updates for scripts
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@@ -96,12 +96,12 @@ popd >> /dev/null
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# copy output to storage
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if [ -z "$suppress_storage_copy" ]; then
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cp "$output_directory_touser"/* "$storage_directory"/
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cp "$output_directory_nottouser"/* "$storage_directory"/
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cp "$cleaned_input_directory"/* "$storage_directory"/
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cp "$output_directory_touser"/* "$storage_directory"/ 2>/dev/null
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cp "$output_directory_nottouser"/* "$storage_directory"/ 2>/dev/null
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cp "$cleaned_input_directory"/* "$storage_directory"/ 2>/dev/null
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fi
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# notify given url of completion
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if [ -n "$notify_url" ]; then
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wget -qO- "$notify_url" # &> /dev/null 2>&1
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wget -qO- -t 1 "$notify_url" # &> /dev/null 2>&1
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fi
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@@ -89,7 +89,15 @@ pid_path="$working_directory/$pid_filename"
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## Process task
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if [ "$task" = "launch" ]; then
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# TODO: verify process isn't running yet
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# verify process isn't running yet
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pid=$(head -n 1 $pid_path)
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# if the pid exists, check the process status using ps
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if ps -p $pid > /dev/null; then
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# if it is in ps, then it's still running
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echo still running
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exit 1
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fi
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piscal_config_file="$working_directory"/piscal.cfg
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# write config file for piscal
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echo $photosynthetic_type > "$piscal_config_file"
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@@ -110,7 +118,7 @@ if [ "$task" = "launch" ]; then
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nohup ${command} > $working_directory/$stderr_filename 2>&1 &
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# write the PID to a temp file to check for completion later
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echo $! > $working_directory/$pid_filename
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echo $! > $pid_path
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echo started
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elif [ "$task" = "get_status" ] || [ "$task" = "get_status_cleaned_input" ]; then
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# if the pid doesn't exist, then process hasn't started
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@@ -140,24 +148,32 @@ elif [ "$task" = "get_status" ] || [ "$task" = "get_status_cleaned_input" ]; the
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echo complete
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if [ "$task" = "get_status" ]; then
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echo "#touser"
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find "$output_directory"/*
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find "$output_directory"/* 2>/dev/null
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cleaned_input_directory="$working_directory/$cleaned_input_directory_name"
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echo "#clninput"
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find "$cleaned_input_directory"/*
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find "$cleaned_input_directory"/* 2>/dev/null
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nottouser_directory="$working_directory/$nottouser_directory_name"
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echo "#nottouser"
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find "$nottouser_directory"/*
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find "$nottouser_directory"/* 2>/dev/null
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exit 0
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fi
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fi
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elif [ "$task" = "cleanup" ]; then
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pid=$(head -n 1 $pid_path)
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# if the pid exists, check the process status using ps
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if ps -p $pid > /dev/null; then
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# if it is in ps, then it's still running
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echo still running
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exit 1
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fi
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rm -rf "$working_directory"
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elif [ "$task" = "kill" ]; then
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# if the pid doesn't exist, then process hasn't started
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if [ ! -f "$pid_path" ]; then
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echo "not started"
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exit
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exit 1
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fi
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pid=$(head -n 1 $pid_path)
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