_document_preprocessor.dir}/${bin.dir}" />
+        <delete dir="${_LVG.dir}/${bin.dir}" />
+        <delete dir="${_NE_contexts.dir}/${bin.dir}" />
+        <delete dir="${_POS_tagger.dir}/${bin.dir}" />
+        <delete dir="${_dependency_parser.dir}/${bin.dir}" />
+        <delete dir="${_drug_ner.dir}/${bin.dir}" />
+        <delete dir="${_smoking_status.dir}/${bin.dir}" />
+        <delete dir="${_side_effects.dir}/${bin.dir}" />
+        <delete dir="${_constituency_parser.dir}/${bin.dir}" />
+        <delete dir="${_coref_resolver.dir}/${bin.dir}" />
+        <delete dir="${_assertion.dir}/${bin.dir}" />
+        <delete dir="${_relation_extractor.dir}/${bin.dir}" />
+   		<echo message="Now deleting filesets for gen'd types"/>
+        <delete>
+            <fileset dir="${_assertion.dir}/${src.dir}" includes="**/types/*.java" />
+            <fileset dir="${_chunker.dir}/${src.dir}" includes="**/type/*.java" />
+            <fileset dir="${_clinical_documents_pipeline.dir}/${src.dir}" includes="**/core/type/*/*.java" />
+            <fileset dir="${_clinical_documents_pipeline.dir}/${src.dir}" includes="**/core/type/*.java" /> <!-- any old types -->
+            <fileset dir="${_context_dependent_tokenizer.dir}/${src.dir}" includes="**/type/*.java" />
+            <fileset dir="${_core.dir}/${src.dir}" includes="**/type/*.java" />
+            <fileset dir="${_coref_resolver.dir}/${src.dir}" includes="**/uima/coref/type/*.java" />
+        	<!-- don't delete what's in core/type/constants -->
+            <fileset dir="${_common_type_system.dir}/${src.dir}" includes="**/core/type/refsem/*.java" />
+            <fileset dir="${_common_type_system.dir}/${src.dir}" includes="**/core/type/relation/*.java" />
+            <fileset dir="${_common_type_system.dir}/${src.dir}" includes="**/core/type/structured/*.java" />
+            <fileset dir="${_common_type_system.dir}/${src.dir}" includes="**/core/type/syntax/*.java" />
+            <fileset dir="${_common_type_system.dir}/${src.dir}" includes="**/core/type/textsem/*.java" />
+            <fileset dir="${_common_type_system.dir}/${src.dir}" includes="**/core/type/textspan/*.java" />
+            <fileset dir="${_common_type_system.dir}/${src.dir}" includes="**/core/type/util/*.java" />
+            <fileset dir="${_dictionary_lookup.dir}/${src.dir}" includes="**/type/*.java" />
+            <fileset dir="${_document_preprocessor.dir}/${src.dir}" includes="**/type/*.java" />
+            <fileset dir="${_LVG.dir}/${src.dir}" includes="**/type/*.java" />
+            <fileset dir="${_NE_contexts.dir}/${src.dir}" includes="**/type/*.java" />
+            <fileset dir="${_POS_tagger.dir}/${src.dir}" includes="**/type/*.java" />
+            <fileset dir="${_dependency_parser.dir}/${src.dir}" includes="**/type/*.java" />
+            <fileset dir="${_pad_termspotter.dir}/${src.dir}" includes="**/core/type/*/*.java" />
+            <fileset dir="${_pad_termspotter.dir}/${src.dir}" includes="**/core/type/*.java" /> <!-- any old types -->
+            <fileset dir="${_pad_termspotter.dir}/${src.dir}" includes="**/pad/type/*.java" />
+            <fileset dir="${_drug_ner.dir}/${src.dir}" includes="**/type/*.java" />
+            <fileset dir="${_smoking_status.dir}/${src.dir}" includes="**/type/*.java" />       <!-- any old types -->
+            <fileset dir="${_smoking_status.dir}/${src.dir}" includes="**/type/*/*.java" />
+            <fileset dir="${_side_effects.dir}/${src.dir}" includes="**/type/*.java" />         <!-- any old types -->
+            <fileset dir="${_side_effects.dir}/${src.dir}" includes="**/type/*/*.java" />
+            <fileset dir="${_constituency_parser.dir}/${src.dir}" includes="**/type/*.java" />
+            <fileset dir="${_coref_resolver.dir}/${src.dir}" includes="**/type/*.java" />
+            <!-- relation-extrator does not have its own types -->
