Merge pull request #274 from pjotrp/pjotr

Add gunicorn support

8 files changed, 93 insertions, 11 deletions

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index a7edb1c2..cbaba76f 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -22,8 +22,25 @@
 # a -c switch, e.g.
 #
 #   env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py
+#
+# For development you may want to run
+#
+#   env GN2_PROFILE=~/opt/gn-latest-guix WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG ./bin/genenetwork2
+#
+# For staging and production we use gunicorn. Run with something like
+# (note you have to provide the server port). Provide a settings file!
+#
+#   env GN2_PROFILE=~/opt/gn-latest-guix SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-prod
+#
+# For development use
+#
+#   env GN2_PROFILE=~/opt/gn-latest-guix SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev
+#
+# For extra flexibility you can also provide gunicorn parameters yourself with something like
+#
+#   env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -gunicorn "--bind 0.0.0.0:5003 --workers=1 wsgi"
 
-SCRIPT=$(readlink -f "$0")
+SCRIPT=$(realpath "$0")
 GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT"))
 GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR)
 
@@ -42,15 +59,27 @@ else
 fi
 echo GN_VERSION=$GN_VERSION
 
+if [ "$1" = "-c" -o "$1" = "-gunicorn" ]; then
+    echo "Can not use $1 switch without default settings file"
+    exit 1
+fi
 # Handle settings parameter (can be .py or .json)
-settings=$1
+if [ ! -z $1 ]; then
+    settings=$(realpath "$1")
+    if [ ! -e $settings ]; then
+        settings=$GN2_BASE_DIR/etc/default_settings.py
+    else
+        shift
+    fi
+fi
+
 ext="${settings##*.}"
-if [ -z "$settings" -o "$ext" = "json" -o "$ext" = "JSON" ]; then
+if [ "$ext" = "json" -o "$ext" = "JSON" ]; then
     overrides=$settings
-    settings=$GN2_BASE_DIR/etc/default_settings.py
 else
-    shift
+    echo $settings
 fi
+
 if [ ! -e $settings ]; then
     echo "ERROR: can not locate settings file - pass it in the command line"
     exit 1
@@ -86,6 +115,9 @@ else
     export PYLMM_COMMAND="$GN2_PROFILE/bin/pylmm_redis"
     export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma"
     export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper"
+    if [ ! -d $PYTHONPATH ] ; then echo "PYTHONPATH not valid "$PYTHONPATH ; exit 1 ; fi
+    if [ ! -d $R_LIBS_SITE ] ; then echo "R_LIBS_SITE not valid "$R_LIBS_SITE ; exit 1 ; fi
+    if [ ! -d $GEM_PATH ] ; then echo "GEM_PATH not valid "$GEM_PATH ; exit 1 ; fi
 fi
 if [ -z $PYTHONPATH ] ; then
     echo "ERROR PYTHONPATH has not been set - use GN2_PROFILE!"
@@ -118,7 +150,33 @@ if [ "$1" = '-c' ] ; then
     echo PYTHONPATH=$PYTHONPATH
     echo RUNNING COMMAND $cmd
     python $cmd
-    exit 0
+    exit $?
+fi
+if [ "$1" = '-gunicorn' ] ; then
+    cd $GN2_BASE_DIR/wqflask
+    cmd=$2
+    echo PYTHONPATH=$PYTHONPATH
+    echo RUNNING gunicorn $cmd
+    gunicorn $cmd
+    exit $?
+fi
+if [ "$1" = '-gunicorn-dev' ] ; then
+    cd $GN2_BASE_DIR/wqflask
+    echo PYTHONPATH=$PYTHONPATH
+    if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
+    cmd="--bind 0.0.0.0:$SERVER_PORT --workers=1 --reload wsgi"
+    echo RUNNING gunicorn $cmd
+    gunicorn $cmd
+    exit $?
+fi
+if [ "$1" = '-gunicorn-prod' ] ; then
+    cd $GN2_BASE_DIR/wqflask
+    echo PYTHONPATH=$PYTHONPATH
+    if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
+    cmd="--bind 0.0.0.0:$SERVER_PORT --workers=32 --max-requests 1000 --timeout 1200 wsgi"
+    echo RUNNING gunicorn $cmd
+    gunicorn $cmd
+    exit $?
 fi
 
 echo "Starting the redis server:"
@@ -127,7 +185,7 @@ dbfilename gn2.rdb
 " | redis-server - &
 
 # Overrides for packages that are not yet public (currently r-auwerx)
-export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib
+# export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib
 
 # Start the flask server running GN2
 cd $GN2_BASE_DIR/wqflask
diff --git a/etc/VERSION b/etc/VERSION
index b624c74a..ca9e199c 100644
--- a/etc/VERSION
+++ b/etc/VERSION
@@ -1 +1 @@
-2.10rc5
+2.11-rc1
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 59e22f1a..699d21f1 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -27,7 +27,7 @@ import sys
 GN_VERSION = open("../etc/VERSION","r").read()
 SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
 SQL_ALCHEMY_POOL_RECYCLE = 3600
-GN_SERVER_URL = "http://localhost:8880/"
+GN_SERVER_URL = "http://localhost:8880/" # REST API server
 
 # ---- Flask configuration (see website)
 TRAP_BAD_REQUEST_ERRORS = True
diff --git a/wqflask/__init__.py b/wqflask/__init__.py
index 315b709e..e69de29b 100644
--- a/wqflask/__init__.py
+++ b/wqflask/__init__.py
@@ -1 +0,0 @@
-from wqflask import app
diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py
new file mode 100644
index 00000000..14a2d689
--- /dev/null
+++ b/wqflask/run_gunicorn.py
@@ -0,0 +1,19 @@
+# Run with gunicorn, see ./bin/genenetwork2 for an example
+#
+# Run standalone with
+#
+#   ./bin/genenetwork2 ./etc/default_settings.py -c run_gunicorn.py
+
+# from flask import Flask
+# application = Flask(__name__)
+
+print "Starting up Gunicorn process"
+
+from wqflask import app
+
+@app.route("/gunicorn")
+def hello():
+    return "<h1 style='color:blue'>Hello There!</h1>"
+
+if __name__ == "__main__":
+    app.run(host='0.0.0.0')
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 50f134db..a0c76e51 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -1,5 +1,7 @@
 # Starts the webserver with the ./bin/genenetwork2 command
 #
+# This uses Werkzeug WSGI, see ./run_gunicorn.py for the alternative
+#
 # Please note, running with host set externally below combined with
 # debug mode is a security risk unless you have a firewall setup, e.g.
 #
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index d8f5616d..4e81c29c 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -766,7 +766,7 @@ def corr_scatter_plot_page():
 def submit_bnw():
     logger.error(request.url)
     template_vars = get_bnw_input(request.form)
-    return render_template("empty_collection.html", **{'tool':'Correlation Matrix'}) 
+    return render_template("empty_collection.html", **{'tool':'Correlation Matrix'})
 
 # Todo: Can we simplify this? -Sam
 def sharing_info_page():
diff --git a/wqflask/wsgi.py b/wqflask/wsgi.py
new file mode 100644
index 00000000..be9c7b37
--- /dev/null
+++ b/wqflask/wsgi.py
@@ -0,0 +1,4 @@
+from run_gunicorn import app as application # expect application as a name
+
+if __name__ == "__main__":
+    application.run()