diff options
Diffstat (limited to 'bin/genenetwork2')
| -rwxr-xr-x | bin/genenetwork2 | 25 |
1 files changed, 19 insertions, 6 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 8886e4bc..2a83a1cd 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -95,6 +95,13 @@ export WQFLASK_OVERRIDES=$overrides # JSON echo WQFLASK_SETTINGS=$settings echo WQFLASK_OVERRIDES=$overrides +# 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 $GN2_PROFILE ] ; then echo "WARNING: GN2_PROFILE has not been set - you need the environment, so I hope you know what you are doing!" export GN2_PROFILE=$(dirname $(dirname $(which genenetwork2))) @@ -108,7 +115,7 @@ 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="$GN2_PROFILE/lib/python2.7/site-packages${PYTHONPATH:+:}$PYTHONPATH" export R_LIBS_SITE=$GN2_PROFILE/site-library export GEM_PATH=$GN2_PROFILE/lib/ruby/gems/2.4.0 export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript @@