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From seanfi...@apache.org
Subject svn commit: r1885073 - in /ctakes/branches/ctakes-4.0.0.1: ./ ctakes-assertion-res/ ctakes-assertion-zoner-res/ ctakes-assertion-zoner/ ctakes-assertion/ ctakes-chunker-res/ ctakes-chunker/ ctakes-clinical-pipeline-res/ ctakes-clinical-pipeline/ ctakes...
Date Sun, 03 Jan 2021 18:12:38 GMT
Author: seanfinan
Date: Sun Jan  3 18:12:37 2021
New Revision: 1885073

URL: http://svn.apache.org/viewvc?rev=1885073&view=rev
Log:
CTAKES-545 : update to use UMLS API Key

Modified:
    ctakes/branches/ctakes-4.0.0.1/   (props changed)
    ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-zoner-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-zoner/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-assertion/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-chunker-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-chunker/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-clinical-pipeline-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-clinical-pipeline/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-constituency-parser-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-constituency-parser/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-context-tokenizer/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-core-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-core/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java
    ctakes/branches/ctakes-4.0.0.1/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/StandardCliOptions.java
    ctakes/branches/ctakes-4.0.0.1/ctakes-coreference-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-coreference/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-dependency-parser-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-dependency-parser/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
    ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTester.java
    ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java
    ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
    ctakes/branches/ctakes-4.0.0.1/ctakes-distribution/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-drug-ner-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-drug-ner/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-examples-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-examples/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-gui-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-gui/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-lvg-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-lvg/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-ne-contexts-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-ne-contexts/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-pos-tagger-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-pos-tagger/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-preprocessor/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-regression-test/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-relation-extractor-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-relation-extractor/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-side-effect-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-side-effect/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-smoking-status-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-smoking-status/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-template-filler/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-temporal-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-temporal/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-type-system/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-utils/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-res/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-uima/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-web/pom.xml
    ctakes/branches/ctakes-4.0.0.1/ctakes-ytex/pom.xml
    ctakes/branches/ctakes-4.0.0.1/pom.xml

Propchange: ctakes/branches/ctakes-4.0.0.1/
------------------------------------------------------------------------------
--- svn:ignore (original)
+++ svn:ignore Sun Jan  3 18:12:37 2021
@@ -1 +1,2 @@
 target
+resources

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-assertion-res</artifactId>
   <name>Apache cTAKES Resources assertion</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-zoner-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-zoner-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-zoner-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-zoner-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-assertion-zoner-res</artifactId>
   <name>Apache cTAKES Resources assertion-zoner</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-zoner/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-zoner/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-zoner/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-assertion-zoner/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 		<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-assertion/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-assertion/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-assertion/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-assertion/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 	<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-chunker-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-chunker-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-chunker-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-chunker-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-chunker-res</artifactId>
   <name>Apache cTAKES Resources ctakes-chunker-res</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-chunker/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-chunker/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-chunker/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-chunker/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
       	<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-clinical-pipeline-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-clinical-pipeline-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-clinical-pipeline-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-clinical-pipeline-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -3,7 +3,7 @@
    <parent>
       <groupId>org.apache.ctakes</groupId>
       <artifactId>ctakes</artifactId>
-      <version>4.0.0</version>
+      <version>4.0.0.1</version>
    </parent>
    <artifactId>ctakes-clinical-pipeline-res</artifactId>
    <name>ctakes-clinical-pipeline-res</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-clinical-pipeline/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-clinical-pipeline/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-clinical-pipeline/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-clinical-pipeline/pom.xml Sun Jan  3 18:12:37 2021
@@ -16,7 +16,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 
 

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-constituency-parser-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-constituency-parser-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-constituency-parser-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-constituency-parser-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-constituency-parser-res</artifactId>
   <name>Apache cTAKES Resources constituency-parser</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-constituency-parser/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-constituency-parser/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-constituency-parser/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-constituency-parser/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies> 
 		<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-context-tokenizer/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-context-tokenizer/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-context-tokenizer/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-context-tokenizer/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 		<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-core-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-core-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-core-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-core-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-core-res</artifactId>
   <name>Apache cTAKES Resources core</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-core/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-core/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-core/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-core/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 	     <dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java Sun Jan  3 18:12:37 2021
@@ -63,6 +63,11 @@ final public class PiperFileRunner {
             builder.set( "umlsPass", umlsPass );
             builder.set( "ctakes.umlspw", umlsPass );
          }
+         final String umlsKey = options.getUmlsApiKey();
+         if ( !umlsKey.isEmpty() ) {
+            builder.set( "umlsKey", umlsKey );
+            builder.set( "ctakes.umls_apikey", umlsKey );
+         }
          // load the piper file
          reader.setCliOptionals( options );
          reader.loadPipelineFile( options.getPiperPath() );
@@ -72,8 +77,10 @@ final public class PiperFileRunner {
          }
          // if an xmi output directory was specified but the piper didn't add the xmi writer, add the
          if ( !xmiOutDir.isEmpty() ) {
-            if ( !builder.getAeNames().stream().map( String::toLowerCase )
-                  .anyMatch( n -> n.contains( "xmiwriter" ) ) ) {
+            if ( !builder.getAeNames()
+                         .stream()
+                         .map( String::toLowerCase )
+                         .anyMatch( n -> n.contains( "xmiwriter" ) ) ) {
                builder.writeXMIs( xmiOutDir );
             }
          }

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/StandardCliOptions.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/StandardCliOptions.java?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/StandardCliOptions.java (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/StandardCliOptions.java Sun Jan  3 18:12:37 2021
@@ -63,9 +63,17 @@ interface StandardCliOptions {
    String getUmlsPassword();
 
    @Option(
+         longName = "key",
+         description = "UMLS API Key.",
+         defaultValue = "" )
+   String getUmlsApiKey();
+
+
+   @Option(
          shortName = "?",
          longName = "help",
          description = "print usage.",
          helpRequest = true )
    boolean isHelpWanted();
+
 }

