Release 2.4.

JULIELab · Mar 28, 2019 · c929305 · c929305
1 parent 90936c7
commit c929305
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Showing 95 changed files with 528 additions and 432 deletions.
diff --git a/jcore-banner-ae-biomedical-english/component.meta b/jcore-banner-ae-biomedical-english/component.meta
@@ -14,7 +14,7 @@
     "maven-artifact": {
         "artifactId": "jcore-banner-ae-biomedical-english",
         "groupId": "de.julielab",
-        "version": "2.4.0-SNAPSHOT"
+        "version": "2.4.0"
     },
     "name": "JCoRe BANNER AE for Biomedical English"
 }
diff --git a/jcore-banner-ae-biomedical-english/pom.xml b/jcore-banner-ae-biomedical-english/pom.xml
@@ -9,7 +9,7 @@
    <parent>
 	<groupId>de.julielab</groupId>
 	<artifactId>jcore-projects</artifactId>
-	<version>2.4.0-SNAPSHOT</version>
+	<version>2.4.0</version>
    </parent>
 
   <dependencies>
@@ -20,7 +20,7 @@
       <dependency>
       	<groupId>de.julielab</groupId>
       	<artifactId>jcore-banner-ae</artifactId>
-      	<version>2.4.0-SNAPSHOT</version>
+      	<version>2.4.0</version>
       </dependency>
       <dependency>
       	<groupId>ch.qos.logback</groupId>

diff --git a/...rc/main/resources/de/julielab/jcore/ae/banner/desc/jcore-banner-ae-biomedical-english.xml b/...rc/main/resources/de/julielab/jcore/ae/banner/desc/jcore-banner-ae-biomedical-english.xml
@@ -1,13 +1,13 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
 <analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
     <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
     <primitive>true</primitive>
     <annotatorImplementationName>de.julielab.jcore.ae.banner.BANNERAnnotator</annotatorImplementationName>
     <analysisEngineMetaData>
         <name>JCoRe BANNER AE for Biomedical English</name>
         <description>This component uses the BANNER named entity recognizer with a model trained on the complete (train and test) dataset of the BioCreative II gene mention challenge.</description>
-        <version>1.0</version>
-        <vendor/>
+        <version>2.4.0</version>
+        <vendor />
         <configurationParameters>
             <configurationParameter>
                 <name>ConfigFile</name>
@@ -46,13 +46,13 @@
         </configurationParameterSettings>
         <typeSystemDescription>
             <imports>
-                <import name="de.julielab.jcore.types.jcore-document-structure-types"/>
-                <import name="de.julielab.jcore.types.jcore-morpho-syntax-types"/>
-                <import name="de.julielab.jcore.types.jcore-semantics-biology-types"/>
+                <import name="de.julielab.jcore.types.jcore-document-structure-types" />
+                <import name="de.julielab.jcore.types.jcore-morpho-syntax-types" />
+                <import name="de.julielab.jcore.types.jcore-semantics-biology-types" />
             </imports>
         </typeSystemDescription>
-        <typePriorities/>
-        <fsIndexCollection/>
+        <typePriorities />
+        <fsIndexCollection />
         <capabilities>
             <capability>
                 <inputs>
@@ -61,7 +61,7 @@
                 <outputs>
                     <type allAnnotatorFeatures="true">de.julielab.jcore.types.Gene</type>
                 </outputs>
-                <languagesSupported/>
+                <languagesSupported />
             </capability>
         </capabilities>
         <operationalProperties>
@@ -70,5 +70,5 @@
             <outputsNewCASes>false</outputsNewCASes>
         </operationalProperties>
     </analysisEngineMetaData>
-    <resourceManagerConfiguration/>
-</analysisEngineDescription>
+    <resourceManagerConfiguration />
+</analysisEngineDescription>
diff --git a/jcore-biosem-ae-bionlp-st09/component.meta b/jcore-biosem-ae-bionlp-st09/component.meta
@@ -14,7 +14,7 @@
     "maven-artifact": {
         "artifactId": "jcore-biosem-ae-bionlp-st09",
         "groupId": "de.julielab",
-        "version": "2.4.0-SNAPSHOT"
+        "version": "2.4.0"
     },
     "name": "JCoRe BioSem AE, BioNLP SharedTask 2009"
 }
diff --git a/jcore-biosem-ae-bionlp-st09/pom.xml b/jcore-biosem-ae-bionlp-st09/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>jcore-projects</artifactId>
-        <version>2.4.0-SNAPSHOT</version>
+        <version>2.4.0</version>
     </parent>
 
     <artifactId>jcore-biosem-ae-bionlp-st09</artifactId>
@@ -17,7 +17,7 @@
         <dependency>
             <groupId>de.julielab</groupId>
             <artifactId>jcore-biosem-ae</artifactId>
-            <version>2.4.0-SNAPSHOT</version>
+            <version>2.4.0</version>
         </dependency>
         <dependency>
             <groupId>junit</groupId>

diff --git a/...-st09/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st09.xml b/...-st09/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st09.xml
@@ -1,21 +1,21 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
 <analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>  <annotatorImplementationName>de.julielab.jcore.ae.biosem.BioSemEventAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>JCoRe BioSEM Event Annotator</name>
-    <description/>
-    <version>2.1.0</version>
-    <vendor/>
-    <configurationParameters/>
-    <configurationParameterSettings/>
+    <description />
+    <version>2.4.0</version>
+    <vendor />
+    <configurationParameters />
+    <configurationParameterSettings />
     <typeSystemDescription>
       <imports>
-        <import name="de.julielab.jcore.types.jcore-semantics-biology-types"/>
+        <import name="de.julielab.jcore.types.jcore-semantics-biology-types" />
       </imports>
     </typeSystemDescription>
-    <typePriorities/>
-    <fsIndexCollection/>
+    <typePriorities />
+    <fsIndexCollection />
     <capabilities>
       <capability>
         <inputs>
@@ -26,7 +26,7 @@
           <type allAnnotatorFeatures="true">de.julielab.jcore.types.EventMention</type>
           <type allAnnotatorFeatures="true">de.julielab.jcore.types.ArgumentMention</type>
         </outputs>
-        <languagesSupported/>
+        <languagesSupported />
       </capability>
     </capabilities>
   <operationalProperties>
@@ -47,7 +47,7 @@
     <externalResources>
       <externalResource>
         <name>TrainedDB</name>
-        <description/>
+        <description />
         <fileResourceSpecifier>
           <fileUrl>file:de/julielab/jcore/ae/biosem/conf/biosemannotator-st09.properties</fileUrl>
         </fileResourceSpecifier>
@@ -61,4 +61,4 @@
       </externalResourceBinding>
     </externalResourceBindings>
   </resourceManagerConfiguration>
-</analysisEngineDescription>
+</analysisEngineDescription>
diff --git a/jcore-biosem-ae-bionlp-st11/component.meta b/jcore-biosem-ae-bionlp-st11/component.meta
@@ -14,7 +14,7 @@
     "maven-artifact": {
         "artifactId": "jcore-biosem-ae-bionlp-st11",
         "groupId": "de.julielab",
-        "version": "2.4.0-SNAPSHOT"
+        "version": "2.4.0"
     },
     "name": "JCoRe BioSem AE, BioNLP SharedTask 2011"
 }
diff --git a/jcore-biosem-ae-bionlp-st11/pom.xml b/jcore-biosem-ae-bionlp-st11/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>jcore-projects</artifactId>
-        <version>2.4.0-SNAPSHOT</version>
+        <version>2.4.0</version>
     </parent>
 
     <artifactId>jcore-biosem-ae-bionlp-st11</artifactId>
@@ -17,7 +17,7 @@
         <dependency>
             <groupId>de.julielab</groupId>
             <artifactId>jcore-biosem-ae</artifactId>
-            <version>2.4.0-SNAPSHOT</version>
+            <version>2.4.0</version>
         </dependency>
         <dependency>
             <groupId>junit</groupId>

diff --git a/...-st11/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st11.xml b/...-st11/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st11.xml
@@ -1,21 +1,21 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
 <analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>  <annotatorImplementationName>de.julielab.jcore.ae.biosem.BioSemEventAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>JCoRe BioSEM Event Annotator</name>
-    <description/>
-    <version>2.1.0</version>
-    <vendor/>
-    <configurationParameters/>
-    <configurationParameterSettings/>
+    <description />
+    <version>2.4.0</version>
+    <vendor />
+    <configurationParameters />
+    <configurationParameterSettings />
     <typeSystemDescription>
       <imports>
-        <import name="de.julielab.jcore.types.jcore-semantics-biology-types"/>
+        <import name="de.julielab.jcore.types.jcore-semantics-biology-types" />
       </imports>
     </typeSystemDescription>
-    <typePriorities/>
-    <fsIndexCollection/>
+    <typePriorities />
+    <fsIndexCollection />
     <capabilities>
       <capability>
         <inputs>
@@ -26,7 +26,7 @@
           <type allAnnotatorFeatures="true">de.julielab.jcore.types.EventMention</type>
           <type allAnnotatorFeatures="true">de.julielab.jcore.types.ArgumentMention</type>
         </outputs>
-        <languagesSupported/>
+        <languagesSupported />
       </capability>
     </capabilities>
   <operationalProperties>
@@ -47,7 +47,7 @@
     <externalResources>
       <externalResource>
         <name>TrainedDB</name>
-        <description/>
+        <description />
         <fileResourceSpecifier>
           <fileUrl>file:de/julielab/jcore/ae/biosem/conf/biosemannotator-st11.properties</fileUrl>
         </fileResourceSpecifier>
@@ -61,4 +61,4 @@
       </externalResourceBinding>
     </externalResourceBindings>
   </resourceManagerConfiguration>
-</analysisEngineDescription>
+</analysisEngineDescription>
diff --git a/jcore-biosem-ae-bionlp-st13/component.meta b/jcore-biosem-ae-bionlp-st13/component.meta
@@ -14,7 +14,7 @@
     "maven-artifact": {
         "artifactId": "jcore-biosem-ae-bionlp-st13",
         "groupId": "de.julielab",
-        "version": "2.4.0-SNAPSHOT"
+        "version": "2.4.0"
     },
     "name": "JCoRe BioSem AE, BioNLP SharedTask 2013"
 }
diff --git a/jcore-biosem-ae-bionlp-st13/pom.xml b/jcore-biosem-ae-bionlp-st13/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>jcore-projects</artifactId>
-        <version>2.4.0-SNAPSHOT</version>
+        <version>2.4.0</version>
     </parent>
 
