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From chen...@apache.org
Subject svn commit: r1712083 [1/3] - in /ctakes/sandbox/ctakes-clinical-deid: ./ GATE/ GATE/pipeline/ GATE/plugins/ GATE/plugins/ANNIE/ GATE/plugins/ANNIE/.annie-defaults-metadata/ GATE/plugins/ANNIE/resources/ GATE/plugins/ANNIE/resources/gazetteer/ GATE/plug...
Date Mon, 02 Nov 2015 16:59:52 GMT
Author: chenpei
Date: Mon Nov  2 16:59:48 2015
New Revision: 1712083

URL: http://svn.apache.org/viewvc?rev=1712083&view=rev
Log:
CTAKES-384- Thanks Azad Dehghan. Initial import of c-deid into sandbox

Added:
    ctakes/sandbox/ctakes-clinical-deid/
    ctakes/sandbox/ctakes-clinical-deid/GATE/
    ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/
    ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/passOne.xgapp
    ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/postProcessing.xgapp
    ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/preProcessing.xgapp
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/ann-job-annie.png   (with props)
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/icon.png   (with props)
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/long-desc.html
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/metadata.xml
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/short-desc.html
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/ANNIE_with_defaults.gapp
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/build.xml
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/creole.xml
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/country.lst
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/lists.def
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/nationality.lst
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/spoken_language.lst
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/us_state.lst
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/us_state_acronym_abbreviation.lst
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/sentenceSplitter/
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/sentenceSplitter/gazetteer/
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/sentenceSplitter/gazetteer/abbreviations.lst
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/sentenceSplitter/gazetteer/lists.def
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/sentenceSplitter/grammar/
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/sentenceSplitter/grammar/cleanup.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/sentenceSplitter/grammar/find-single-nl.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/sentenceSplitter/grammar/find.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/sentenceSplitter/grammar/main-single-nl.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/sentenceSplitter/grammar/main.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/sentenceSplitter/grammar/no-splits.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/sentenceSplitter/grammar/prepare.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/sentenceSplitter/grammar/split.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/tokeniser/
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/tokeniser/AlternateTokeniser.rules
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/tokeniser/DefaultTokeniser.rules
    ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/tokeniser/postprocess.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/AGE.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/COUNTRY.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/DOCTOR.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/FAX.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/ID_NUM.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/MEDICALREC_NUM.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/PATIENT.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/PHONE.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/STATE.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/STREET.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/USERNAME.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/ZIP.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/postproc/
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/postproc/PostProc_boundary_adjustment.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/postproc/PostProc_copy_ann1.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/postproc/PostProc_copy_ann2.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/postproc/PostProc_priority_sorting.jape
    ctakes/sandbox/ctakes-clinical-deid/GATE/rule-set/postproc/README
    ctakes/sandbox/ctakes-clinical-deid/LICENSE
    ctakes/sandbox/ctakes-clinical-deid/README
    ctakes/sandbox/ctakes-clinical-deid/bin/
    ctakes/sandbox/ctakes-clinical-deid/bin/co/
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/controller/
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/controller/Controller.class   (with props)
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/controller/Document.class   (with props)
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/io/
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/io/Output.class   (with props)
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/pipeline/
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/pipeline/firstpass/
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/pipeline/firstpass/PassOne.class   (with props)
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/pipeline/firstpass/ner/
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/pipeline/firstpass/ner/EmailNER.class   (with props)
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/pipeline/firstpass/ner/UrlNER.class   (with props)
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/pipeline/other/
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/pipeline/other/PostProcess.class   (with props)
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/pipeline/other/PreProcess.class   (with props)
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/pipeline/secondpass/
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/pipeline/secondpass/Extract.class   (with props)
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/pipeline/secondpass/Input.class   (with props)
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/pipeline/secondpass/Overlap.class   (with props)
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/pipeline/secondpass/PassTwo.class   (with props)
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/ui/
    ctakes/sandbox/ctakes-clinical-deid/bin/co/dehghan/cdeid/ui/Deid.class   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/
    ctakes/sandbox/ctakes-clinical-deid/libs/ant-1.9.3.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/ant-launcher-1.9.3.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/aopalliance-1.0.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/apache-mime4j-core-0.7.2.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/apache-mime4j-dom-0.7.2.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/bcmail-jdk15-1.45.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/bcprov-jdk15-1.45.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/commons-codec-1.9.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/commons-compress-1.8.1.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/commons-io-2.4.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/commons-lang-2.6.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/commons-logging-1.1.3.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/flying-saucer-core-9.0.4.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/fontbox-1.8.8.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/gate-asm-5.0.3.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/gate-compiler-jdt-4.3.2-P20140317-1600.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/gate.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/gateLauncher.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/hamcrest-core-1.3.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/ivy-2.3.0.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/jackson-annotations-2.3.0.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/jackson-core-2.3.2.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/jackson-databind-2.3.2.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/java-getopt-1.0.13.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/jaxen-1.1.6.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/jdom-1.1.3.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/jempbox-1.8.8.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/joda-time-2.6.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/junit-4.11.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/log4j-1.2.17.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/nekohtml-1.9.14.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/pdfbox-app-1.8.10.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/poi-3.11.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/poi-ooxml-3.11.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/poi-ooxml-schemas-3.11.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/poi-scratchpad-3.11.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/spring-aop-2.5.6.SEC01.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/spring-beans-2.5.6.SEC01.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/spring-core-2.5.6.SEC01.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/stax2-api-3.1.1.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/tika-core-1.7.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/tika-parsers-1.7.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/validationtools.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/woodstox-core-lgpl-4.2.0.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/xercesImpl-2.9.1.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/xmlbeans-2.6.0.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/xmlunit-1.5.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/xpp3-1.1.4c.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/libs/xstream-1.4.7.jar   (with props)
    ctakes/sandbox/ctakes-clinical-deid/src/
    ctakes/sandbox/ctakes-clinical-deid/src/co/
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/controller/
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/controller/Controller.java
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/io/
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/io/Output.java
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/pipeline/
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/pipeline/firstpass/
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/pipeline/firstpass/PassOne.java
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/pipeline/firstpass/ner/
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/pipeline/firstpass/ner/EmailNER.java
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/pipeline/firstpass/ner/UrlNER.java
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/pipeline/other/
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/pipeline/other/PostProcess.java
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/pipeline/other/PreProcess.java
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/pipeline/secondpass/
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/pipeline/secondpass/Input.java
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/pipeline/secondpass/PassTwo.java
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/ui/
    ctakes/sandbox/ctakes-clinical-deid/src/co/dehghan/cdeid/ui/Deid.java

Added: ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/passOne.xgapp
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/passOne.xgapp?rev=1712083&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/passOne.xgapp (added)
+++ ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/passOne.xgapp Mon Nov  2 16:59:48 2015
@@ -0,0 +1,851 @@
+<gate.util.persistence.GateApplication>
+  <urlList class="gate.util.persistence.CollectionPersistence">
+    <localList>
+      <gate.util.persistence.PersistenceManager-URLHolder>
+        <urlString>$gatehome$plugins/ANNIE/</urlString>
+      </gate.util.persistence.PersistenceManager-URLHolder>
+    </localList>
+    <collectionType>java.util.ArrayList</collectionType>
+  </urlList>
+  <application class="gate.util.persistence.SerialAnalyserControllerPersistence">
+    <prList class="gate.util.persistence.CollectionPersistence">
+      <localList>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>annotationSetName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>longestMatchOnly</string>
+                <boolean>true</boolean>
+              </entry>
+              <entry>
+                <string>wholeWordsOnly</string>
+                <boolean>true</boolean>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.gazetteer.DefaultGazetteer</resourceType>
+          <resourceName>GazSet</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>gazetteerFeatureSeparator</string>
+                <string>:</string>
+              </entry>
+              <entry>
+                <string>listsURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../plugins/ANNIE/resources/gazetteer/lists.def</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>caseSensitive</string>
+                <boolean>false</boolean>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>passOne</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>AGE</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/AGE.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>passOne</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>COUNTRY</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/COUNTRY.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>passOne</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>DOCTOR</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/DOCTOR.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>passOne</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>FAX</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/FAX.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>passOne</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>ID NUM</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/ID_NUM.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>passOne</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>MEDICALRECORD NUM</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/MEDICALREC_NUM.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>passOne</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>PATIENT</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/PATIENT.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>passOne</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>PHONE</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/PHONE.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>passOne</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>STATE</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/STATE.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>passOne</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>STREET</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/STREET.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>passOne</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>USERNAME</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/USERNAME.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>passOne</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>ZIP</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/ZIP.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+      </localList>
+      <collectionType>java.util.ArrayList</collectionType>
+    </prList>
+    <resourceType>gate.creole.SerialAnalyserController</resourceType>
+    <resourceName>Pass One</resourceName>
+    <initParams class="gate.util.persistence.MapPersistence">
+      <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+      <localMap/>
+    </initParams>
+    <features class="gate.util.persistence.MapPersistence">
+      <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+      <localMap/>
+    </features>
+  </application>
+</gate.util.persistence.GateApplication>
\ No newline at end of file

Added: ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/postProcessing.xgapp
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/postProcessing.xgapp?rev=1712083&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/postProcessing.xgapp (added)
+++ ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/postProcessing.xgapp Mon Nov  2 16:59:48 2015
@@ -0,0 +1,219 @@
+<gate.util.persistence.GateApplication>
+  <urlList class="gate.util.persistence.CollectionPersistence">
+    <localList>
+      <gate.util.persistence.PersistenceManager-URLHolder>
+        <urlString>$gatehome$plugins/ANNIE/</urlString>
+      </gate.util.persistence.PersistenceManager-URLHolder>
+    </localList>
+    <collectionType>java.util.ArrayList</collectionType>
+  </urlList>
+  <application class="gate.util.persistence.SerialAnalyserControllerPersistence">
+    <prList class="gate.util.persistence.CollectionPersistence">
+      <localList>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>final_predictions</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <string>passTwo</string>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>PP Ann1</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/postproc/PostProc_copy_ann1.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>final_predictions</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <string>passOne</string>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>PP Ann2</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/postproc/PostProc_copy_ann2.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>enableDebugging</string>
+                <boolean>false</boolean>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <string>final_predictions</string>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <string>passTwo</string>
+              </entry>
+              <entry>
+                <string>ontology</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.Transducer</resourceType>
+          <resourceName>PP Priority Sort</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>binaryGrammarURL</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>annotationAccessors</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>grammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$relpath$../rule-set/postproc/PostProc_priority_sorting.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>operators</string>
+                <null/>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+      </localList>
+      <collectionType>java.util.ArrayList</collectionType>
+    </prList>
+    <resourceType>gate.creole.SerialAnalyserController</resourceType>
+    <resourceName>Post-processing pipeline</resourceName>
+    <initParams class="gate.util.persistence.MapPersistence">
+      <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+      <localMap/>
+    </initParams>
+    <features class="gate.util.persistence.MapPersistence">
+      <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+      <localMap/>
+    </features>
+  </application>
+</gate.util.persistence.GateApplication>
\ No newline at end of file

Added: ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/preProcessing.xgapp
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/preProcessing.xgapp?rev=1712083&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/preProcessing.xgapp (added)
+++ ctakes/sandbox/ctakes-clinical-deid/GATE/pipeline/preProcessing.xgapp Mon Nov  2 16:59:48 2015
@@ -0,0 +1,123 @@
+<gate.util.persistence.GateApplication>
+  <urlList class="gate.util.persistence.CollectionPersistence">
+    <localList>
+      <gate.util.persistence.PersistenceManager-URLHolder>
+        <urlString>$gatehome$plugins/ANNIE/</urlString>
+      </gate.util.persistence.PersistenceManager-URLHolder>
+    </localList>
+    <collectionType>java.util.ArrayList</collectionType>
+  </urlList>
+  <application class="gate.util.persistence.SerialAnalyserControllerPersistence">
+    <prList class="gate.util.persistence.CollectionPersistence">
+      <localList>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>annotationSetName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.tokeniser.DefaultTokeniser</resourceType>
+          <resourceName>ANNIE English Tokeniser_00015</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>tokeniserRulesURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$gatehome$plugins/ANNIE/resources/tokeniser/DefaultTokeniser.rules</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>transducerGrammarURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$gatehome$plugins/ANNIE/resources/tokeniser/postprocess.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+        <gate.util.persistence.LanguageAnalyserPersistence>
+          <runtimeParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>corpus</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>outputASName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>inputASName</string>
+                <null/>
+              </entry>
+              <entry>
+                <string>document</string>
+                <null/>
+              </entry>
+            </localMap>
+          </runtimeParams>
+          <resourceType>gate.creole.splitter.SentenceSplitter</resourceType>
+          <resourceName>ANNIE Sentence Splitter_00018</resourceName>
+          <initParams class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap>
+              <entry>
+                <string>gazetteerListsURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$gatehome$plugins/ANNIE/resources/sentenceSplitter/gazetteer/lists.def</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+              <entry>
+                <string>encoding</string>
+                <string>UTF-8</string>
+              </entry>
+              <entry>
+                <string>transducerURL</string>
+                <gate.util.persistence.PersistenceManager-URLHolder>
+                  <urlString>$gatehome$plugins/ANNIE/resources/sentenceSplitter/grammar/main-single-nl.jape</urlString>
+                </gate.util.persistence.PersistenceManager-URLHolder>
+              </entry>
+            </localMap>
+          </initParams>
+          <features class="gate.util.persistence.MapPersistence">
+            <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+            <localMap/>
+          </features>
+        </gate.util.persistence.LanguageAnalyserPersistence>
+      </localList>
+      <collectionType>java.util.ArrayList</collectionType>
+    </prList>
+    <resourceType>gate.creole.SerialAnalyserController</resourceType>
+    <resourceName>PreProcessing</resourceName>
+    <initParams class="gate.util.persistence.MapPersistence">
+      <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+      <localMap/>
+    </initParams>
+    <features class="gate.util.persistence.MapPersistence">
+      <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+      <localMap/>
+    </features>
+  </application>
+</gate.util.persistence.GateApplication>
\ No newline at end of file

Added: ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/ann-job-annie.png
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/ann-job-annie.png?rev=1712083&view=auto
==============================================================================
Binary file - no diff available.

Propchange: ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/ann-job-annie.png
------------------------------------------------------------------------------
    svn:mime-type = application/octet-stream

Added: ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/icon.png
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/icon.png?rev=1712083&view=auto
==============================================================================
Binary file - no diff available.

Propchange: ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/icon.png
------------------------------------------------------------------------------
    svn:mime-type = application/octet-stream

Added: ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/long-desc.html
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/long-desc.html?rev=1712083&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/long-desc.html (added)
+++ ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/long-desc.html Mon Nov  2 16:59:48 2015
@@ -0,0 +1,59 @@
+<p><img src="ann-job-annie.png" style="float: right"/><strong>ANNIE</strong> is 
+a named entity recognition pipeline that identifies basic entity types, such 
+as <em>Person</em>, <em>Location</em>, <em>Organization</em>, <em>Money</em> 
+amounts, <em>Time</em> and <em>Date</em> expressions.</p>
+
+<p>It is the prototypical information extraction pipeline distributed
+with the <a href="http://gate.ac.uk">GATE framework</a> and forms the base of 
+many more complex GATE-based IE applications.</p>
+
+<p><button class="btn btn-info" data-toggle="collapse" data-target="#ldAnnotationDetails"><i class="icon-info-sign icon-white"></i> Annotation details</button></p>
+
+<div class="collapse clearfix" id="ldAnnotationDetails">
+<table>
+  <tr>
+    <td colspan="2"><b>Default annotations</b></td>
+  </tr>
+  <tr>
+    <td><tt>:Person</tt></td>
+    <td rowspan="4">Standard named entity types</td>
+  </tr>
+  <tr>
+    <td><tt>:Location</tt></td>
+  </tr>
+  <tr>
+    <td><tt>:Organization</tt></td>
+  </tr>
+  <tr>
+    <td><tt>:Date</tt></td>
+  </tr>
+  <tr>
+    <td><tt>:Address</tt></td>
+    <td>Includes email and IP addresses as well as street addresses</td>
+  </tr>
+  <tr>
+    <td colspan="2"><b>Additional annotations available if selected</b></td>
+  </tr>
+  <tr>
+    <td><tt>:Money</tt></td>
+    <td>Monetary amounts</td>
+  </tr>
+  <tr>
+    <td><tt>:Percent</tt></td>
+    <td>Expressions representing percentages</td>
+  </tr>
+  <tr>
+    <td><tt>:Token</tt></td>
+    <td>The individual tokens of the text, with "category" feature for POS</td>
+  </tr>
+  <tr>
+    <td><tt>:SpaceToken</tt></td>
+    <td>The spaces between tokens</td>
+  </tr>
+  <tr>
+    <td><tt>:Sentence</tt></td>
+    <td>Sentences detected by the sentence splitter</td>
+  </tr>
+</table>
+</div>
+

Added: ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/metadata.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/metadata.xml?rev=1712083&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/metadata.xml (added)
+++ ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/metadata.xml Mon Nov  2 16:59:48 2015
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<metadata xmlns="http://gate.ac.uk/ns/pipeline-metadata">
+  <pipeline-name>ANNIE Named Entity Recognizer</pipeline-name>
+  <slug>annie-named-entity-recognizer</slug>
+  <ordering>10</ordering>
+  <annotation-selectors>:Address, :Date, :Location, :Organization, :Person</annotation-selectors>
+  <additional-annotations>:Money, :Percent, :Token, :SpaceToken, :Sentence</additional-annotations>
+  <tags>
+    <tag>English</tag>
+    <tag>Named Entity</tag>
+  </tags>
+</metadata>

Added: ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/short-desc.html
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/short-desc.html?rev=1712083&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/short-desc.html (added)
+++ ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/.annie-defaults-metadata/short-desc.html Mon Nov  2 16:59:48 2015
@@ -0,0 +1,3 @@
+The ANNIE named entity recognition service. Identifies names of 
+<em>persons</em>, <em>locations</em>, <em>organizations</em>, as well as 
+<em>money amounts</em>, <em>time and date expressions</em>. 
\ No newline at end of file

Added: ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/ANNIE_with_defaults.gapp
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/ANNIE_with_defaults.gapp?rev=1712083&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/ANNIE_with_defaults.gapp (added)
+++ ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/ANNIE_with_defaults.gapp Mon Nov  2 16:59:48 2015
@@ -0,0 +1,189 @@
+<gate.util.persistence.GateApplication>
+  <urlList class="gate.util.persistence.CollectionPersistence">
+    <localList>
+      <gate.util.persistence.PersistenceManager-URLHolder>
+        <urlString>$relpath$.</urlString>
+      </gate.util.persistence.PersistenceManager-URLHolder>
+    </localList>
+    <collectionType>java.util.ArrayList</collectionType>
+  </urlList>
+  <application class="gate.util.persistence.ConditionalSerialAnalyserControllerPersistence">
+    <strategiesList class="gate.util.persistence.CollectionPersistence">
+      <localList>
+        <gate.util.persistence.AnalyserRunningStrategyPersistence>
+          <runMode>1</runMode>
+          <pr class="gate.util.persistence.PRPersistence">
+            <runtimeParams class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </runtimeParams>
+            <resourceType>gate.creole.annotdelete.AnnotationDeletePR</resourceType>
+            <resourceName>Document Reset PR</resourceName>
+            <initParams class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </initParams>
+            <features class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </features>
+          </pr>
+        </gate.util.persistence.AnalyserRunningStrategyPersistence>
+        <gate.util.persistence.AnalyserRunningStrategyPersistence>
+          <runMode>1</runMode>
+          <pr class="gate.util.persistence.LanguageAnalyserPersistence">
+            <runtimeParams class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </runtimeParams>
+            <resourceType>gate.creole.tokeniser.DefaultTokeniser</resourceType>
+            <resourceName>ANNIE English Tokeniser</resourceName>
+            <initParams class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </initParams>
+            <features class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </features>
+          </pr>
+        </gate.util.persistence.AnalyserRunningStrategyPersistence>
+        <gate.util.persistence.AnalyserRunningStrategyPersistence>
+          <runMode>1</runMode>
+          <featureName></featureName>
+          <featureValue></featureValue>
+          <pr class="gate.util.persistence.LanguageAnalyserPersistence">
+            <runtimeParams class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </runtimeParams>
+            <resourceType>gate.creole.gazetteer.DefaultGazetteer</resourceType>
+            <resourceName>ANNIE Gazetteer</resourceName>
+            <initParams class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+		<localMap/>
+            </initParams>
+            <features class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </features>
+          </pr>
+        </gate.util.persistence.AnalyserRunningStrategyPersistence>
+        <gate.util.persistence.AnalyserRunningStrategyPersistence>
+          <runMode>1</runMode>
+          <featureName></featureName>
+          <featureValue></featureValue>
+          <pr class="gate.util.persistence.LanguageAnalyserPersistence">
+            <runtimeParams class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </runtimeParams>
+            <resourceType>gate.creole.splitter.SentenceSplitter</resourceType>
+            <resourceName>ANNIE Sentence Splitter</resourceName>
+            <initParams class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </initParams>
+            <features class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </features>
+          </pr>
+        </gate.util.persistence.AnalyserRunningStrategyPersistence>
+        <gate.util.persistence.AnalyserRunningStrategyPersistence>
+          <runMode>1</runMode>
+          <pr class="gate.util.persistence.LanguageAnalyserPersistence">
+            <runtimeParams class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </runtimeParams>
+            <resourceType>gate.creole.POSTagger</resourceType>
+            <resourceName>ANNIE POS Tagger</resourceName>
+            <initParams class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </initParams>
+            <features class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </features>
+          </pr>
+        </gate.util.persistence.AnalyserRunningStrategyPersistence>
+        <gate.util.persistence.AnalyserRunningStrategyPersistence>
+          <runMode>1</runMode>
+          <pr class="gate.util.persistence.LanguageAnalyserPersistence">
+            <runtimeParams class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </runtimeParams>
+            <resourceType>gate.creole.ANNIETransducer</resourceType>
+            <resourceName>ANNIE NE Transducer</resourceName>
+            <initParams class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </initParams>
+            <features class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </features>
+          </pr>
+        </gate.util.persistence.AnalyserRunningStrategyPersistence>
+        <gate.util.persistence.AnalyserRunningStrategyPersistence>
+          <runMode>1</runMode>
+          <featureName></featureName>
+          <featureValue></featureValue>
+          <pr class="gate.util.persistence.LanguageAnalyserPersistence">
+            <runtimeParams class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </runtimeParams>
+            <resourceType>gate.creole.orthomatcher.OrthoMatcher</resourceType>
+            <resourceName>ANNIE OrthoMatcher</resourceName>
+            <initParams class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </initParams>
+            <features class="gate.util.persistence.MapPersistence">
+              <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+              <localMap/>
+            </features>
+          </pr>
+        </gate.util.persistence.AnalyserRunningStrategyPersistence>
+      </localList>
+      <collectionType>java.util.ArrayList</collectionType>
+    </strategiesList>
+    <prList class="gate.util.persistence.CollectionPersistence">
+      <localList>
+        <gate.util.persistence.PRPersistence reference="../../../strategiesList/localList/gate.util.persistence.AnalyserRunningStrategyPersistence/pr"/>
+        <gate.util.persistence.LanguageAnalyserPersistence reference="../../../strategiesList/localList/gate.util.persistence.AnalyserRunningStrategyPersistence[2]/pr"/>
+        <gate.util.persistence.LanguageAnalyserPersistence reference="../../../strategiesList/localList/gate.util.persistence.AnalyserRunningStrategyPersistence[3]/pr"/>
+        <gate.util.persistence.LanguageAnalyserPersistence reference="../../../strategiesList/localList/gate.util.persistence.AnalyserRunningStrategyPersistence[4]/pr"/>
+        <gate.util.persistence.LanguageAnalyserPersistence reference="../../../strategiesList/localList/gate.util.persistence.AnalyserRunningStrategyPersistence[5]/pr"/>
+        <gate.util.persistence.LanguageAnalyserPersistence reference="../../../strategiesList/localList/gate.util.persistence.AnalyserRunningStrategyPersistence[6]/pr"/>
+        <gate.util.persistence.LanguageAnalyserPersistence reference="../../../strategiesList/localList/gate.util.persistence.AnalyserRunningStrategyPersistence[7]/pr"/>
+      </localList>
+      <collectionType>java.util.ArrayList</collectionType>
+    </prList>
+    <resourceType>gate.creole.ConditionalSerialAnalyserController</resourceType>
+    <resourceName>ANNIE</resourceName>
+    <initParams class="gate.util.persistence.MapPersistence">
+      <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+      <localMap/>
+    </initParams>
+    <features class="gate.util.persistence.MapPersistence">
+      <mapType>gate.util.SimpleFeatureMapImpl</mapType>
+      <localMap>
+        <entry>
+          <string>gate.gui.icon</string>
+          <string>annie-application</string>
+        </entry>
+        <entry>
+          <string>gate.app.MetadataURL</string>
+          <gate.util.persistence.PersistenceManager-URLHolder>
+            <urlString>$relpath$.annie-defaults-metadata/metadata.xml</urlString>
+          </gate.util.persistence.PersistenceManager-URLHolder>
+        </entry>
+      </localMap>
+    </features>
+  </application>
+</gate.util.persistence.GateApplication>