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-coreference-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-coreference-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-coreference-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-coreference-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-coreference-res</artifactId>
   <name>Apache cTAKES Resources coreference</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-coreference/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-coreference/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-coreference/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-coreference/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 	     <dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-dependency-parser-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-dependency-parser-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-dependency-parser-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-dependency-parser-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-dependency-parser-res</artifactId>
   <name>Apache cTAKES Resources dependency-parser</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-dependency-parser/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-dependency-parser/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-dependency-parser/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-dependency-parser/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 	     <dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
    <parent>
       <groupId>org.apache.ctakes</groupId>
       <artifactId>ctakes</artifactId>
-      <version>4.0.0</version>
+      <version>4.0.0.1</version>
    </parent>
    <artifactId>ctakes-dictionary-lookup-fast-res</artifactId>
    <name>Apache cTAKES Resources dictionary-lookup-fast-res</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 	     <dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java Sun Jan  3 18:12:37 2021
@@ -23,22 +23,25 @@ import org.apache.ctakes.utils.env.Envir
 import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;
 
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.net.HttpURLConnection;
 import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Properties;
 
-
 /**
  * Used to validate UMLS license / user.
  * <p/>
- * TODO  Authentication before download would be nice, or perhaps an encrypted download
- * Author: SPF
- * Affiliation: CHIP-NLP
- * Date: 2/19/14
+ * download Author: SPF Affiliation: CHIP-NLP Date: 2/19/14
+ * <p/>
+ * UPDATED to use the API_KEY based authentication scheme of the UMLS For
+ * maximum compatibility with existing configurations we permit umls_user =
+ * "umls_api_key" and umls_password = "<APIKEY>" settings or simply set the
+ * ctakes.umls_apikey system property pabramowitsch (11/2020)
  */
 public enum UmlsUserApprover {
 
@@ -49,93 +52,210 @@ public enum UmlsUserApprover {
    }
 
    // properties, matches new
+   public final static String OLD_USER_PARAM = "ctakes.umlsuser";
+   public final static String OLD_PASS_PARAM = "ctakes.umlspw";
+
    public final static String URL_PARAM = "umlsUrl";
-   public final static String VENDOR_PARAM = "umlsVendor";
    public final static String USER_PARAM = "umlsUser";
    public final static String PASS_PARAM = "umlsPass";
+   public final static String KEY_PARAM = "umlsKey";
 
-   // environment, matches old
-   private final static String UMLSADDR_PARAM = "ctakes.umlsaddr";
-   private final static String UMLSVENDOR_PARAM = "ctakes.umlsvendor";
-   final static String UMLSUSER_PARAM = "ctakes.umlsuser";
-   final static String UMLSPW_PARAM = "ctakes.umlspw";
+   public final static String API_KEY_LABEL = "umls_api_key";
+   public final static String OLDY_KEY_PROP = "ctakes.umls_apikey";
 
    static final private Logger LOGGER = Logger.getLogger( "UmlsUserApprover" );
 
    static final private String CHANGEME = "CHANGEME";
-   
+   static final private String CHANGE_ME = "CHANGE_ME";
+   // forget about copies of this URL sprinkled around the other libraries
+   static private final String OLD_USER_PASS_URL = "https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser";
+   static final private String UTS_APIKEY_URL = "https://utslogin.nlm.nih.gov/cas/v1/api-key";
+
+   static private final String WHERE_DEFAULT = "Default Value";
+   static private final String WHERE_ENV = "User Environment or Piper Variable";
+   static private final String WHERE_XML = "Property Xml";
+
+   static private final String NEW_AUTH_MESSAGE
+         = "\n\n\n"
+           + "Starting 2021 NIH is using a new method for UMLS license authentication.  \n\n"
+           + "To use the UMLS dictionary you must obtain a UMLS API Key.  \n"
+           + "After obtaining a Key, there are several methods to utilize it with Apache cTAKES.  \n\n"
+           + "You may specify the value of your Key with a single parameter: \n"
+           + OLDY_KEY_PROP + " in your Operating System, \n"
+           + KEY_PARAM + " in your Operating System, \n"
+           + KEY_PARAM + " in your Piper File, \n"
+           + KEY_PARAM + " in your Dictionary Properties XML, \n"
+           + "--key in your Piper Runner command line, \n"
+           + "-D" + OLDY_KEY_PROP + " in your Java command parameters, or \n"
+           + "-D" + KEY_PARAM + " in your Java command parameters.  \n\n"
+           + "The single key settings above will be preferred over the pre-2021 [UserName , Password] method.  \n"
+           + "The pre-2021 [UserName , Password] method may still be used if the username is set to \n"
+           + API_KEY_LABEL + " and the password is set to the value of your Key.  \n\n"
+           + "For more information visit https://uts.nlm.nih.gov/  \n\n\n";
+
    // cache of valid users
    static private final Collection<String> _validUsers = new ArrayList<>();
 
+
    /**
     * validate the UMLS license / user
     *
     * @param uimaContext contains information about the UMLS license / user
-    * @param properties  -
-    * @return true if the server at umlsaddr approves of the vendor, user, password combination
+    * @param properties  possibly containing the attribs we need If not, we will
+    *                    look in the environment and sysprops.
+    * @return true if the server at umlsaddr approves of the vendor, user, password
+    * combination
     */
    public boolean isValidUMLSUser( final UimaContext uimaContext, final Properties properties ) {
-      String umlsUrl = EnvironmentVariable.getEnv( UMLSADDR_PARAM, uimaContext );
-      if ( umlsUrl == null || umlsUrl.equals( EnvironmentVariable.NOT_PRESENT ) ) {
-         umlsUrl = properties.getProperty( URL_PARAM );
-      }
-      String vendor = EnvironmentVariable.getEnv( UMLSVENDOR_PARAM, uimaContext );
-      if ( vendor == null || vendor.equals( EnvironmentVariable.NOT_PRESENT ) ) {
-         vendor = properties.getProperty( VENDOR_PARAM );
-      }
-      String user = EnvironmentVariable.getEnv( UMLSUSER_PARAM, uimaContext );
-      if ( user == null || user.equals( EnvironmentVariable.NOT_PRESENT ) ) {
-         user = properties.getProperty( USER_PARAM );
-      }
-      String pass = EnvironmentVariable.getEnv( UMLSPW_PARAM, uimaContext );
-      if ( pass == null || pass.equals( EnvironmentVariable.NOT_PRESENT ) ) {
-         pass = properties.getProperty( PASS_PARAM );
+      final String apiUrl = getUrl( properties );
+      final String umlsApiKey = getApiKey( uimaContext, properties );
+      if ( umlsApiKey != null ) {
+         return isValidUMLSUser( apiUrl, umlsApiKey );
       }
-      return isValidUMLSUser( umlsUrl, vendor, user, pass );
+      // emulate U&P style
+      final String user = getUser( uimaContext, properties );
+      final String pass = getPassOrKey( uimaContext, properties );
+      return isValidUMLSUser( apiUrl, null, user, pass );
    }
 
