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Posted to commits@ctakes.apache.org by se...@apache.org on 2021/01/03 18:12:38 UTC
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...
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>