Added: ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/build.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/build.xml?rev=1712083&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/build.xml (added)
+++ ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/build.xml Mon Nov  2 16:59:48 2015
@@ -0,0 +1,174 @@
+<?xml version="1.0"?>
+<!-- $Id: build.xml 16174 2012-10-29 13:58:16Z ian_roberts $ -->
+<project name="GATE Tokenisers" default="jar" basedir=".">
+    <description>
+        GATE see http://gate.ac.uk
+    </description>
+  <!-- set global properties for this build -->
+  <!-- Prevent Ant from warning about includeantruntime not being set -->
+  <property name="build.sysclasspath" value="ignore" />
+
+  <!-- Name of the output jar file -->
+  <property name="jarFile"  location="heptag_wrapper.jar"/>
+  
+  <!-- Sources -->
+  <property name="srcDir" location="src"/>
+  
+  <!-- Output directory for the build process -->
+  <property name="outputDir"  location="classes"/>
+
+  <!-- Libraries directory for the build process -->
+  <property name="libDir"  location="lib"/>
+  
+  <!-- Extensions directory for the build process -->
+  <property name="extDir"  location="lib/ext"/>
+
+  <!-- Documentation directory -->
+  <property name="docDir"  location="doc"/>
+  
+  <!-- Use the new 1.3+ compiler -->
+  <property name="build.compiler"  value="modern"/>
+
+  
+  <!-- tools.jar path -->
+  <path id="tools.jar.path" location="../bin/tools14.jar"/>
+  
+  <!-- The build CLASSPATH -->
+  <path id="build.class.path">
+    <fileset file="../../bin/gate.jar"/>
+    <fileset file="lib/heptag.jar"/>
+  </path>
+  
+  <!-- Prints out some information messages -->
+  <echo level="info">
+    This is the ANT build script for a CREOLE GATE component (http://gate.ac.uk).
+    Type &quot;ant help&quot; for details about the targets available.
+    GATE ${gate.version}, build ${gate.build}</echo>
+    
+  <!-- Prints out details about the targets -->
+  <target name="help">
+    <echo level="info">
+      This is the ANT build script for gate (http://gate.ac.uk).
+      The following targets are available
+        -all (default target): compiles GUK and GATE classes and makes the gate.jar archive.
+        
+        -compile: compiles all the .java files
+        -resources: copies the resources to the output directory (${outputDir})
+        -jar: creates the gate.jar archive
+        -run: starts GATE
+        -clean: cleans up the output from all previous builds
+        
+        -doc: creates the Javadoc and Java2HTML documentation
+        -docclean: deletes all built documentation
+        -jape: rebuilds the JAPE parser files and associated documentation
+        -guk: compiles the GUK classes and builds the guk.jar archive
+        -gukdemo: starts the GUK Editor (a.k.a. GATE Unicode Editor)
+        -test: runs the GATE test suite
+        
+        -distro: make a GATE distribution (calls all build tasks in the process)
+    </echo>
+  </target>
+  
+
+	<!-- This target compiles all the classes -->  
+  <target name="compile"
+          description="compile the source " >
+    <!-- Compile the java code from ${srcDir} into ${buildDir} -->
+    <javac srcdir="${srcDir}" 
+		       destdir="${outputDir}"
+           includes="gate/**"
+           source="1.4"
+           target="1.4"
+					 classpathref="build.class.path"/>
+  </target>
+	
+  <!-- Make gate.jar archive -->
+	<target name="jar" depends="compile">
+		<jar destfile="${jarFile}" 
+         update="false"
+         index="true">
+      <fileset dir="${outputDir}/"
+               includes="gate/**"/>
+    </jar>
+	</target>
+  
+  
+  <!-- Clear all build output -->
+  <target name="clean">
+    <delete includeemptydirs="true">
+      <fileset dir="${outputDir}" excludes="**/CVS,**/CVS/**,**/.cvsignore"/>
+    </delete>
+  </target>
+  
+  <!-- Dummy javadoc as there are no sources but gate core wants the target -->
+  <target name="javadoc">
+  </target>
+  
+  <!-- Make documentation - internal -->
+  <target name="internaljavadoc">
+    <javadoc access="private" 
+              destdir="${docDir}/javadoc/internal"
+              classpathref="run.class.path"
+              Extdirs="${extDir}"
+              Encoding="UTF-8"
+              Use="yes"
+              Windowtitle="GATE JavaDoc"
+              link="http://docs.oracle.com/javase/6/docs/api/"
+              docencoding="UTF-8"
+              charset="UTF-8"
+              source="1.6"
+              breakiterator="true">
+      <fileset dir="${srcDir}"/>        
+    </javadoc>
+  </target>
+
+  
+  <!-- Convert the source to HTML using the java2html utility -->
+  <target name="java2html">
+    <java jar="${buildDir}/lib/j2h.jar"
+          fork="true"
+          spawn="false">
+      <jvmarg value="-Dfile.encoding=UTF-8"/>
+      <arg value="-d"/> <arg file="${docDir}/java2html/"/>
+      <arg value="-js"/> <arg file="${srcDir}"/>
+      <arg value="-jd"/> <arg file="${docDir}/javadoc"/>
+      <arg value="-m"/> <arg value="4"/>
+      <arg value="-t"/> <arg value="2"/>
+      <arg value="-n"/> <arg value="&quot;GATE source&quot;"/>
+    </java>
+  </target>
+ 
+  <target name="doc" depends="javadoc, internaljavadoc, java2html"/>
+ 
+  
+  <!-- Clear all built documentation -->
+  <target name="docclean">
+    <delete includeemptydirs="true">
+      <fileset dir="${docDir}/javadoc" excludes="**/CVS,**/CVS/**,**/.cvsignore,internal,internal/**"/>
+    </delete>
+    <delete includeemptydirs="true">
+      <fileset dir="${docDir}/javadoc/internal" excludes="**/CVS,**/CVS/**,**/.cvsignore"/>
+    </delete>
+    <delete includeemptydirs="true">
+      <fileset dir="${docDir}/java2html" excludes="**/CVS,**/CVS/**,**/.cvsignore"/>
+    </delete>
+  </target>
+    
+  <target name="test" depends="jar">
+    <junit fork="true" 
+           showoutput="yes"
+           printsummary="yes">
+      <classpath refid="run.class.path"/>
+      <sysproperty key="gate.config" value="${buildDir}/gate.xml"/>
+      <jvmarg value="-Djava.ext.dirs=${extDir}"/>
+      <formatter type="plain"
+                 usefile="false"/>
+      <formatter type="xml"
+                 if="write.xml"/>
+      <test name="gate.TestGate"
+            outfile="testResult"
+            todir="${buildDir}"/>
+    </junit>
+  </target>  
+</project>
+

