Piscal Queue working more resilient to error

Core/Remote/piscal_manager.sh

@@ -1,27 +1,33 @@
 #!/bin/bash
 # piscal manager script
 
-usage="$(basename "$0") [-h] -d directory_name [-f input_filename|-s] -- script to manage Piscal
+usage="$(basename "$0") [-h] -d directory_name -p photosynthetic_type [-s|-c|-k] -- script to manage Piscal
 
 where:
     -h  show this help text
     -d  working directory name
-    -f  input filename
-    -s  job status"
+    -p  photosynthetic type
+    -s  start job
+    -c  cleanup directory
+    -k  kill job"
+
+# Initialize variables:
+# http://stackoverflow.com/a/246128/99492
+base_directory="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+directory_name=""
+photosynthetic_type="C3_photosynthesis_leafweb" #default
+task="get_status" # default task
+input_directory_name="input"
+pid_filename="piscal.pid"
+stderr_filename="piscal.err"
+output_directory_name="output/fitresult/touser"
+cleaned_input_directory_name="output/clninput"
+launcher="$base_directory/piscal_launcher.sh"
 
 # http://stackoverflow.com/a/14203146/99492
 # http://wiki.bash-hackers.org/howto/getopts_tutorial
 
-# Initialize variables:
-base_directory="/home/poprhythm/LeafWeb"
-directory_name=""
-input_filename=""
-task="start" # default task
-pid_filename="piscal.pid"
-out_filename="piscal.out"
-launcher="$base_directory/piscal_launcher.sh"
-
-while getopts "hd:f:s" opt; do
+while getopts "hd:f:p:sck" opt; do
     #echo "$opt = $OPTARG"
     case "$opt" in
     h )
@@ -31,12 +37,17 @@ while getopts "hd:f:s" opt; do
     d )
         directory_name=$OPTARG
         ;;
-    f )
-        input_filename=$OPTARG
-        task="start"
+    p )
+        photosynthetic_type=$OPTARG
         ;;
     s )
-        task="get_status"
+        task="launch"
+        ;;
+    c )
+        task="cleanup"
+        ;;
+    k )
+        task="kill"
         ;;
     \?) printf "illegal option: -%s\n" "$OPTARG" >&2
         echo "$usage" >&2
@@ -44,55 +55,83 @@ while getopts "hd:f:s" opt; do
         ;;
     esac
 done
+
+## Examine directories
 if [ -z "$directory_name" ]; then
     echo "directory name required (-d)"
     exit 1
 fi
 working_directory="$base_directory/$directory_name"
 if [ ! -d "$working_directory" ]; then
-    echo "directory $working_directory not found"
+    echo "working directory $working_directory not found"
     exit 1
 fi
-if [ "$task" = "start" ]; then
-    if [ -z "$input_filename" ]; then
-        echo "input filename required (-f)"
-        exit 1
-    fi
+input_directory="$working_directory/$input_directory_name"
+if [ ! -d "$input_directory" ]; then
+    echo "input directory $input_directory not found"
+    exit 1
+fi
+pid_path="$working_directory/$pid_filename"
+
+## Process task
+if [ "$task" = "launch" ]; then
+    piscal_config_file="$working_directory"/piscal.cfg
+    # write config file for piscal
+    echo $photosynthetic_type > "$piscal_config_file"
+    find "$input_directory" -maxdepth 1 -type f\
+        -printf '%P\n'\
+        >> "$piscal_config_file"
     
-    if [ ! -f "$working_directory/$input_filename" ]; then
-        echo "input filename $working_directory/$input_filename not found"
-        exit 1
-    fi
-    
-    command="$launcher -d $working_directory -f $input_filename"
-    nohup ${command} > $working_directory/$out_filename 2>&1 &
+    command="$launcher -d $working_directory -f piscal.cfg"
+    # launch it, sending error output to file
+    nohup ${command} > $working_directory/$stderr_filename 2>&1 &
 
     # write the PID to a temp file to check for completion later
     echo $! > $working_directory/$pid_filename
     echo started
 elif [ "$task" = "get_status" ]; then
-    pid_path="$working_directory/$pid_filename"
-    
-    # if the pid doesn't exist, then process never started
+    # if the pid doesn't exist, then process hasn't started
     if [ ! -f "$pid_path" ]; then
-        echo "no pid file found"
-        exit 1
+        echo "not started"
+        exit
     fi
-    
+
     pid=$(head -n 1 $pid_path)
     # if the pid exists, check the process status using ps
     if ps -p $pid > /dev/null; then
         # if it is in ps, then it's still running
         echo running
     else
-        # otherwise, it is complete, check the output for success/error
-        # TODO: examine output for errors, etc
-        #cat piscal.out
-        if [ ! -d "$working_directory/output" ]; then
-            echo "output directory $working_directory/output not found"
+        # otherwise, it is complete, check for runtime errors
+        if [ -s "$working_directory/$stderr_filename" ]; then
+            cat "$working_directory/$stderr_filename"
             exit 1
         fi
-        echo success
-        find "$working_directory/output"/*
+        
+        output_directory="$working_directory/$output_directory_name"
+        if [ ! -d "$output_directory" ]; then
+            echo "output directory $output_directory not found"
+            exit 1
+        fi
+        
+        echo complete
+        find "$output_directory"/*
     fi
-fi
+elif [ "$task" = "cleanup" ]; then
+    rm -rf "$working_directory"
+    echo hi
+elif [ "$task" = "kill" ]; then
+    # if the pid doesn't exist, then process hasn't started
+    if [ ! -f "$pid_path" ]; then
+        echo "not started"
+        exit
+    fi
+
+    pid=$(head -n 1 $pid_path)
+    # if the pid exists, check the process status using ps
+    if ps -p $pid > /dev/null; then
+        # if it is in ps, then it's still running
+        kill $pid
+    fi
+    echo killed
+fi