Use separate pid_log_paster_args variable

to store --pid-file and --log-file options of `./scripts/paster.py` .

https://github.com/galaxyproject/galaxy/pull/6239 fixed 3 bugs:

- `GALAXY_RUN_ALL=1 ./run.sh` was reusing the same pid and log files for
  all Galaxy processes;
- `./run.sh restart` was always using `paster.pid` and `paster.log` instead
  of the configured files
- `./run.sh status` was always using `paster.pid`

but also introduced a regression, i.e. the plain `./run.sh` started
writing to the log file instead of the standard output (console).

This fixes the regression by using a separate variable for these options
instead of conflating them in `paster_args` or `server_args`.

run.sh

@@ -78,8 +78,9 @@ if [ "$run_server" = "python" -a -n "$GALAXY_RUN_ALL" ]; then
         exit 1
     fi
     for server in $servers; do
+        echo "Executing: python $server_args --server-name=\"$server\" --pid-file=\"$server.pid\" --log-file=\"$server.log\""
+        python $server_args --server-name="$server" --pid-file="$server.pid" --log-file="$server.log"
         if [ -n "$wait_arg_set" -a -n "$daemon_or_restart_arg_set" ]; then
-            python ./scripts/paster.py serve "$GALAXY_CONFIG_FILE" --server-name="$server" --pid-file="$server.pid" --log-file="$server.log" $paster_args
             while true; do
                 sleep 1
                 printf "."
@@ -95,13 +96,10 @@ if [ "$run_server" = "python" -a -n "$GALAXY_RUN_ALL" ]; then
                 [ -n "$latest_pid" ] && [ "$latest_pid" -eq "$current_pid_in_file" ] && break
             done
             echo
-        else
-            echo "Handling $server with log file $server.log..."
-            python ./scripts/paster.py serve "$GALAXY_CONFIG_FILE" --server-name="$server" --pid-file="$server.pid" --log-file="$server.log" $paster_args
         fi
     done
 else
-    echo "executing: $run_server $server_args"
+    echo "Executing: $run_server $server_args $pid_log_paster_args"
     # args are properly quoted so use eval
-    eval $run_server $server_args
+    eval $run_server $server_args $pid_log_paster_args
 fi

run_reports.sh

@@ -48,5 +48,5 @@ if [ -n "$GALAXY_REPORTS_CONFIG_DIR" ]; then
 fi
 
 find_server ${GALAXY_REPORTS_CONFIG:-none} reports
-echo "executing: $run_server $server_args"
-eval $run_server $server_args
+echo "Executing: $run_server $server_args $pid_log_paster_args"
+eval $run_server $server_args $pid_log_paster_args

run_tool_shed.sh

@@ -37,5 +37,5 @@ if [ -z "$TOOL_SHED_CONFIG_FILE" ]; then
 fi
 
 find_server ${TOOL_SHED_CONFIG_FILE:-none} tool_shed
-echo "executing: $run_server $server_args"
-eval $run_server $server_args
+echo "Executing: $run_server $server_args $pid_log_paster_args"
+eval $run_server $server_args $pid_log_paster_args

scripts/common_startup_functions.sh

@@ -22,30 +22,33 @@ parse_common_args() {
             --stop-daemon|stop)
                 common_startup_args="$common_startup_args --stop-daemon"
                 paster_args="$paster_args --stop-daemon"
-                uwsgi_args="$uwsgi_args --stop $PID_FILE"
+                pid_log_paster_args="--pid-file \"$PID_FILE\""
+                uwsgi_args="$uwsgi_args --stop \"$PID_FILE\""
                 stop_daemon_arg_set=1
                 shift
                 ;;
             --restart|restart)
-                if [ "$1" = "--restart" ]
-                then
-                    paster_args="$paster_args restart"
-                else
-                    paster_args="$paster_args $1"
-                fi
-                uwsgi_args="$uwsgi_args --reload $PID_FILE"
+                paster_args="$paster_args restart"
+                pid_log_paster_args="--pid-file \"$PID_FILE\" --log-file \"$LOG_FILE\""
+                uwsgi_args="$uwsgi_args --reload \"$PID_FILE\""
                 restart_arg_set=1
                 daemon_or_restart_arg_set=1
                 shift
                 ;;
             --daemon|start)
                 paster_args="$paster_args --daemon"
+                pid_log_paster_args="--pid-file \"$PID_FILE\" --log-file \"$LOG_FILE\""
                 # --daemonize2 waits until after the application has loaded
                 # to daemonize, thus it stops if any errors are found
-                uwsgi_args="--master --daemonize2 $LOG_FILE --pidfile2 $PID_FILE $uwsgi_args"
+                uwsgi_args="--master --daemonize2 \"$LOG_FILE\" --pidfile2 \"$PID_FILE\" $uwsgi_args"
                 daemon_or_restart_arg_set=1
                 shift
                 ;;
+            --status|status)
+                paster_args="$paster_args $1"
+                pid_log_paster_args="--pid-file \"$PID_FILE\""
+                shift
+                ;;
             --wait)
                 wait_arg_set=1
                 shift
@@ -115,8 +118,9 @@ find_server() {
             server_args="$(python ./scripts/get_uwsgi_args.py $arg_getter_args)"
         fi
         server_args="$server_args $uwsgi_args"
+        pid_log_paster_args=""
     else
         run_server="python"
-        server_args="./scripts/paster.py serve $server_config --pid-file $PID_FILE --log-file $LOG_FILE $paster_args"
+        server_args="./scripts/paster.py serve $server_config $paster_args"
     fi
 }