+        </delete>
+   		<echo message="Done deleting filesets for gen'd types"/>
+        <delete dir="${docs.dir}/api" />
+        <delete quiet="true" failonerror="false" includeemptydirs="true">
+            <fileset dir="." includes="**/.classpath **/resources/launch/" />
+        </delete>
+    </target>
+
+
+    <!-- - - - - - - - - - - - - - - - -->
+    <!-- Build all projects.           -->
+    <!-- - - - - - - - - - - - - - - - -->
+    <target name="all" depends="generate_types,build_all,javadoc.generate" description="Generates necessary type system files, compiles all source files, and build Javadoc API documentations." />
+
+    <target name="build_all" depends="build_base, build_extensions, build_other" description="Compiles all source files." />
+    <target name="build_base" depends="_common_type_system.build,_core.build,_document_preprocessor.build,_POS_tagger.build,_chunker.build,_context_dependent_tokenizer.build,_LVG.build,_dictionary_lookup.build,_NE_contexts.build,_clinical_documents_pipeline.build,_dependency_parser.build,_assertion.build" description="Gens types (xml to .java) and Compiles .java to .class." />
+    <target name="build_extensions" depends="_pad_termspotter.build,_drug_ner.build,_smoking_status.build,_side_effects.build,_constituency_parser.build,_coref_resolver.build,_relation_extractor.build" description="Compiles optional parts of cTAKES." />
+    <target name="build_other" depends="comparexcas.build" description="Compiles Utilities such as CompareXcas." />
+
+    <!-- - - - - - - - - - - - - - - - - -->
+    <!-- Run CVD in a separate process.  -->
+    <!-- - - - - - - - - - - - - - - - - -->
+    <target name="testrun" description="Run UIMA CVD to process a sample note.">
+        <java fork="true" classname="org.apache.uima.tools.cvd.CVD" classpathref="testrun.cp">
+            <arg value="-desc" />
+            <arg file="${_clinical_documents_pipeline.dir}/${desc.dir}/analysis_engine/AggregatePlaintextProcessor.xml" />
+        </java>
+    </target>
+
+    <!-- - - - - - - - - - - - - - - - - -->
+    <!-- Run CPE in a separate process.  -->
+    <!-- - - - - - - - - - - - - - - - - -->
+    <target name="testcpe" description="Run UIMA CPE to process multiple notes.">
+        <java fork="true" classname="org.apache.uima.tools.cpm.CpmFrame" classpathref="testrun.cp" />
+    </target>
+
+    <!-- - - - - - - - - - - - - -->
+    <!-- Type system generators  -->
+    <!-- - - - - - - - - - - - - -->
+    <target name="generate_types" depends="_common_type_system.type,_clinical_documents_pipeline.type,_pad_termspotter.type,_pad_subsection.type,_drug_ner.type,_smoking_status.type,_side_effects.type,_coref_resolver1.type,_coref_resolver2.type,_assertion.type" unless="-types.ready" description="JCasGen type systems files for every project that has types.">
+    <!-- avoid generating more than once, jcasgen and jcasgen_merge are not intelligent enough to only generate outdated types -->
+        <property name="types.ready" value="true" />
+    </target>
+
+    <target name="-types.ready">
+        <condition>
+            <isset property="generate_typesd" />
+        </condition>
+    </target>
+
+    <target name="_clinical_documents_pipeline.type"> <!-- DOESN'T NEED TO GENERATE, referenced all dependent projects -->
+        <exec executable="${uima.home}/bin/${jcasgener}.${jext}">
+            <env key="ECLIPSE_HOME" value="${eclipse.home}" />
+            <env key="UIMA_HOME" value="${uima.home}" />
+            <env key="TEMP" value="${env.TEMP}" />
+            <arg value="${_clinical_documents_pipeline.dir}/${desc.dir}/analysis_engine/AggregatePlaintextProcessor.xml" />
+            <arg value="${_clinical_documents_pipeline.dir}/${src.dir}" />
+        </exec>
+    </target>
+
+    <target name="_common_type_system.type">
+   		<echo message="uima.home=${uima.home}"/>
+   		<echo message="eclipse.home=${eclipse.home}"/>
+        <exec executable="${uima.home}/bin/${jcasgener}.${jext}">
+            <env key="ECLIPSE_HOME" value="${eclipse.home}" />
+            <env key="UIMA_HOME" value="${uima.home}" />
+            <env key="TEMP" value="${env.TEMP}" />
+            <arg value="${_common_type_system.dir}/${desc.dir}/common_type_system.xml" />
+            <arg value="${_common_type_system.dir}/${src.dir}" />
+        </exec>
+    </target>
+
+    <target name="_pad_termspotter.type">
+        <exec executable="${uima.home}/bin/${jcasgener}.${jext}">
+            <env key="ECLIPSE_HOME" value="${eclipse.home}" />
+            <env key="UIMA_HOME" value="${uima.home}" />
+            <env key="TEMP" value="${env.TEMP}" />
+            <arg value="${_pad_termspotter.dir}/${desc.dir}/type_system/PADSiteAndTerm.xml" />
+            <arg value="${_pad_termspotter.dir}/${src.dir}" />
+        </exec>
+    </target>
+
+    <target name="_pad_subsection.type">
+        <exec executable="${uima.home}/bin/${jcasgener}.${jext}">
+            <env key="ECLIPSE_HOME" value="${eclipse.home}" />
+            <env key="UIMA_HOME" value="${uima.home}" />
+            <env key="TEMP" value="${env.TEMP}" />
+            <arg value="${_pad_termspotter.dir}/${desc.dir}/type_system/SubSection.xml" />
+            <arg value="${_pad_termspotter.dir}/${src.dir}" />
+        </exec>
+    </target>
+
+    <target name="_drug_ner.type">
+        <exec executable="${uima.home}/bin/${jcasgener}.${jext}">
+            <env key="ECLIPSE_HOME" value="${eclipse.home}" />
+            <env key="UIMA_HOME" value="${uima.home}" />
+            <env key="TEMP" value="${env.TEMP}" />
+            <arg value="${_drug_ner.dir}/${desc.dir}/type_system/NERTypeSystem.xml" />
+            <arg value="${_drug_ner.dir}/${src.dir}" />
+        </exec>
+    </target>
+
+
+    <target name="_smoking_status.type">
+        <exec executable="${uima.home}/bin/${jcasgener}.${jext}">
+            <env key="ECLIPSE_HOME" value="${eclipse.home}" />
+            <env key="UIMA_HOME" value="${uima.home}" />
+            <env key="TEMP" value="${env.TEMP}" />
+            <arg value="${_smoking_status.dir}/${desc.dir}/type_system/SmokingProductionTypeSystem.xml" />
+            <arg value="${_smoking_status.dir}/${src.dir}" />
+        </exec>
+    </target>
+
+	<target name="_side_effects.type">
+        <exec executable="${uima.home}/bin/${jcasgener}.${jext}">
+            <env key="ECLIPSE_HOME" value="${eclipse.home}" />
+            <env key="UIMA_HOME" value="${uima.home}" />
+            <env key="TEMP" value="${env.TEMP}" />
+            <arg value="${_side_effects.dir}/${desc.dir}/type_system/SideEffectTypeSystem.xml" />
+            <arg value="${_side_effects.dir}/${src.dir}" />
+        </exec>
+    </target>
+
+    <target name="_coref_resolver1.type">
+        <exec executable="${uima.home}/bin/${jcasgener}.${jext}">
+            <env key="ECLIPSE_HOME" value="${eclipse.home}" />
+            <env key="UIMA_HOME" value="${uima.home}" />
+            <env key="TEMP" value="${env.TEMP}" />
+            <arg value="${_coref_resolver.dir}/${desc.dir}/type-system/VecInst.xml" />
+            <arg value="${_coref_resolver.dir}/${src.dir}" />
+        </exec>
+    </target>
+
+    <target name="_coref_resolver2.type">
+        <exec executable="${uima.home}/bin/${jcasgener}.${jext}">
+            <env key="ECLIPSE_HOME" value="${eclipse.home}" />
+            <env key="UIMA_HOME" value="${uima.home}" />
+            <env key="TEMP" value="${env.TEMP}" />
+            <arg value="${_coref_resolver.dir}/${desc.dir}/type-system/CorefTypes.xml" />
+            <arg value="${_coref_resolver.dir}/${src.dir}" />
+        </exec>
+    </target>
+
+    <target name="_assertion.type">
