diff --git a/jcore-medical-pos-pipeline/runPipeline.sh b/jcore-medical-pos-pipeline/runPipeline.sh index b528f93..4b14526 100755 --- 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 $* diff --git a/jcore-medical-pos-pipeline/src/main/java/de/julielab/jcore/pipelines/MedicalPOSPipeline.java b/jcore-medical-pos-pipeline/src/main/java/de/julielab/jcore/pipeline/MedicalPOSPipeline.java similarity index 99% rename from jcore-medical-pos-pipeline/src/main/java/de/julielab/jcore/pipelines/MedicalPOSPipeline.java rename to jcore-medical-pos-pipeline/src/main/java/de/julielab/jcore/pipeline/MedicalPOSPipeline.java index 637a52b..7a8c1fa 100644 --- a/jcore-medical-pos-pipeline/src/main/java/de/julielab/jcore/pipelines/MedicalPOSPipeline.java +++ b/jcore-medical-pos-pipeline/src/main/java/de/julielab/jcore/pipeline/MedicalPOSPipeline.java @@ -1,4 +1,4 @@ -package de.julielab.jcore.pipelines; +package de.julielab.jcore.pipeline; import static org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineDescription; import static org.apache.uima.fit.factory.CollectionReaderFactory.createReaderDescription; diff --git a/jcore-relation-extraction-pipeline/cpe-pipeline.xml b/jcore-relation-extraction-pipeline/cpe-pipeline.xml deleted file mode 100644 index 7b5e2da..0000000 --- a/jcore-relation-extraction-pipeline/cpe-pipeline.xml +++ /dev/null @@ -1,64 +0,0 @@ - - - - - - - - - - inDirectory - - inFiles/ - - - - - - - - - - - - - - - - - - - - - - - - - outDirectory - - outFiles/ - - - - bioEventServiceMode - - false/ - - - - - - - - - - - - - - -1 - immediate - - - - diff --git a/jcore-relation-extraction-pipeline/installComponents.sh b/jcore-relation-extraction-pipeline/installComponents.sh deleted file mode 100755 index 31948e0..0000000 --- a/jcore-relation-extraction-pipeline/installComponents.sh +++ /dev/null @@ -1,37 +0,0 @@ -#!/bin/bash - -lib_dir=target/dependency - -### Check whether Maven is installed -if !(hash mvn 2>/dev/null); then - echo "" - echo "[Maven] Maven is not installed. Aborting."; - echo "[Maven] Please install it to use the automatic project dependency copying process." - exit 1; -else - if [ -d "$lib_dir" ]; then - echo "" - echo "[Maven] jar library directory \""$lib_dir"\" already exists. Skipping Maven dependency copying." - echo "[Maven] Please execute \"mvn clean\" from the command line and re-run this script if you want a clean installation." - else - mvn dependency:copy-dependencies - fi -fi - -### Check whether UIMA is installed and the environment variable is set -if [ -z "$UIMA_HOME" ]; then - echo "" - echo "[UIMA] UIMA is either not installed or the environment variable is not set. Aborting."; - echo "[UIMA] Please make sure you have UIMA installed if you want to use the prebuilt CPEs." - echo "" - exit 1; -else - echo "[UIMA] Your UIMA environment variable is \""$UIMA_HOME"\"" - if [ ! -d "$UIMA_HOME" ]; then - echo "" - echo "[UIMA] \""$UIMA_HOME"\" seems to be no valid directory. Aborting." - echo "" - exit 1; - fi - echo "" -fi diff --git a/jcore-relation-extraction-pipeline/pom.xml b/jcore-relation-extraction-pipeline/pom.xml index ebe1cd4..9e998ad 100644 --- a/jcore-relation-extraction-pipeline/pom.xml +++ b/jcore-relation-extraction-pipeline/pom.xml @@ -9,6 +9,11 @@ jcore-relation-extraction-pipeline JCoRe Relation Extraction Pipeline + + de.julielab + jcore-types + 2.2.2 + de.julielab jcore-bionlp09event-reader @@ -31,4 +36,4 @@ JULIE Lab Jena, Germany http://www.julielab.de - \ No newline at end of file + diff --git a/jcore-relation-extraction-pipeline/runPipeline.sh b/jcore-relation-extraction-pipeline/runPipeline.sh index 53b3199..859132b 100755 --- a/jcore-relation-extraction-pipeline/runPipeline.sh +++ b/jcore-relation-extraction-pipeline/runPipeline.sh @@ -2,6 +2,32 @@ java_libs=target/dependency +### Check whether Maven is installed and install dependencies +if !(hash mvn 2>/dev/null); then + echo "" + echo "[Maven] Maven is not installed. Aborting."; + echo "[Maven] Please install it to use the automatic project dependency copying process." + exit 1; +else + if [ -d "$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/jcore-relation-extraction-pipeline/src/main/java/de/julielab/jcore/pipeline/relationextraction/BioSEMApplication.java b/jcore-relation-extraction-pipeline/src/main/java/de/julielab/jcore/pipeline/relationextraction/BioSEMApplication.java index caba7b4..279b5a9 100644 --- a/jcore-relation-extraction-pipeline/src/main/java/de/julielab/jcore/pipeline/relationextraction/BioSEMApplication.java +++ b/jcore-relation-extraction-pipeline/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();