Update stop-its shell script

updates parsing and adds comments and output statements for logs

roles/usegalaxy-eu.fix-stop-ITs/templates/stop-ITs.sh.j2

@@ -1,18 +1,30 @@
 #!/bin/sh
+TODAY=$(date +"%d-%m-%y %H:%M:%S")
 DAY=86400
 . {{ galaxy_root }}/.bashrc
 cd ~
 for job in $(gxadmin query queue-detail --all | grep running | grep interactive_tool | awk '{print $3}')
 do
+    # Get job working directory
     JWD=$(python3 /usr/local/bin/galaxy_jwd get $job)
-    pushd $JWD
-    ClusterID=$( head -n 1 job_condor.log | awk '{print $2}' | awk -F. '{print $1"."$2}' | sed 's/^(//' )
-    if [ "$(condor_q -global $ClusterID -autoformat JobStartDate)" == "undefined" ] || [ "$(condor_q -global $ClusterID -autoformat JobStartDate)" == "" ]
-    then
+
+    # Get external/Condor job ID from either external_id file or job_condor.log file from JWD
+    if [ -f $JWD/external_id ]; then
+        ClusterID=$(cat $JWD/external_id | tr -d '"')
+    elif [ -f $JWD/job_condor.log ]; then
+        ClusterID=$(head -n 1 $JWD/job_condor.log | sed -n 's/.*(\([0-9]*\)\..*/\1/p')
+    fi
+
+    # If cluster ID is found
+    if [ ! -z "$ClusterID" ]; then
+        # Check if job is running for more than 24 hrs and remove it
+        if [ "$(condor_q -global $ClusterID -autoformat JobStartDate)" == "undefined" ] || [ "$(condor_q -global $ClusterID -autoformat JobStartDate)" == "" ]; then
+            echo "Removing condor job $ClusterID (Galaxy job id: $job) on $TODAY"
+            condor_rm $ClusterID
+
+        elif [ $(($(date +"%s") - $(condor_q -global $ClusterID -autoformat JobStartDate))) -ge $DAY ]; then
+            echo "Removing condor job $ClusterID (Galaxy job id: $job) on $TODAY"
             condor_rm $ClusterID
-    elif [ $(($(date +"%s") - $(condor_q -global $ClusterID -autoformat JobStartDate))) -ge $DAY ]
-    then
-        condor_rm $ClusterID
+        fi
     fi
-    popd
 done