+        <exec executable="${uima.home}/bin/${jcasgener}.${jext}">
+            <env key="ECLIPSE_HOME" value="${eclipse.home}" />
+            <env key="UIMA_HOME" value="${uima.home}" />
+            <env key="TEMP" value="${env.TEMP}" />
+            <arg value="${_assertion.dir}/${desc.dir}/medfactsTypeSystem.xml" />
+            <arg value="${_assertion.dir}/${src.dir}" />
+        </exec>
+    </target>
+
+    <!-- - - - - - -->
+    <!-- Compilers -->
+    <!-- - - - - - -->
+    <target name="_chunker.build" depends="generate_types,_core.build,_POS_tagger.build">
+        <mkdir dir="${_chunker.dir}/${bin.dir}" />
+        <javac destdir="${_chunker.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_chunker.dir}/${src.dir}" />
+            <src path="${_chunker.dir}/scripts/java" />
+            <src path="${_chunker.dir}/test/src" />
+            <classpath refid="_chunker.cp" />
+        </javac>
+    </target>
+
+    <target name="_clinical_documents_pipeline.build" depends="generate_types,_chunker.build,_context_dependent_tokenizer.build,_core.build,_dictionary_lookup.build,_document_preprocessor.build,_LVG.build,_NE_contexts.build,_POS_tagger.build">
+        <mkdir dir="${_clinical_documents_pipeline.dir}/${bin.dir}" />
+        <javac destdir="${_clinical_documents_pipeline.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_clinical_documents_pipeline.dir}/${src.dir}" />
+            <classpath refid="_clinical_documents_pipeline.cp" />
+        </javac>
+    </target>
+
+    <target name="_context_dependent_tokenizer.build" depends="generate_types,_core.build">
+        <mkdir dir="${_context_dependent_tokenizer.dir}/${bin.dir}" />
+        <javac destdir="${_context_dependent_tokenizer.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_context_dependent_tokenizer.dir}/${src.dir}" />
+            <classpath refid="_context_dependent_tokenizer.cp" />
+        </javac>
+    </target>
+
+    <target name="_core.build" depends="generate_types">  
+	   	<!-- <property name="myuimahome" refid="uima.home"/> -->
+   		<echo message="uima.home=${uima.home}"/>
+        <mkdir dir="${_core.dir}/${bin.dir}" />
+        <javac destdir="${_core.dir}/${bin.dir}"  includeantruntime="false" debug="${compile.debug}">
+            <src path="${_core.dir}/${src.dir}" />
+            <src path="${_core.dir}/test" />
+            <classpath refid="_core.cp" />
+        </javac>
+    </target>
+
+    <target name="_common_type_system.build" depends="generate_types">
+	   	<!-- <property name="myclasspath" refid="_common_type_system.cp"/> -->
+   		<!-- <echo message="classpath= ${myclasspath}"/> -->
+        <mkdir dir="${_common_type_system.dir}/${bin.dir}" />
+        <javac destdir="${_common_type_system.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_common_type_system.dir}/${src.dir}" />
+            <classpath refid="_common_type_system.cp" />
+        </javac>
+   </target>
+	
+    <target name="_dictionary_lookup.build" depends="generate_types,_core.build">
+        <mkdir dir="${_dictionary_lookup.dir}/${bin.dir}" />
+        <javac destdir="${_dictionary_lookup.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_dictionary_lookup.dir}/${src.dir}" />
+            <src path="${_dictionary_lookup.dir}/scripts/java" />
+            <classpath refid="_dictionary_lookup.cp" />
+        </javac>
+    </target>
+
+    <target name="_document_preprocessor.build" depends="generate_types,_core.build">
+        <mkdir dir="${_document_preprocessor.dir}/${bin.dir}" />
+        <javac destdir="${_document_preprocessor.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_document_preprocessor.dir}/${src.dir}" />
+            <src path="${_document_preprocessor.dir}/test" />
+            <classpath refid="_document_preprocessor.cp" />
+        </javac>
+    </target>
+