Added: ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/creole.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/creole.xml?rev=1712083&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/creole.xml (added)
+++ ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/creole.xml Mon Nov  2 16:59:48 2015
@@ -0,0 +1,90 @@
+<?xml version="1.0"?>
+<!-- $Id: creole.xml 17154 2013-12-01 16:44:44Z markagreenwood $ -->
+<!-- creole.xml directory file for ANNIE Processing resources -->
+<CREOLE-DIRECTORY>
+
+	<!-- PROCESSING RESOURCES -->
+
+	<!-- creole.xml for the Unicode tokeniser -->
+	<RESOURCE>
+		<CLASS>gate.creole.tokeniser.SimpleTokeniser</CLASS>			
+	</RESOURCE>
+
+	<!-- creole.xml for the Englishtokeniser -->
+	<RESOURCE>
+		<CLASS>gate.creole.tokeniser.DefaultTokeniser</CLASS>			
+	</RESOURCE>
+
+	<!-- creole.xml for gazetteer -->
+	<RESOURCE>
+		<CLASS>gate.creole.gazetteer.DefaultGazetteer</CLASS>
+	</RESOURCE>
+
+	<!-- creole.xml for a SharedDefaultGazetteer instance -->
+	<RESOURCE>
+		<CLASS>gate.creole.gazetteer.SharedDefaultGazetteer</CLASS>
+	</RESOURCE>
+
+	<!-- creole.xml for Hash Gazetteer (ex Natural)-->
+	<RESOURCE>
+		<CLASS>com.ontotext.gate.gazetteer.HashGazetteer</CLASS>
+	</RESOURCE>
+
+	<!-- creole.xml for JapeTransducer -->
+	<RESOURCE>
+		<CLASS>gate.creole.Transducer</CLASS>
+	</RESOURCE>
+
+	<!-- creole.xml for ANNIE Transducer -->
+	<RESOURCE>
+		<CLASS>gate.creole.ANNIETransducer</CLASS>
+	</RESOURCE>
+
+	<!-- creole.xml for Sentence splitter-->
+	<RESOURCE>
+		<CLASS>gate.creole.splitter.SentenceSplitter</CLASS>
+	</RESOURCE>
+
+	<!-- creole.xml for RegEx Sentence splitter-->
+	<RESOURCE>
+		<CLASS>gate.creole.splitter.RegexSentenceSplitter</CLASS>
+	</RESOURCE>
+
+	<!-- creole.xml for HepTag (Mark Hepple's POS tagger)-->
+	<RESOURCE>
+		<CLASS>gate.creole.POSTagger</CLASS>		
+	</RESOURCE>
+
+	<!-- creole.xml for namematch -->
+	<RESOURCE>
+		<CLASS>gate.creole.orthomatcher.OrthoMatcher</CLASS>
+	</RESOURCE>
+
+	<!--  creole.xml for the coreferencer -->
+	<RESOURCE>
+		<CLASS>gate.creole.coref.Coreferencer</CLASS>
+	</RESOURCE>
+
+	<!--  creole.xml for the coreferencer -->
+	<RESOURCE>
+		<CLASS>gate.creole.coref.NominalCoref</CLASS>		
+	</RESOURCE>
+
+	<!--  creole.xml for the document reset -->
+	<RESOURCE>
+		<CLASS>gate.creole.annotdelete.AnnotationDeletePR</CLASS>
+	</RESOURCE>
+
+	<!-- VISUAL RESOURCES -->
+
+	<!-- creole.xml for the jape viewer -->
+	<RESOURCE>
+		<CLASS>gate.gui.jape.JapeViewer</CLASS>
+	</RESOURCE>
+
+	<!-- Gazetteer editor -->	
+	<RESOURCE>
+		<CLASS>gate.gui.GazetteerEditor</CLASS>
+	</RESOURCE>
+
+</CREOLE-DIRECTORY>

