diff options
Diffstat (limited to 'bin/genenetwork2')
| -rwxr-xr-x | bin/genenetwork2 | 81 |
1 files changed, 49 insertions, 32 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 8886e4bc..b3a8d8c2 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -15,20 +15,29 @@ # installation path of genenetwork). Say your profile is in # ~/opt/gn-latest-guix # -# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 # # You can pass in your own settings file, e.g. # -# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_settings.py +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ~/my_settings.py # -# To run a maintenance script with settings (instead of the webserver) add that with -# a -c switch, e.g. +# To run a maintenance python script with settings (instead of the +# webserver) run from the base-dir with settings file and add that +# script with a -c switch, e.g. # -# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ./maintenance/gen_select_dataset.py +# +# To run any script in the environment +# +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD" +# +# To get a python REPL(!) +# +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -cli python # # For development you may want to run # -# env GN2_PROFILE=~/opt/gn-latest-guix WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG ./bin/genenetwork2 +# env GN2_PROFILE=~/opt/gn-latest 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! @@ -68,32 +77,36 @@ 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) -if [ ! -z $1 ]; then - settings=$(realpath "$1") - if [ ! -e $settings ]; then - settings=$GN2_BASE_DIR/etc/default_settings.py - else - shift - fi -fi -ext="${settings##*.}" -if [ "$ext" = "json" -o "$ext" = "JSON" ]; then - overrides=$settings +settings=$1 +if [ -z $settings ]; then + settings=$GN2_BASE_DIR/etc/default_settings.py else - echo $settings + shift fi +settings=$(realpath $settings) + +# ext="${settings##*.}" +# if [ "$ext" = "json" -o "$ext" = "JSON" ]; then +# overrides=$settings +# else +# echo $settings +# fi if [ ! -e $settings ]; then echo "ERROR: can not locate settings file - pass it in the command line" exit 1 fi -export WQFLASK_SETTINGS=$settings # Python -export WQFLASK_OVERRIDES=$overrides # JSON -echo WQFLASK_SETTINGS=$settings -echo WQFLASK_OVERRIDES=$overrides +export GN2_SETTINGS=$settings # Python +echo GN2_SETTINGS=$settings + +# This is a temporary hack to inject ES - should have added python2-elasticsearch package to guix instead +# if [ -z $ELASTICSEARCH_PROFILE ]; then +# echo -e "WARNING: Elastic Search profile has not been set - use ELASTICSEARCH_PROFILE"; +# else +# PYTHONPATH="$PYTHONPATH${PYTHONPATH:+:}$ELASTICSEARCH_PROFILE/lib/python2.7/site-packages" +# fi if [ -z $GN2_PROFILE ] ; then echo "WARNING: GN2_PROFILE has not been set - you need the environment, so I hope you know what you are doing!" @@ -108,9 +121,8 @@ if [ -z $GN2_PROFILE ]; then read -p "PRESS [ENTER] TO CONTINUE..." else export PATH=$GN2_PROFILE/bin:$PATH - export PYTHONPATH=$GN2_PROFILE/lib/python2.7/site-packages + export PYTHONPATH="$GN2_PROFILE/lib/python2.7/site-packages" # never inject another PYTHONPATH!! export R_LIBS_SITE=$GN2_PROFILE/site-library - export GEM_PATH=$GN2_PROFILE/lib/ruby/gems/2.4.0 export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0" export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0" @@ -124,9 +136,12 @@ else 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 + while IFS=":" read -ra PPATH; do + for PPART in "${PPATH[@]}"; do + if [ ! -d $PPART ] ; then echo "$PPART in PYTHONPATH not valid $PYTHONPATH" ; exit 1 ; fi + done + done <<< "$PYTHONPATH" 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!" @@ -157,18 +172,20 @@ if [ "$1" = '-c' ] ; then cd $GN2_BASE_DIR/wqflask cmd=${2#wqflask/} echo PYTHONPATH=$PYTHONPATH - echo RUNNING COMMAND $cmd - python $cmd + shift ; shift + echo RUNNING COMMAND $cmd $* + python $cmd $* 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 + shift ; shift + echo RUNNING COMMAND $cmd $* + $cmd $* exit $? fi if [ "$1" = '-gunicorn' ] ; then |