+    <target name="_LVG.build" depends="generate_types,_chunker.build,_core.build">
+        <mkdir dir="${_LVG.dir}/${bin.dir}" />
+        <javac destdir="${_LVG.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_LVG.dir}/${src.dir}" />
+            <classpath refid="_LVG.cp" />
+        </javac>
+    </target>
+
+    <target name="_NE_contexts.build" depends="generate_types,_core.build">
+        <mkdir dir="${_NE_contexts.dir}/${bin.dir}" />
+        <javac destdir="${_NE_contexts.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_NE_contexts.dir}/${src.dir}" />
+            <src path="${_NE_contexts.dir}/test/src" />
+            <classpath refid="_NE_contexts.cp" />
+        </javac>
+    </target>
+
+    <target name="_POS_tagger.build" depends="generate_types,_core.build">
+        <mkdir dir="${_POS_tagger.dir}/${bin.dir}" />
+        <javac destdir="${_POS_tagger.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_POS_tagger.dir}/${src.dir}" />
+            <src path="${_POS_tagger.dir}/scripts/java" />
+            <src path="${_POS_tagger.dir}/test/src" />
+            <classpath refid="_POS_tagger.cp" />
+        </javac>
+    </target>
+
+    <target name="_dependency_parser.build" depends="generate_types,_core.build,_LVG.build,_POS_tagger.build,_chunker.build,_context_dependent_tokenizer.build">
+        <mkdir dir="${_dependency_parser.dir}/${bin.dir}" />
+        <javac destdir="${_dependency_parser.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_dependency_parser.dir}/${src.dir}" />
+            <classpath refid="_dependency_parser.cp" />
+        </javac>
+    </target>
+
+    <target name="_pad_termspotter.build" depends="generate_types,build_base" >
+        <mkdir dir="${_pad_termspotter.dir}/${bin.dir}" />
+        <javac destdir="${_pad_termspotter.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_pad_termspotter.dir}/${src.dir}" />
+            <classpath refid="_pad_termspotter.cp" />
+        </javac>
+    </target>
+    <target name="_drug_ner.build" depends="generate_types,build_base" >
+        <mkdir dir="${_drug_ner.dir}/${bin.dir}" />
+        <javac destdir="${_drug_ner.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_drug_ner.dir}/${src.dir}" />
+            <classpath refid="_drug_ner.cp" />
+        </javac>
+    </target>
+    <target name="_smoking_status.build" depends="generate_types,build_base" >
+        <mkdir dir="${_smoking_status.dir}/${bin.dir}" />
+        <javac destdir="${_smoking_status.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_smoking_status.dir}/${src.dir}" />
+            <classpath refid="_smoking_status.cp" />
+        </javac>
+    </target>
+    <target name="_side_effects.build" depends="generate_types,build_base" >
+        <mkdir dir="${_side_effects.dir}/${bin.dir}" />
+        <javac destdir="${_side_effects.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_side_effects.dir}/${src.dir}" />
+            <classpath refid="_side_effects.cp" />
+        </javac>
+    </target>
+    <target name="_constituency_parser.build" depends="generate_types,build_base" >
+        <mkdir dir="${_constituency_parser.dir}/${bin.dir}" />
+        <javac destdir="${_constituency_parser.dir}/${bin.dir}" srcdir="${_constituency_parser.dir}/${src.dir}" debug="${compile.debug}">
+            <src path="${_constituency_parser.dir}/${src.dir}" />
+            <classpath refid="_constituency_parser.cp" />
+        </javac>
+    </target>
+    <target name="_coref_resolver.build" depends="generate_types,build_base,_constituency_parser.build" >
+        <mkdir dir="${_coref_resolver.dir}/${bin.dir}" />
+        <javac destdir="${_coref_resolver.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_coref_resolver.dir}/${src.dir}" />
+            <classpath refid="_coref_resolver.cp" />
+        </javac>
+    </target>
+	