Added: ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/country.lst
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/country.lst?rev=1712083&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/country.lst (added)
+++ ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/country.lst Mon Nov  2 16:59:48 2015
@@ -0,0 +1,191 @@
+Afghanistan
+Africa
+Albania
+Algeria
+Andorra
+Angola
+Arabia
+Argentina
+Armenia
+Australia
+Austria
+Bahama
+Bahrain
+Bangladesh
+Belarus
+Belgium
+Belize
+Benin
+Bermuda
+Bhutan
+Bissau
+Bosnia
+Botswana
+Brazil
+Britain
+Brunei
+Bulgaria
+Burma
+Burundi
+Cambodia
+Cameroon
+Canada
+Chad
+Chile
+China
+Colombia
+Columbia
+Congo
+Croatia
+Cuba
+Cyprus
+Czech
+Denmark
+Djibouti
+Dominican
+Ecuador
+Egypt
+Emirates
+Eritrea
+Estonia
+Ethiopia
+Fiji
+Finland
+France
+Gabon
+Gambia
+Germany
+Georgia
+Ghana
+Greece
+Grenada
+Guatemala
+Guiana
+Guinea
+Guyana
+Haiti
+Holland
+Honduras
+Hungary
+Iceland
+India
+Indonesia
+Iran
+Iraq
+Ireland
+Italy
+Jamaica
+Japan
+Jordan
+Kazakhstan
+Kenya
+Kiribati
+Korea
+Kosovo
+Kuwait
+Kyrgyzstan
+Lanka
+Laos
+Latvia
+Lebanon
+Leone
+Libya
+Liechtenstein
+Lithuania
+Luxembourg
+Malawi
+Malaysia
+Maldives
+Mali
+Malta
+Mauritania
+Mauritia
+Mexico
+Micronesia
+Moldovia
+Mongolia
+Morocco
+Mozambique
+Myanmar
+Namibia
+Nepal
+Netherland
+Netherlands
+Nicaragua
+Niger
+Nigeria
+Norway
+Oman
+Pakistan
+Palau
+Palestine
+Panama
+Papua
+Paraguay
+Peru
+Philippines
+Portugal
+Poland
+Qatar
+Rica
+Romania
+Russia
+Rwanda
+Salvador
+Scotland
+Senegal
+Serbia
+Sierra
+Singapore
+Slovakia
+Slovenia
+Somalia
+Spain
+Sudan
+Suriname
+Swaziland
+Sweden
+Swedish
+Switzerland
+Syria
+Taiwan
+Tajikstan
+Tajikistan
+Tanzania
+Thailand
+Tibet
+Timor
+Tonga
+Tunisia
+Turkey
+Turkmenistan
+Tuvalua
+Uganda
+Ukrain
+Ukraine
+Uruguay
+Uzbekistan
+Venezuela
+Verde
+Vietnam
+Wales
+Yemen
+Zaire
+Zambia
+Zealand
+Zimbabwe
+Israel
+Herzegovina
+England
+America
+Puerto Rico
+Sri Lanka
+Costa Rica
+United Kingdom
+UK
+United States
+Ivory Coast
+Saudi Arabia
+South Korea
+North Korea
+Trinidad and Tobago

Added: ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/lists.def
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/lists.def?rev=1712083&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/lists.def (added)
+++ ctakes/sandbox/ctakes-clinical-deid/GATE/plugins/ANNIE/resources/gazetteer/lists.def Mon Nov  2 16:59:48 2015
@@ -0,0 +1,5 @@
+country.lst:location:country
+nationality.lst:location:country
+spoken_language.lst:location:country
+us_state_acronym_abbreviation.lst:location:state_a_a
+us_state.lst:location:state




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