    /**
-    * validate the UMLS license / user
+    * validate the UMLS license / user Functionality overridden to deal with new
+    * UMLS API
     *
     * @param umlsUrl -
-    * @param vendor  -
-    * @param user    -
-    * @param pass    -
-    * @return true if the server at umlsaddr approves of the vendor, user, password combination
-    */
-   public boolean isValidUMLSUser( final String umlsUrl, final String vendor,
-                                   final String user, final String pass ) {
-      final String cacheCode = umlsUrl + vendor + user + pass;
-      if ( _validUsers.contains( cacheCode ) ) {
-         return true;
+    * @param vendor  IGNORED -
+    * @param user    NOW needs to be the value "umls_api_key" -
+    * @param apikey  THE API KEY -
+    * @return true if the server at umlsaddr approves of the vendor, user, password
+    * combination
+    */
+   public boolean isValidUMLSUser( String umlsUrl, final String vendor, final String user, final String apikey ) {
+      if ( !isValid( USER_PARAM, user ) || !user.equals( API_KEY_LABEL ) ) {
+         LOGGER.error( NEW_AUTH_MESSAGE );
+         return false;
       }
-      String data;
-      try {
-         data = URLEncoder.encode( "licenseCode", "UTF-8" ) + "=" + URLEncoder.encode( vendor, "UTF-8" );
-         data += "&" + URLEncoder.encode( "user", "UTF-8" ) + "=" + URLEncoder.encode( user, "UTF-8" );
-         data += "&" + URLEncoder.encode( "password", "UTF-8" ) + "=" + URLEncoder.encode( pass, "UTF-8" );
-      } catch ( UnsupportedEncodingException unseE ) {
-         LOGGER.error( "Could not encode URL for " + user + " with vendor license " + vendor );
+      if ( !isValid( PASS_PARAM, apikey ) || apikey.length() <= 24 ) {
+         LOGGER.error( NEW_AUTH_MESSAGE );
          return false;
       }
-      
-      // Potentially someone could have a user ID of CHANGEME or a password of CHANGEME but don't allow those
-      // to make it easy for us to detect that the user or password was not set correctly.
-      if (user.equals(CHANGEME)) {
-    	  LOGGER.info( "Not checking UMLS Account for user " + user + ":" );
-    	  LOGGER.error("  User " + CHANGEME + " not allowed, verify you are setting " + USER_PARAM + " or " + UMLSUSER_PARAM + " properly.");
-    	  return false;
-      }
-      if (pass.equals(CHANGEME)) {
-    	  LOGGER.info( "Not checking UMLS Account for user " + user + " password " + pass );
-    	  LOGGER.error("  Password " + CHANGEME + " not allowed, verify you are setting " + PASS_PARAM + " or " + UMLSPW_PARAM + " properly.");
-    	  return false;
+      if ( _validUsers.contains( apikey ) ) {
+         return true;
+      }
+      // last chance for an override
+      if ( !isValid( umlsUrl ) ) {
+         umlsUrl = getUrl();
+         if ( !isValid( umlsUrl ) ) {
+            umlsUrl = UTS_APIKEY_URL;
+         }
       }
+      return isValidUMLSUser( umlsUrl, apikey );
+   }
 