+    <target name="_assertion.build" depends="generate_types,_dependency_parser.build" >
+        <mkdir dir="${_assertion.dir}/${bin.dir}" />
+        <javac destdir="${_assertion.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_assertion.dir}/${src.dir}" />
+            <classpath refid="_assertion.cp" />
+        </javac>
+    </target>
+	
+    <target name="_relation_extractor.build" depends="generate_types,build_base" >
+        <mkdir dir="${_relation_extractor.dir}/${bin.dir}" />
+        <javac destdir="${_relation_extractor.dir}/${bin.dir}" debug="${compile.debug}">
+            <src path="${_relation_extractor.dir}/${src.dir}" />
+            <classpath refid="_relation_extractor.cp" />
+        </javac>
+    </target>
+	
+
+    <target name="build_runtime_classpath">
+        <property name="testrun_classpath" refid="testrun.cp"/>
+        <echo message="export CLASSPATH=&quot;${testrun_classpath}&quot;" file="runtime_classpath.txt"/>
+    </target>
+	
+	<!-- - - - - - - - - - - -->
+    <!-- Javadoc generators  -->
+    <!-- - - - - - - - - - - -->
+    <target name="javadoc.generate" depends="_javadoc2009.generate,_javadoc2011.generate,_javadoc2012a.generate,_javadoc2012b.generate" />
+	
+    <target name="_javadoc2009.generate" description="Generates Javadoc HTML pages.">
+        <mkdir dir="${docs.dir}/api" />
+        <javadoc destdir="${docs.dir}/api" windowtitle="Clinical Text Analysis and Knowledge Extraction System API">
+            <doctitle><![CDATA[<h1>cTAKES ${pipeline.version} Java API Documentation</h1>]]></doctitle>
+            <bottom><![CDATA[Copyright &copy; 2012 The Apache Software Foundation. All Rights Reserved.]]></bottom>
+            <packageset dir="${_chunker.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />
+            <packageset dir="${_clinical_documents_pipeline.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />
+            <packageset dir="${_context_dependent_tokenizer.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />
+            <packageset dir="${_core.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />     	
+            <packageset dir="${_dictionary_lookup.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />
+            <packageset dir="${_document_preprocessor.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />
+            <packageset dir="${_LVG.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />
+            <packageset dir="${_NE_contexts.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />
+            <packageset dir="${_POS_tagger.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />
+            <packageset dir="${_dependency_parser.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />
+            <packageset dir="${_pad_termspotter.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />
+            <packageset dir="${_drug_ner.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />     	
+        </javadoc>
+    </target>
+
+    <target name="_javadoc2011.generate" description="Generates Javadoc HTML pages.">
+        <mkdir dir="${docs.dir}/api" />
+        <javadoc destdir="${docs.dir}/api" windowtitle="Clinical Text Analysis and Knowledge Extraction System API">
+            <doctitle><![CDATA[<h1>cTAKES ${pipeline.version} Java API Documentation</h1>]]></doctitle>
+            <bottom><![CDATA[Copyright &copy; 2012 The Apache Software Foundation. All Rights Reserved.]]></bottom>
+            <packageset dir="${_smoking_status.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />
+            <packageset dir="${_side_effects.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />
+            <packageset dir="${_constituency_parser.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />
+            <packageset dir="${_coref_resolver.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />
+        </javadoc>
