diff options
| -rwxr-xr-x | bin/genenetwork2 | 72 | ||||
| -rw-r--r-- | etc/VERSION | 2 | ||||
| -rw-r--r-- | etc/default_settings.py | 2 | ||||
| -rw-r--r-- | wqflask/__init__.py | 1 | ||||
| -rw-r--r-- | wqflask/run_gunicorn.py | 19 | ||||
| -rw-r--r-- | wqflask/runserver.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 2 | ||||
| -rw-r--r-- | wqflask/wsgi.py | 4 |
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() |