+   /**
+    * New UTS authentication method
+    *
+    * @param umlsUrl    -
+    * @param umlsApiKey -
+    * @return true if the umls api key can be authenticated
+    */
+   static private boolean isValidUMLSUser( final String umlsUrl, final String umlsApiKey ) {
+      if ( _validUsers.contains( umlsApiKey ) ) {
+         return true;
+      }
+      return authenticate( umlsUrl, umlsApiKey );
+   }
+
+   /**
+    * @return the url to the authentication service
+    */
+   static private String getUrl() {
+      // get explicitly from the JVM in case any component
+      // still has the old URL mentioned
+      return getUrl( System.getProperties() );
+   }
+
+   /**
+    * @param properties properties from either the xml file or the user environment
+    * @return a user defined url or the default
+    */
+   static private String getUrl( final Properties properties ) {
+      String where = WHERE_ENV;
+      String umlsUrl = EnvironmentVariable.getEnv( URL_PARAM );
+      if ( !isValid( umlsUrl ) || umlsUrl.equals( OLD_USER_PASS_URL ) ) {
+         umlsUrl = properties.getProperty( URL_PARAM );
+         if ( isValid( umlsUrl ) && !umlsUrl.equals( OLD_USER_PASS_URL ) ) {
+            where = WHERE_XML;
+         }
+      }
+      if ( !isValid( umlsUrl ) || umlsUrl.equals( OLD_USER_PASS_URL ) ) {
+         umlsUrl = UTS_APIKEY_URL;
+         where = WHERE_DEFAULT;
+      }
+      LOGGER.debug( "Using umlsURL set using: " + where );
+      return umlsUrl;
+   }
+
+
+   /**
+    * Check for parameter value in the uimacontext, environment and properties xml.
+    *
+    * @param uimaContext -
+    * @param properties  -
+    * @param name        -
+    * @param oldParam    the old environment variable style.  ctakes.umls{something}
+    * @param param       the new environment variable or piper file style.  umls{something}
+    * @return the obtained value or null
+    */
+   static private String getParamValue( final UimaContext uimaContext, final Properties properties,
+                                        final String name,
+                                        final String oldParam, final String param ) {
+      String where = WHERE_ENV + " " + param;
+      String value = EnvironmentVariable.getEnv( param, uimaContext );
+      if ( !isValid( value ) ) {
+         value = properties.getProperty( param );
+         if ( isValid( param, value ) ) {
+            where = WHERE_XML + " " + param;
+         } else {
+            value = null;
+         }
+      }
+      if ( value == null ) {
+         value = EnvironmentVariable.getEnv( oldParam, uimaContext );
+         if ( isValid( value ) ) {
+            where = WHERE_ENV + " " + oldParam;
+         }
+      }
+      if ( value != null ) {
+         LOGGER.debug( name + " set using: " + where );
+      }
+      return value;
+   }
+
+   static private String getApiKey( final UimaContext uimaContext, final Properties properties ) {
+      return getParamValue( uimaContext, properties, "UMLS API Key", OLDY_KEY_PROP, KEY_PARAM );
+   }
+
+   static private String getPassOrKey( final UimaContext uimaContext, final Properties properties ) {
+      return getParamValue( uimaContext, properties, "UMLS API Key", OLD_PASS_PARAM, PASS_PARAM );
+   }
+
+   static private String getUser( final UimaContext uimaContext, final Properties properties ) {
+      return getParamValue( uimaContext, properties, "UMLS User", OLD_USER_PARAM, USER_PARAM );
+   }
+
+   /**
+    * @param umlsUrl -
+    * @param apiKey  -
+    * @return true if the api key is valid according to the server at umlsUrl
+    */
+   static private boolean authenticate( final String umlsUrl, String apiKey ) {
       try ( DotLogger dotter = new DotLogger() ) {
-         LOGGER.info( "Checking UMLS Account at " + umlsUrl + " for user " + user + ":" );
+         apiKey = apiKey.trim();
+         LOGGER.info( "Checking UMLS Account at " + umlsUrl + ":" );
+         String data = "apikey=" + apiKey;
          final URL url = new URL( umlsUrl );
-         final URLConnection connection = url.openConnection();
+         final HttpURLConnection connection = (HttpURLConnection) url.openConnection();
+         connection.setRequestMethod( "POST" );
          connection.setDoOutput( true );
          final OutputStreamWriter writer = new OutputStreamWriter( connection.getOutputStream() );
          writer.write( data );
@@ -143,21 +263,25 @@ public enum UmlsUserApprover {
          boolean isValidUser = false;
          final BufferedReader reader = new BufferedReader( new InputStreamReader( connection.getInputStream() ) );
          String line;
-         while ( (line = reader.readLine()) != null ) {
+         while ( ( line = reader.readLine() ) != null ) {
             final String trimline = line.trim();
             if ( trimline.isEmpty() ) {
                break;
             }
-            isValidUser = trimline.equalsIgnoreCase( "<Result>true</Result>" )
-                          || trimline.equalsIgnoreCase( "<?xml version='1.0' encoding='UTF-8'?><Result>true</Result>" );
          }
+         // not used, but in case of problems we may want to see what is returned
+         LOGGER.debug( "UTS response: " + line );
          writer.close();
          reader.close();
+         // This method gets a ticket getting token. If it's successful, thats all we
+         // need to know
+         isValidUser = ( connection.getResponseCode() == HttpURLConnection.HTTP_CREATED );
          if ( isValidUser ) {
-            LOGGER.info( "  UMLS Account at " + umlsUrl + " for user " + user + " has been validated" );
-            _validUsers.add( cacheCode );
+            LOGGER.info( "  UMLS Account has been validated" );
+            _validUsers.add( apiKey );
          } else {
-            LOGGER.error( "  UMLS Account at " + umlsUrl + " is not valid for user " + user + " with " + pass );
+            LOGGER.error( "  UMLS Account at " + umlsUrl + " is not valid." );
+            LOGGER.error( NEW_AUTH_MESSAGE );
          }
          return isValidUser;
       } catch ( IOException ioE ) {
@@ -166,5 +290,45 @@ public enum UmlsUserApprover {
       }
    }
 
+   /**
+    * used for unit testing
+    */
+   public void resetUserCache() {
+      _validUsers.clear();
+   }
+
+   /**
+    * @param value -
+    * @return true if the value is not null, not empty and not a "NOT_PRESENT" constant
+    */
+   static private boolean isValid( final String value ) {
+      return value != null
+             && !value.trim()
+                      .isEmpty()
+             && !value.equals( EnvironmentVariable.NOT_PRESENT );
+   }
+
+   /**
+    * If the value is equal to "CHANGEME" or "CHANGE_ME" a message is logged telling the user to set a value.
+    *
+    * @param name  -
+    * @param value -
+    * @return true if the value is not null, not empty and not a "NOT_PRESENT" constant
+    */
+   static private boolean isValid( final String name, final String value ) {
+      if ( isValid( value ) ) {
+         if ( value.trim()
+                   .equals( CHANGEME ) || value.trim()
+                                               .equals( CHANGE_ME ) ) {
+            // Potentially someone could have a user ID of CHANGEME or a password of CHANGEME but don't allow those
+            // to make it easy for us to detect that the user or password was not set correctly.
+            LOGGER.error( "  " + name + " " + value + " not allowed.  It is a placeholder reminder." );
+            return false;
+         }
+         return true;
+      }
+      return false;
+   }
+
 
 }

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTester.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTester.java?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTester.java (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTester.java Sun Jan  3 18:12:37 2021
@@ -3,8 +3,8 @@ package org.apache.ctakes.dictionary.loo
 import org.apache.ctakes.utils.env.EnvironmentVariable;
 import org.apache.log4j.Logger;
 
-import static org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover.UMLSPW_PARAM;
-import static org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover.UMLSUSER_PARAM;
+import static org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover.OLD_PASS_PARAM;
+import static org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover.OLD_USER_PARAM;
 
 /**
  * @author SPF , chip-nlp
@@ -19,11 +19,11 @@ final public class UmlsUserTester {
    }
 
    static public boolean canTestUmlsUser() {
-      String user = EnvironmentVariable.getEnv( UMLSUSER_PARAM, null );
+      String user = EnvironmentVariable.getEnv( OLD_USER_PARAM, null );
       if ( user == null || user.equals( EnvironmentVariable.NOT_PRESENT ) ) {
          return false;
       }
-      String pass = EnvironmentVariable.getEnv( UMLSPW_PARAM, null );
+      String pass = EnvironmentVariable.getEnv( OLD_PASS_PARAM, null );
       return pass != null && !pass.equals( EnvironmentVariable.NOT_PRESENT );
    }
 

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-dictionary-lookup-res</artifactId>
   <name>Apache cTAKES Resources dictionary-lookup</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/pom.xml Sun Jan  3 18:12:37 2021
@@ -19,25 +19,26 @@
     under the License.
 