     <artifactId>jcore-biosem-ae-bionlp-st13</artifactId>
@@ -21,7 +21,7 @@
         <dependency>
             <groupId>de.julielab</groupId>
             <artifactId>jcore-biosem-ae</artifactId>
-            <version>2.4.0-SNAPSHOT</version>
+            <version>2.4.0</version>
         </dependency>
         <dependency>
             <groupId>ch.qos.logback</groupId>

diff --git a/...-st13/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st13.xml b/...-st13/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st13.xml
@@ -1,21 +1,21 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
 <analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>  <annotatorImplementationName>de.julielab.jcore.ae.biosem.BioSemEventAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>JCoRe BioSEM Event Annotator</name>
-    <description/>
-    <version>2.1.0</version>
-    <vendor/>
-    <configurationParameters/>
-    <configurationParameterSettings/>
+    <description />
+    <version>2.4.0</version>
+    <vendor />
+    <configurationParameters />
+    <configurationParameterSettings />
     <typeSystemDescription>
       <imports>
-        <import name="de.julielab.jcore.types.jcore-semantics-biology-types"/>
+        <import name="de.julielab.jcore.types.jcore-semantics-biology-types" />
       </imports>
     </typeSystemDescription>
-    <typePriorities/>
-    <fsIndexCollection/>
+    <typePriorities />
+    <fsIndexCollection />
     <capabilities>
       <capability>
         <inputs>
@@ -26,7 +26,7 @@
           <type allAnnotatorFeatures="true">de.julielab.jcore.types.EventMention</type>
           <type allAnnotatorFeatures="true">de.julielab.jcore.types.ArgumentMention</type>
         </outputs>
-        <languagesSupported/>
+        <languagesSupported />
       </capability>
     </capabilities>
   <operationalProperties>
@@ -47,7 +47,7 @@
     <externalResources>
       <externalResource>
         <name>TrainedDB</name>
-        <description/>
+        <description />
         <fileResourceSpecifier>
           <fileUrl>file:de/julielab/jcore/ae/biosem/conf/biosemannotator-st13.properties</fileUrl>
         </fileResourceSpecifier>
@@ -61,4 +61,4 @@
       </externalResourceBinding>
     </externalResourceBindings>
   </resourceManagerConfiguration>
-</analysisEngineDescription>
+</analysisEngineDescription>
diff --git a/jcore-jnet-ae-biomedical-english/component.meta b/jcore-jnet-ae-biomedical-english/component.meta
@@ -14,7 +14,7 @@
     "maven-artifact": {
         "artifactId": "jcore-jnet-ae-biomedical-english",
         "groupId": "de.julielab",
-        "version": "2.4.0-SNAPSHOT"
+        "version": "2.4.0"
     },
     "name": "JCoRe JNET AE, Biomedical English"
 }
diff --git a/jcore-jnet-ae-biomedical-english/pom.xml b/jcore-jnet-ae-biomedical-english/pom.xml
@@ -6,14 +6,14 @@
   <description>This project employs the jcore-jnet-ae (Named Entity Tagger) with a model trained on the PennBioIE corpus.</description>
   <parent>
   	<artifactId>jcore-projects</artifactId>
-  	<version>2.4.0-SNAPSHOT</version>
+  	<version>2.4.0</version>
   	<groupId>de.julielab</groupId>
   </parent>
   <dependencies>
   	<dependency>
   		<groupId>de.julielab</groupId>
   		<artifactId>jcore-jnet-ae</artifactId>
-  		<version>2.4.0-SNAPSHOT</version>
+  		<version>2.4.0</version>
   	</dependency>
       <dependency>
           <groupId>junit</groupId>