+    </target>
+
+    <target name="_javadoc2012a.generate" description="Generates Javadoc HTML pages.">
+        <mkdir dir="${docs.dir}/api" />
+        <javadoc destdir="${docs.dir}/api" windowtitle="Clinical Text Analysis and Knowledge Extraction System API">
+            <doctitle><![CDATA[<h1>cTAKES ${pipeline.version} Java API Documentation</h1>]]></doctitle>
+            <bottom><![CDATA[Copyright &copy; 2012 The Apache Software Foundation. All Rights Reserved.]]></bottom>
+            <packageset dir="${_common_type_system.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />          	
+        </javadoc>
+    </target>
+
+    <target name="_javadoc2012b.generate" description="Generates Javadoc HTML pages.">
+        <mkdir dir="${docs.dir}/api" />
+        <javadoc destdir="${docs.dir}/api" windowtitle="Clinical Text Analysis and Knowledge Extraction System API">
+            <doctitle><![CDATA[<h1>cTAKES ${pipeline.version} Java API Documentation</h1>]]></doctitle>
+            <bottom><![CDATA[Copyright: &copy; 2012 The Apache Software Foundation. All Rights Reserved.]]></bottom>
+            <packageset dir="${_relation_extractor.dir}/${src.dir}" defaultexcludes="yes" excludes="**/type" />     	
+        </javadoc>
+    </target>
+
+
+    <!-- - - - - - - - - - -->
+    <!-- Build CompareXcas -->
+    <!-- - - - - - - - - - -->
+    <target name="comparexcas.build" description="Build CompareXcas, which can compare two XCAS files without reading a type system file.">
+        <mkdir dir="${_utils_project.dir}/${bin.dir}" />
+        <javac srcdir="${_utils_project.dir}/${src.dir}" destdir="${_utils_project.dir}/${bin.dir}" debug="${compile.debug}"/>
+    </target>
+
+    <!-- - - - - - - - - - - - - - - - - - - - - - -->
+    <!-- Zip CompareXcas                           -->
+    <!-- - - - - - - - - - - - - - - - - - - - - - -->
+    <target name="comparexcas.zip" description="Zip CompareXcas.">
+        <zip basedir="${_utils_project.dir}" destfile="./utils.zip" compress="true" />
+    </target>
+
+    <!-- - - - - - - - - - - - - - - - - - - - - - -->
+    <!-- Extract Eclipse workspace metadata files  -->
+    <!-- - - - - - - - - - - - - - - - - - - - - - -->
+    <target name="eclipse.metadata.extract" description="Extract Eclipse metadata files.">
+        <untar src="eclipse.specific.tar.gz" dest="." compression="gzip" />
+    </target>
+
+</project>

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Added: incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step2.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/SHARPn-cTAKES/files%20for%20pipeline%20root/build_step2.properties?rev=1403908&view=auto
==============================================================================
--- incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step2.properties (added)
+++ incubator/ctakes/branches/SHARPn-cTAKES/files for pipeline root/build_step2.properties Tue Oct 30 22:47:40 2012
@@ -0,0 +1,10 @@
+uima.dir=/Apps/ApacheSoftwareFoundation/uima/uimaj-2.4.0-bin
+eclipse.home=/Apps/eclipse-java-helios-win32/eclipse
+# CTAKES_HOME is the output directory 
+CTAKES_HOME=C:\\cTAKES\\2.6\\building-2.6\\cTAKES-2.6-incubating.alpha-005
+workspace.home=C:/Apps_data/Workspaces/Apache_cTAKES
+typeSystem.target=${CTAKES_HOME}/cTAKESdesc/typesystem/cTAKESTypes.xml
+typeSystem.dir=${CTAKES_HOME}/cTAKESdesc/typesystem
+projectList=common-type-system,chunker,clinical documents pipeline,context dependent tokenizer,core,dependency parser,dictionary lookup,document preprocessor,Drug NER,LVG,NE contexts,PAD term spotter,POS tagger,SideEffect,smoking status,Constituency Parser,coref-resolver,assertion,relation-extractor
+<!-- temp directory - some versions of jcasgen requires this to be set -->
+tempDir=/Apps/_data_/Temp
\ No newline at end of file

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