 -->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+			xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>ctakes-dictionary-lookup</artifactId>
 	<name>Apache cTAKES dictionary lookup</name>
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
-		<dependencies>
-	     <dependency>
+	<dependencies>
+		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-dictionary-lookup-res</artifactId>
-		</dependency>		    
+		</dependency>
 		<dependency>
-         <groupId>org.hsqldb</groupId>
+			<groupId>org.hsqldb</groupId>
 			<artifactId>hsqldb</artifactId>
-         <version>2.3.4</version>
-      </dependency>
+			<version>2.3.4</version>
+		</dependency>
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>
@@ -47,6 +48,10 @@
 			<artifactId>ctakes-core</artifactId>
 		</dependency>
 		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dictionary-lookup-fast</artifactId>
+		</dependency>
+		<dependency>
 			<groupId>log4j</groupId>
 			<artifactId>log4j</artifactId>
 		</dependency>
@@ -57,7 +62,7 @@
 		<dependency>
 			<groupId>org.apache.lucene</groupId>
 			<artifactId>lucene-queries</artifactId>
-		</dependency>		
+		</dependency>
 		<dependency>
 			<groupId>org.apache.lucene</groupId>
 			<artifactId>lucene-queryparser</artifactId>
@@ -65,7 +70,7 @@
 		<dependency>
 			<groupId>org.apache.lucene</groupId>
 			<artifactId>lucene-analyzers-common</artifactId>
-		</dependency>				
+		</dependency>
 		<dependency>
 			<groupId>jdom</groupId>
 			<artifactId>jdom</artifactId>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java Sun Jan  3 18:12:37 2021
@@ -18,16 +18,12 @@
  */
 package org.apache.ctakes.dictionary.lookup.ae;
 
+import org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover;
 import org.apache.ctakes.utils.env.EnvironmentVariable;
 import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import java.io.*;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-
 /**
  * UIMA annotator that identified entities based on lookup.
  * Special implementation to pre bundle the UMLS SnowmedCT/RxNorm dictionaries
@@ -54,7 +50,8 @@ public class ThreadedUmlsDictionaryLooku
       final String umlsUser = EnvironmentVariable.getEnv( UMLSUSER_PARAM, aContext );
       final String umlsPassword = EnvironmentVariable.getEnv( UMLSPW_PARAM, aContext );
       _logger.info( "Using " + UMLSADDR_PARAM + ": " + umlsAddress + ": " + umlsUser );
-      if ( !isValidUMLSUser( umlsAddress, umlsVendor, umlsUser, umlsPassword ) ) {
+      if ( !UmlsUserApprover.getInstance()
+                            .isValidUMLSUser( umlsAddress, null, umlsUser, umlsPassword ) ) {
          _logger.error( "Error: Invalid UMLS License.  " +
                         "A UMLS License is required to use the UMLS dictionary lookup. \n" +
                         "Error: You may request one at: https://uts.nlm.nih.gov/license.html \n" +
@@ -64,44 +61,44 @@ public class ThreadedUmlsDictionaryLooku
       }
    }
 
-   public static boolean isValidUMLSUser( final String umlsaddr, final String vendor,
-                                          final String username, final String password ) {
-      String data;
-      try {
-         data = URLEncoder.encode( "licenseCode", "UTF-8" ) + "=" + URLEncoder.encode( vendor, "UTF-8" );
-         data += "&" + URLEncoder.encode( "user", "UTF-8" ) + "=" + URLEncoder.encode( username, "UTF-8" );
-         data += "&" + URLEncoder.encode( "password", "UTF-8" ) + "=" + URLEncoder.encode( password, "UTF-8" );
-      } catch ( UnsupportedEncodingException unseE ) {
-         LOGGER.error( "Could not encode URL for " + username + " with vendor license " + vendor );
-         return false;
-      }
-      try {
-         final URL url = new URL( umlsaddr );
-         final URLConnection connection = url.openConnection();
-         connection.setDoOutput( true );
-         try ( final OutputStreamWriter writer = new OutputStreamWriter( connection.getOutputStream() );
-               final BufferedReader reader = new BufferedReader( new InputStreamReader( connection
-                     .getInputStream() ) ) ) {
-
-            writer.write( data );
-            writer.flush();
-            boolean result = false;
-
-            String line;
-            while ( (line = reader.readLine()) != null ) {
-               final String trimline = line.trim();
-               if ( trimline.isEmpty() ) {
-                  break;
-               }
-               result = trimline.equalsIgnoreCase( "<Result>true</Result>" )
-                        || trimline.equalsIgnoreCase( "<?xml version='1.0' encoding='UTF-8'?><Result>true</Result>" );
-            }
-            return result;
-         }
-      } catch ( IOException ioE ) {
-         LOGGER.error( ioE.getMessage() );
-         return false;
-      }
-   }
+//   public static boolean isValidUMLSUser( final String umlsaddr, final String vendor,
+//                                          final String username, final String password ) {
+//      String data;
+//      try {
+//         data = URLEncoder.encode( "licenseCode", "UTF-8" ) + "=" + URLEncoder.encode( vendor, "UTF-8" );
+//         data += "&" + URLEncoder.encode( "user", "UTF-8" ) + "=" + URLEncoder.encode( username, "UTF-8" );
+//         data += "&" + URLEncoder.encode( "password", "UTF-8" ) + "=" + URLEncoder.encode( password, "UTF-8" );
+//      } catch ( UnsupportedEncodingException unseE ) {
+//         LOGGER.error( "Could not encode URL for " + username + " with vendor license " + vendor );
+//         return false;
+//      }
+//      try {
+//         final URL url = new URL( umlsaddr );
+//         final URLConnection connection = url.openConnection();
+//         connection.setDoOutput( true );
+//         try ( final OutputStreamWriter writer = new OutputStreamWriter( connection.getOutputStream() );
+//               final BufferedReader reader = new BufferedReader( new InputStreamReader( connection
+//                     .getInputStream() ) ) ) {
+//
+//            writer.write( data );
+//            writer.flush();
+//            boolean result = false;
+//
+//            String line;
+//            while ( (line = reader.readLine()) != null ) {
+//               final String trimline = line.trim();
+//               if ( trimline.isEmpty() ) {
+//                  break;
+//               }
+//               result = trimline.equalsIgnoreCase( "<Result>true</Result>" )
+//                        || trimline.equalsIgnoreCase( "<?xml version='1.0' encoding='UTF-8'?><Result>true</Result>" );
+//            }
+//            return result;
+//         }
+//      } catch ( IOException ioE ) {
+//         LOGGER.error( ioE.getMessage() );
+//         return false;
+//      }
+//   }
 
