Merge rolling_restart.sh in run.sh by adding --wait parameter.

Also add the following combination:

GALAXY_RUN_ALL=1 ./run.sh --daemon --wait

which, by preventing servers from starting simultaneously, is useful when
multiple servers are configured before creating the database, or when updating
to a new Galaxy release containing a database upgrade.

rolling_restart.sh

@@ -1,61 +1,3 @@
 #!/bin/sh
 
-cd `dirname $0`
-
-# If there is a .venv/ directory, assume it contains a virtualenv that we
-# should run this instance in.
-if [ -d .venv ];
-then
-    . .venv/bin/activate
-fi
-
-python ./scripts/check_python.py
-[ $? -ne 0 ] && exit 1
-
-./scripts/common_startup.sh
-
-if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then
-    python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR"
-fi
-
-if [ -z "$GALAXY_CONFIG_FILE" ]; then
-    if [ -f universe_wsgi.ini ]; then
-        GALAXY_CONFIG_FILE=universe_wsgi.ini
-    elif [ -f config/galaxy.ini ]; then
-        GALAXY_CONFIG_FILE=config/galaxy.ini
-    else
-        GALAXY_CONFIG_FILE=config/galaxy.ini.sample
-    fi
-    export GALAXY_CONFIG_FILE
-fi
-
-servers=`sed -n 's/^\[server:\(.*\)\]/\1/  p' $GALAXY_CONFIG_FILE | xargs echo`
-for server in $servers; do
-    # If there's a pid
-    if [ -e $server.pid ]; then
-        # Then kill it
-        echo "Killing $server"
-        pid=`cat $server.pid`
-        kill $pid
-    else
-        # Otherwise just continue
-        echo "$server not running"
-    fi
-    # Start the server (and background) (should this be nohup'd?)
-    python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@
-    while true; do
-        sleep 1
-        printf "."
-        # Grab the current pid from the pid file
-        if ! current_pid_in_file=$(cat $server.pid); then
-            echo "A Galaxy process died, interrupting" >&2
-            exit 1
-        fi
-        # Search for all pids in the logs and tail for the last one
-        latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $server.log -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1`
-        # If they're equivalent, then the current pid file agrees with our logs
-        # and we've succesfully started
-        [ -n "$latest_pid" ] && [ $latest_pid -eq $current_pid_in_file ] && break
-    done
-    echo
-done
+GALAXY_RUN_ALL=1 ./run.sh restart --wait

run.sh

@@ -49,9 +49,31 @@ if [ -n "$GALAXY_RUN_ALL" ]; then
         echo 'ERROR: $GALAXY_RUN_ALL cannot be used without the `--daemon`, `--stop-daemon` or `restart` arguments to run.sh'
         exit 1
     fi
+    (echo "$@" | grep -q -e '--daemon\|restart') && (echo "$@" | grep -q -e '--wait')
+    WAIT=$?
+    ARGS=`echo "$@" | sed 's/--wait//'`
     for server in $servers; do
-        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 $@
+        if [ $WAIT -eq 0 ]; then
+            python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $ARGS
+            while true; do
+                sleep 1
+                printf "."
+                # Grab the current pid from the pid file
+                if ! current_pid_in_file=$(cat $server.pid); then
+                    echo "A Galaxy process died, interrupting" >&2
+                    exit 1
+                fi
+                # Search for all pids in the logs and tail for the last one
+                latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $server.log -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1`
+                # If they're equivalent, then the current pid file agrees with our logs
+                # and we've succesfully started
+                [ -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 $@
+        fi
     done
 else
     # Handle only 1 server, whose name can be specified with --server-name parameter (defaults to "main")