standarized java path; changed relation extraction pipeline to pure java

application
JULIELab · Sep 27, 2016 · 45e5019 · 45e5019
1 parent 1b56a13
commit 45e5019
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Showing 7 changed files with 40 additions and 108 deletions.
diff --git a/jcore-medical-pos-pipeline/runPipeline.sh b/jcore-medical-pos-pipeline/runPipeline.sh
@@ -21,7 +21,7 @@ else
 fi
 
 ### compiles the java file
-if [ ! -f "target/classes/de/julielab/jcore/pipelines/MedicalPOSPipeline.class" ]; then
+if [ ! -f "target/classes/de/julielab/jcore/pipeline/MedicalPOSPipeline.class" ]; then
 	echo "[Maven] Compiling sources for the first time"
 	mvn compile
 fi
@@ -30,4 +30,4 @@ fi
 export CLASSPATH=`for i in $java_libs/*.jar; do echo -n "$i:";done;echo -n ""`
 
 ### run the pipeline with given arguments
-java -cp $CLASSPATH"./target/classes" de.julielab.jcore.pipelines.MedicalPOSPipeline $*
+java -cp $CLASSPATH"./target/classes" de.julielab.jcore.pipeline.MedicalPOSPipeline $*
diff --git a/...b/jcore/pipelines/MedicalPOSPipeline.java → ...ab/jcore/pipeline/MedicalPOSPipeline.java b/...b/jcore/pipelines/MedicalPOSPipeline.java → ...ab/jcore/pipeline/MedicalPOSPipeline.java
@@ -1,4 +1,4 @@
-package de.julielab.jcore.pipelines;
+package de.julielab.jcore.pipeline;
 
 import static org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineDescription;
 import static org.apache.uima.fit.factory.CollectionReaderFactory.createReaderDescription;

diff --git a/jcore-relation-extraction-pipeline/cpe-pipeline.xml b/jcore-relation-extraction-pipeline/cpe-pipeline.xml
diff --git a/jcore-relation-extraction-pipeline/installComponents.sh b/jcore-relation-extraction-pipeline/installComponents.sh
diff --git a/jcore-relation-extraction-pipeline/pom.xml b/jcore-relation-extraction-pipeline/pom.xml
@@ -9,6 +9,11 @@
     <artifactId>jcore-relation-extraction-pipeline</artifactId>
     <name>JCoRe Relation Extraction Pipeline</name>
     <dependencies>
+        <dependency>
+            <groupId>de.julielab</groupId>
+            <artifactId>jcore-types</artifactId>
+            <version>2.2.2</version>
+        </dependency>
         <dependency>
             <groupId>de.julielab</groupId>
             <artifactId>jcore-bionlp09event-reader</artifactId>
@@ -31,4 +36,4 @@
         <name>JULIE Lab Jena, Germany</name>
         <url>http://www.julielab.de</url>
     </organization>
-</project>
+</project>
diff --git a/jcore-relation-extraction-pipeline/runPipeline.sh b/jcore-relation-extraction-pipeline/runPipeline.sh
@@ -2,6 +2,32 @@
 
 java_libs=target/dependency
 
+### Check whether Maven is installed and install dependencies
+if !(hash mvn 2>/dev/null); then
+	echo ""
+	echo "[Maven] Maven is not installed. Aborting.";
+	echo "[Maven] Please install it to use the automatic project dependency copying process."
+	exit 1;
+else
+	if [ -d "$java_libs" ]; then
+		echo ""
+		echo "[Maven] jar library directory \""$java_libs"\" already exists. Skipping Maven dependency copying."
+		echo "[Maven] Please execute \"mvn clean\" from the command line and re-run this script if you want a clean installation."
+		echo "[Maven] You can safely ignore this if you don't encounter any problems."
+		echo ""
+	else
+		mvn dependency:copy-dependencies
+	fi
+fi
+
+### compiles the java file
+if [ ! -f "target/classes/de/julielab/jcore/pipeline/relationextraction/BioSEMApplication.class" ]; then
+	echo "[Maven] Compiling sources for the first time"
+	mvn compile
+fi
+
+### add dependencies to java classpath
 export CLASSPATH=`for i in $java_libs/*.jar; do echo -n "$i:";done;echo -n ""`
 
-$UIMA_HOME/bin/runCPE.sh cpe-pipeline.xml
+### run the pipeline with given arguments
+java -cp $CLASSPATH"./target/classes" de.julielab.jcore.pipeline.relationextraction.BioSEMApplication $*
diff --git a/...peline/src/main/java/de/julielab/jcore/pipeline/relationextraction/BioSEMApplication.java b/...peline/src/main/java/de/julielab/jcore/pipeline/relationextraction/BioSEMApplication.java
@@ -34,12 +34,14 @@ public void run(String in, String out) {
     private void initializeComponents(String in, String out) {
         try {
             // init ST Reader
-            reader = CollectionReaderFactory.createReader(EventReader.class, EventReader.DIRECTORY_PARAM, in,
+            reader = CollectionReaderFactory.createReader(EventReader.class,
+            		EventReader.DIRECTORY_PARAM, in,
                     EventReader.BIOEVENT_SERVICE_MODE_PARAM, false);
             // init BioSEM Event Extractor AE
             relationExtractor = AnalysisEngineFactory.createEngine(AE_DESCRIPTOR);
             // init ST Writer
-            consumer = AnalysisEngineFactory.createEngine(EventConsumer.class, EventConsumer.DIRECTORY_PARAM, out,
+            consumer = AnalysisEngineFactory.createEngine(EventConsumer.class,
+            		EventConsumer.DIRECTORY_PARAM, out,
                     EventConsumer.BIOEVENT_SERVICE_MODE_PARAM, false);
         } catch (ResourceInitializationException e) {
             e.printStackTrace();