 }

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java Sun Jan  3 18:12:37 2021
@@ -22,6 +22,7 @@ import org.apache.commons.io.FileUtils;
 import org.apache.ctakes.core.pipeline.PipeBitInfo;
 import org.apache.ctakes.core.resource.FileResourceImpl;
 import org.apache.ctakes.core.resource.JdbcConnectionResourceImpl;
+import org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover;
 import org.apache.ctakes.utils.env.EnvironmentVariable;
 import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;
@@ -30,16 +31,10 @@ import org.apache.uima.fit.factory.Analy
 import org.apache.uima.fit.factory.ExternalResourceFactory;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
 import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
 
 /**
  * UIMA annotator that identified entities based on lookup.
@@ -81,7 +76,8 @@ public class UmlsDictionaryLookupAnnotat
          UMLSPW = EnvironmentVariable.getEnv( UMLSPW_PARAM, aContext );
 
          iv_logger.info( "Using " + UMLSADDR_PARAM + ": " + UMLSAddr + ": " + UMLSUser );
-         if ( !isValidUMLSUser( UMLSAddr, UMLSVendor, UMLSUser, UMLSPW ) ) {
+         if ( !UmlsUserApprover.getInstance()
+                               .isValidUMLSUser( UMLSAddr, UMLSVendor, UMLSUser, UMLSPW ) ) {
             iv_logger.error(
                   "Error: Invalid UMLS License.  A UMLS License is required to use the UMLS dictionary lookup. \n" +
                   "Error: You may request one at: https://uts.nlm.nih.gov/license.html \n" +
@@ -94,67 +90,76 @@ public class UmlsDictionaryLookupAnnotat
       }
    }
 
