oxo2-json2inferences SCRIPT_DIR

Author: henrietteharmse

oxo2-dataload/oxo2-json2inferences/explanations2json.sh

@@ -14,7 +14,7 @@ NEMO_INFERENCES=$1
 OUTPUT_FILE=$2
 
 # Define the path to the JAR file
-JAR_FILE="oxo2-json2inferences/target/oxo2-json2inferences-1.0.0-SNAPSHOT.jar"
+JAR_FILE="$SCRIPT_DIR/oxo2-json2inferences/target/oxo2-json2inferences-1.0.0-SNAPSHOT.jar"
 
 # Check if the JAR file exists
 if [ ! -f "$JAR_FILE" ]; then

oxo2-dataload/oxo2-json2inferences/inferences2trace.sh

@@ -14,7 +14,7 @@ INPUT_FILE=$1
 OUTPUT_FILE=$2
 
 # Define the path to the JAR file
-JAR_FILE="oxo2-json2inferences/target/oxo2-json2inferences-1.0.0-SNAPSHOT.jar"
+JAR_FILE="$SCRIPT_DIR/oxo2-json2inferences/target/oxo2-json2inferences-1.0.0-SNAPSHOT.jar"
 
 # Check if the JAR file exists
 if [ ! -f "$JAR_FILE" ]; then

oxo2-dataload/oxo2-sssom2json/src/main/java/uk/ac/ebi/spot/oxo/sssom2json/SSSOM2JSON.java

@@ -118,8 +118,6 @@ public static void main(String[] args) throws IOException {
     private static void processMappingSets(String inputDirectory, String outputDirectory) throws IOException {
         Stream<Path> directoriesOfMappingSets = getDirectories(inputDirectory);
 
-        // List<Path> listOfDirectoriesOfMappingSets = directoriesOfMappingSets.collect(Collectors.toList());
-
         String mappingSetDirectory = outputDirectory + File.separator + "mappingSet";
         String mappingDirectory = outputDirectory + File.separator + "mapping";
 

oxo2-dataload/sssom2json.sh

@@ -16,11 +16,9 @@ if [ -d "$OUTPUT_DIR" ]; then
   rm -rf "$OUTPUT_DIR"
 fi
 
-# Root directory for scripts
-SCRIPT_PATH=$(dirname $(readlink -f $0))
 
 # Run the SSSOM2JSON
-java $JAVA_OPTS -jar $SCRIPT_PATH/oxo2-sssom2json/target/oxo2-sssom2json-1.0.0-SNAPSHOT.jar -i $INPUT_DIR -o $OUTPUT_DIR
+java $JAVA_OPTS -jar $SCRIPT_DIR/oxo2-sssom2json/target/oxo2-sssom2json-1.0.0-SNAPSHOT.jar -i $INPUT_DIR -o $OUTPUT_DIR
 
 # Check if the command was successful
 if [ $? -eq 0 ]; then