diff options
Diffstat (limited to 'bin/genenetwork2')
| -rwxr-xr-x | bin/genenetwork2 | 82 |
1 files changed, 61 insertions, 21 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index d926d6a1..889401fd 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -1,53 +1,93 @@ #! /bin/bash # -# This will run the GN2 server (with default settings if none supplied). Pass in -# your own settings file, e.g. +# This will run the GN2 server (with default settings if none +# supplied). Pass in your own settings file, e.g. # # ./bin/genenetwork2 ~/my_settings.py # +# But better is to retain the defaults and override them with +# JSON file (see the deploy docs). +# +# ./bin/genenetwork2 ~/my_overrides.json +# # To run a maintenance script with settings (instead of the webserver) add that with # a -c switch, e.g. # -# ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py +# ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py # # Environment settings can be used to preconfigure as well as a # settings.py file. +# +# GN2_BASE_PATH is base directory of wqflask source code +# SCRIPT=$(readlink -f "$0") -GN2_BASE_PATH=$(dirname $(dirname "$SCRIPT")) +GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT")) -GN2_GUIX_PATH=$GN2_BASE_PATH/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg -if [ -d $GN2_GUIX_PATH ]; then - echo GN2 is running from GUIX - GN2_BASE_PATH=$GN2_GUIX_PATH -fi -echo $GN2_BASE_PATH +echo GN2_BASE_DIR=$GN2_BASE_DIR -# Handle settings parameter + +# Handle settings parameter (can be .py or .json) settings=$1 -if [ -z $settings ]; then - # get default - settings=$GN2_BASE_PATH/etc/default_settings.py +ext="${settings##*.}" +if [ -z "$settings" -o "$ext" = "json" -o "$ext" = "JSON" ]; then + overrides=$settings + settings=$GN2_BASE_DIR/etc/default_settings.py else shift fi if [ ! -e $settings ]; then - echo "ERROR: can not locate settings file - pass it in the command line" - exit 1 + GUIX_ETC=$GN2_BASE_DIR/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg + if [ -d $GUIX_ETC ]; then + echo INFO: GN2 is actually running from GNU Guix + else + echo "ERROR: can not locate settings file - pass it in the command line" + exit 1 + fi +fi +export WQFLASK_SETTINGS=$settings # Python +export WQFLASK_OVERRIDES=$overrides # JSON + +echo WQFLASK_SETTINGS=$settings +echo WQFLASK_OVERRIDES=$overrides + +# ---- Checks and balances +if [ -z $GUIX_ETC ]; then + if [ -z $GN2_PROFILE ] ; then + echo "WARNING: GN2_PROFILE has not been set - I hope you know what you are doing" + else + export PYTHONPATH=$GN2_PROFILE/lib/python2.7/site-packages + export R_LIBS_SITE=$GN2_PROFILE/site-library + export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0" + export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0" + export XDG_DATA_DIRS="$GN2_PROFILE/share" + export GIO_EXTRA_MODULES="$GN2_PROFILE/lib/gio/modules" + fi + if [ -z $PYTHONPATH ] ; then + echo "WARNING PYTHONPATH has not been set" + fi + if [ ! -d $R_LIBS_SITE ] ; then + echo "ERROR: R_LIBS_SITE has not been set correctly (we only allow one path)" + echo "Paste in the output of, for example," + echo "guix package -p /usr/local/guix-profiles/gn2-staging --search-paths" + exit 1 + fi fi -export WQFLASK_SETTINGS=$settings # We may change this one: -export PYTHONPATH=$GN2_BASE_PATH/wqflask:$PYTHONPATH +export PYTHONPATH=$GN2_BASE_DIR/wqflask:$PYTHONPATH # TEMPDIR defaults to /tmp if nothing else if [ -z $TEMPDIR ]; then TEMPDIR="/tmp" fi +set|grep $GN2_PROFILE +set|grep TEMPDIR + # Now handle command parameter -c -if [ $1 = '-c' ] ; then - cd $GN2_BASE_PATH/wqflask +if [ "$1" = '-c' ] ; then + cd $GN2_BASE_DIR/wqflask cmd=${2#wqflask/} echo PYTHONPATH=$PYTHONPATH echo RUNNING COMMAND $cmd @@ -61,6 +101,6 @@ dbfilename gn2.rdb " | redis-server - & # Start the flask server running GN2 -cd $GN2_BASE_PATH/wqflask +cd $GN2_BASE_DIR/wqflask echo "Starting with $settings" /usr/bin/env python runserver.py |