Merge branch 'testing' of https://github.com/genenetwork/genenetwork2

1 files changed, 95 insertions, 8 deletions

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 5e791885..8886e4bc 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -1,5 +1,14 @@
 #! /bin/bash
 #
+# This is the startup script for GN2. It sets the environment variables to pick
+# up a Guix profile and allows for overriding parameters.
+#
+# Typical usage
+#
+#   env GN2_PROFILE=~/opt/genenetwork2-phewas ./bin/genenetwork2 ~/my_settings.py
+#
+# Where GN2_PROFILE points to the GNU Guix profile used for deployment.
+#
 # This will run the GN2 server (with default settings if none
 # supplied). Typically you need a GNU Guix profile which is set with
 # an environment variable (this profile is dictated by the
@@ -16,8 +25,27 @@
 # 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 "$0")
+echo SCRIPT=$SCRIPT
+echo GN2_PROFILE=$GN2_PROFILE
 GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT"))
 GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR)
 
@@ -36,15 +64,27 @@ 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
@@ -61,6 +101,8 @@ if [ -z $GN2_PROFILE ] ; then
     if [ -d $GN2_PROFILE ]; then
         echo "Best guess is $GN2_PROFILE"
     fi
+    echo "ERROR: always set GN2_PROFILE"
+    exit 1
 fi
 if [ -z $GN2_PROFILE ]; then
     read -p "PRESS [ENTER] TO CONTINUE..."
@@ -79,7 +121,12 @@ else
     export PLINK_COMMAND="$GN2_PROFILE/bin/plink2"
     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 [ -z $GEMMA_WRAPPER_COMMAND ]; then
+        export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper"
+    fi
+    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!"
@@ -105,14 +152,51 @@ set|grep guix
 set|grep $GN2_PROFILE
 set|grep TMPDIR
 
-# Now handle command parameter -c
+# Now handle command parameter -c which runs python
 if [ "$1" = '-c' ] ; then
     cd $GN2_BASE_DIR/wqflask
     cmd=${2#wqflask/}
     echo PYTHONPATH=$PYTHONPATH
     echo RUNNING COMMAND $cmd
     python $cmd
-    exit 0
+    exit $?
+fi
+# Now handle command parameter -cli which runs in bash
+if [ "$1" = "-cli" ] ; then
+    echo "HERE"
+    cd $GN2_BASE_DIR/wqflask
+    cmd=$2
+    echo PYTHONPATH=$PYTHONPATH
+    echo RUNNING COMMAND $cmd
+    $cmd
+    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 --timeout 180 --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 $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
+    PID=$TMPDIR/gunicorn.$USER.pid
+    cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID -k eventlet --workers 20 --keep-alive 1200 --max-requests 1000 --timeout 1200 wsgi"
+    echo RUNNING gunicorn $cmd
+    gunicorn $cmd
+    exit $?
 fi
 
 echo "Starting the redis server:"
@@ -120,6 +204,9 @@ echo -n "dir $TMPDIR
 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
+
 # Start the flask server running GN2
 cd $GN2_BASE_DIR/wqflask
 echo "Starting with $settings"