-   public static boolean isValidUMLSUser( String umlsaddr, String vendor, String username, String password )
-         throws Exception {
-      String data = URLEncoder.encode( "licenseCode", "UTF-8" ) + "="
-                    + URLEncoder.encode( vendor, "UTF-8" );
-      data += "&" + URLEncoder.encode( "user", "UTF-8" ) + "="
-              + URLEncoder.encode( username, "UTF-8" );
-      data += "&" + URLEncoder.encode( "password", "UTF-8" ) + "="
-              + URLEncoder.encode( password, "UTF-8" );
-      URL url = new URL( umlsaddr );
-      URLConnection conn = url.openConnection();
-      conn.setDoOutput( true );
-      try ( OutputStreamWriter wr = new OutputStreamWriter( conn.getOutputStream() ) ) {
-         wr.write( data );
-         wr.flush();
-      }
-      try ( BufferedReader rd = new BufferedReader( new InputStreamReader( conn.getInputStream() ) ) ) {
-         boolean result = false;
-         String line;
-         while ( (line = rd.readLine()) != null ) {
-            if ( line.trim().length() > 0 ) {
-               result = line.trim().equalsIgnoreCase( "<Result>true</Result>" )
-                        ||
-                        line.trim().equalsIgnoreCase( "<?xml version='1.0' encoding='UTF-8'?><Result>true</Result>" );
-            }
-         }
-         return result;
-      }
-   }
-
-  @SuppressWarnings("resource")
-  public static AnalysisEngineDescription createAnnotatorDescription() throws ResourceInitializationException, MalformedURLException {
-      InputStream lookUpStream = UmlsDictionaryLookupAnnotator.class.getClassLoader().getResourceAsStream("org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml");
-      File lookupFile = new File("/tmp/LookupDesc_Db.xml");
+//   public static boolean isValidUMLSUser( String umlsaddr, String vendor, String username, String password )
+//         throws Exception {
+//      String data = URLEncoder.encode( "licenseCode", "UTF-8" ) + "="
+//                    + URLEncoder.encode( vendor, "UTF-8" );
+//      data += "&" + URLEncoder.encode( "user", "UTF-8" ) + "="
+//              + URLEncoder.encode( username, "UTF-8" );
+//      data += "&" + URLEncoder.encode( "password", "UTF-8" ) + "="
+//              + URLEncoder.encode( password, "UTF-8" );
+//      URL url = new URL( umlsaddr );
+//      URLConnection conn = url.openConnection();
+//      conn.setDoOutput( true );
+//      try ( OutputStreamWriter wr = new OutputStreamWriter( conn.getOutputStream() ) ) {
+//         wr.write( data );
+//         wr.flush();
+//      }
+//      try ( BufferedReader rd = new BufferedReader( new InputStreamReader( conn.getInputStream() ) ) ) {
+//         boolean result = false;
+//         String line;
+//         while ( (line = rd.readLine()) != null ) {
+//            if ( line.trim().length() > 0 ) {
+//               result = line.trim().equalsIgnoreCase( "<Result>true</Result>" )
+//                        ||
+//                        line.trim().equalsIgnoreCase( "<?xml version='1.0' encoding='UTF-8'?><Result>true</Result>" );
+//            }
+//         }
+//         return result;
+//      }
+//   }
+
+   @SuppressWarnings( "resource" )
+   public static AnalysisEngineDescription createAnnotatorDescription()
+         throws ResourceInitializationException, MalformedURLException {
+      InputStream lookUpStream = UmlsDictionaryLookupAnnotator.class.getClassLoader()
+                                                                    .getResourceAsStream(
+                                                                          "org/apache/ctakes/dictionary/lookup"
+                                                                          + "/LookupDesc_Db.xml" );
+      File lookupFile = new File( "/tmp/LookupDesc_Db.xml" );
       try {
-          FileUtils.copyInputStreamToFile(lookUpStream, lookupFile);
-      } catch (IOException e) {
-          throw new RuntimeException("Error copying temporary InpuStream org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml to /tmp/LookupDesc_Db.xml.", e);
+         FileUtils.copyInputStreamToFile( lookUpStream, lookupFile );
+      } catch ( IOException e ) {
+         throw new RuntimeException(
+               "Error copying temporary InpuStream org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml to "
+               + "/tmp/LookupDesc_Db.xml.",
+               e );
       }
       return AnalysisEngineFactory.createEngineDescription( UmlsDictionaryLookupAnnotator.class,
-             UMLSADDR_PARAM,
-             "https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser",
-             UMLSVENDOR_PARAM,
-             "NLM-6515182895",
-             "LookupDescriptor",
-             ExternalResourceFactory.createExternalResourceDescription(
-                   FileResourceImpl.class,
-                   lookupFile.toURI().toURL() ),
-             "DbConnection",
-             ExternalResourceFactory.createExternalResourceDescription(
-                   JdbcConnectionResourceImpl.class,
-                   "",
-                   JdbcConnectionResourceImpl.PARAM_DRIVER_CLASS,
-                   "org.hsqldb.jdbcDriver",
-                   JdbcConnectionResourceImpl.PARAM_URL,
-                   // Should be the following but it's WAY too slow
-                   "jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/umls" ),
-             //"jdbc:hsqldb:file:target/unpacked/org/apache/ctakes/dictionary/lookup/umls2011ab/umls"),
-             "RxnormIndexReader",
-             ExternalResourceFactory.createExternalResourceDescription(
-                   JdbcConnectionResourceImpl.class,
-                   "",
+                                                            UMLSADDR_PARAM,
+                                                            "https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser",
+                                                            UMLSVENDOR_PARAM,
+                                                            "NLM-6515182895",
+                                                            "LookupDescriptor",
+                                                            ExternalResourceFactory.createExternalResourceDescription(
+                                                                  FileResourceImpl.class,
+                                                                  lookupFile.toURI()
+                                                                            .toURL() ),
+                                                            "DbConnection",
+                                                            ExternalResourceFactory.createExternalResourceDescription(
+                                                                  JdbcConnectionResourceImpl.class,
+                                                                  "",
+                                                                  JdbcConnectionResourceImpl.PARAM_DRIVER_CLASS,
+                                                                  "org.hsqldb.jdbcDriver",
+                                                                  JdbcConnectionResourceImpl.PARAM_URL,
+                                                                  // Should be the following but it's WAY too slow
+                                                                  "jdbc:hsqldb:res:/org/apache/ctakes/dictionary"
+                                                                  + "/lookup/umls2011ab/umls" ),
+                                                            //"jdbc:hsqldb:file:target/unpacked/org/apache/ctakes/dictionary/lookup/umls2011ab/umls"),
+                                                            "RxnormIndexReader",
+                                                            ExternalResourceFactory.createExternalResourceDescription(
+                                                                  JdbcConnectionResourceImpl.class,
+                                                                  "",
                    JdbcConnectionResourceImpl.PARAM_DRIVER_CLASS,
                    "org.hsqldb.jdbcDriver",
                    JdbcConnectionResourceImpl.PARAM_URL,

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-distribution/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-distribution/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-distribution/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-distribution/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-      <version>4.0.0</version>
+      <version>4.0.0.1</version>
 	</parent>
 	<packaging>pom</packaging>
 

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-drug-ner-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-drug-ner-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-drug-ner-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-drug-ner-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -3,7 +3,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-drug-ner-res</artifactId>
   <name>Apache cTAKES Resources drug-ner</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-drug-ner/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-drug-ner/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-drug-ner/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-drug-ner/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 		<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-examples-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-examples-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-examples-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-examples-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -3,7 +3,7 @@
    <parent>
       <groupId>org.apache.ctakes</groupId>
       <artifactId>ctakes</artifactId>
-      <version>4.0.0</version>
+      <version>4.0.0.1</version>
    </parent>
    <artifactId>ctakes-examples-res</artifactId>
    <name>ctakes-examples-res</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-examples/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-examples/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-examples/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-examples/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
     <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-examples</artifactId>
   <name>ctakes-examples</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-gui-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-gui-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-gui-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-gui-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -4,7 +4,7 @@
    <parent>
       <groupId>org.apache.ctakes</groupId>
       <artifactId>ctakes</artifactId>
-      <version>4.0.0</version>
+      <version>4.0.0.1</version>
    </parent>
 
    <artifactId>ctakes-gui-res</artifactId>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-gui/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-gui/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-gui/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-gui/pom.xml Sun Jan  3 18:12:37 2021
@@ -4,7 +4,7 @@
    <parent>
       <groupId>org.apache.ctakes</groupId>
       <artifactId>ctakes</artifactId>
-      <version>4.0.0</version>
+      <version>4.0.0.1</version>
    </parent>
 
    <artifactId>ctakes-gui</artifactId>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-lvg-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-lvg-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-lvg-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-lvg-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-lvg-res</artifactId>
   <name>Apache cTAKES Resources lvg</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-lvg/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-lvg/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-lvg/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-lvg/pom.xml Sun Jan  3 18:12:37 2021
@@ -27,7 +27,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>  
 		<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-ne-contexts-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-ne-contexts-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-ne-contexts-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-ne-contexts-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-ne-contexts-res</artifactId>
   <name>Apache cTAKES Resources ne-contexts</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-ne-contexts/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-ne-contexts/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-ne-contexts/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-ne-contexts/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 		<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-pos-tagger-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-pos-tagger-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-pos-tagger-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-pos-tagger-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-pos-tagger-res</artifactId>
   <name>Apache cTAKES Resources pos-tagger</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-pos-tagger/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-pos-tagger/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-pos-tagger/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-pos-tagger/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies> 
 		<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-preprocessor/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-preprocessor/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-preprocessor/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-preprocessor/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
       <!--<dependency>-->

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-regression-test/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-regression-test/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-regression-test/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-regression-test/pom.xml Sun Jan  3 18:12:37 2021
@@ -3,7 +3,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-regression-test</artifactId>
   <name>Apache cTAKES Regression-test</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-relation-extractor-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-relation-extractor-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-relation-extractor-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-relation-extractor-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-relation-extractor-res</artifactId>
   <name>Apache cTAKES Resources relation-extractor</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-relation-extractor/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-relation-extractor/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-relation-extractor/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-relation-extractor/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 		<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-side-effect-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-side-effect-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-side-effect-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-side-effect-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-side-effect-res</artifactId>
   <name>Apache cTAKES Resources side-effect</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-side-effect/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-side-effect/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-side-effect/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-side-effect/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	
 	<dependencies>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-smoking-status-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-smoking-status-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-smoking-status-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-smoking-status-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-smoking-status-res</artifactId>
   <name>Apache cTAKES Resources smoking-status</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-smoking-status/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-smoking-status/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-smoking-status/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-smoking-status/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	
 	<dependencies>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-template-filler/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-template-filler/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-template-filler/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-template-filler/pom.xml Sun Jan  3 18:12:37 2021
@@ -27,7 +27,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 		<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-temporal-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-temporal-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-temporal-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-temporal-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -24,7 +24,7 @@
   <parent>
     <groupId>org.apache.ctakes</groupId>
     <artifactId>ctakes</artifactId>
-    <version>4.0.0</version>
+    <version>4.0.0.1</version>
   </parent>
   <artifactId>ctakes-temporal-res</artifactId>
   <name>Apache cTAKES Resources temporal</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-temporal/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-temporal/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-temporal/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-temporal/pom.xml Sun Jan  3 18:12:37 2021
@@ -27,7 +27,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 		<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-type-system/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-type-system/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-type-system/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-type-system/pom.xml Sun Jan  3 18:12:37 2021
@@ -27,7 +27,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 		<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-utils/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-utils/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-utils/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-utils/pom.xml Sun Jan  3 18:12:37 2021
@@ -26,7 +26,7 @@
 	<parent>
 		<artifactId>ctakes</artifactId>
 		<groupId>org.apache.ctakes</groupId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 		<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-res/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-res/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-res/pom.xml Sun Jan  3 18:12:37 2021
@@ -14,7 +14,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<artifactId>ctakes-ytex-res</artifactId>
 	<name>Apache cTAKES Resources ctakes-ytex-res</name>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-uima/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-uima/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-uima/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-uima/pom.xml Sun Jan  3 18:12:37 2021
@@ -16,7 +16,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 		<dependency>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-web/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-web/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-web/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-ytex-web/pom.xml Sun Jan  3 18:12:37 2021
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<artifactId>ctakes-ytex-web</artifactId>
 	<packaging>war</packaging>

Modified: ctakes/branches/ctakes-4.0.0.1/ctakes-ytex/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/ctakes-ytex/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/ctakes-ytex/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/ctakes-ytex/pom.xml Sun Jan  3 18:12:37 2021
@@ -16,7 +16,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>4.0.0</version>
+		<version>4.0.0.1</version>
 	</parent>
 	<dependencies>
 		<!-- begin non ASF compliant dependencies -->

Modified: ctakes/branches/ctakes-4.0.0.1/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-4.0.0.1/pom.xml?rev=1885073&r1=1885072&r2=1885073&view=diff
==============================================================================
--- ctakes/branches/ctakes-4.0.0.1/pom.xml (original)
+++ ctakes/branches/ctakes-4.0.0.1/pom.xml Sun Jan  3 18:12:37 2021
@@ -19,12 +19,13 @@
     under the License.
 
 -->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+			xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.apache.ctakes</groupId>
 	<artifactId>ctakes</artifactId>
-	<version>4.0.0</version>
+	<version>4.0.0.1</version>
 	<packaging>pom</packaging>
 	<name>Apache cTAKES</name>
 	<url>http://ctakes.apache.org</url>
@@ -32,9 +33,9 @@
 	<scm>
 		<!-- In child modules, Maven will append ${artifactId} to the following 
 			URLs -->
-		<connection>scm:svn:https://svn.apache.org/repos/asf/ctakes/tags/ctakes-4.0.0-rc3</connection>
-		<developerConnection>scm:svn:https://svn.apache.org/repos/asf/ctakes/tags/ctakes-4.0.0-rc3</developerConnection>
-		<url>https://svn.apache.org/repos/asf/ctakes/tags/ctakes-4.0.0-rc3</url>
+		<connection>scm:svn:https://svn.apache.org/repos/asf/ctakes/tags/ctakes-4.0.0.1</connection>
+		<developerConnection>scm:svn:https://svn.apache.org/repos/asf/ctakes/tags/ctakes-4.0.0.1</developerConnection>
+		<url>https://svn.apache.org/repos/asf/ctakes/tags/ctakes-4.0.0.1</url>
 	</scm>
 	<issueManagement>
 		<system>jira</system>
@@ -76,7 +77,7 @@
 		</mailingList>
 	</mailingLists>
 	<properties>
-		<ctakes.version>4.0.0</ctakes.version>
+		<ctakes.version>4.0.0.1</ctakes.version>
 		<maven.compiler.source>1.8</maven.compiler.source>
 		<maven.compiler.target>1.8</maven.compiler.target>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>



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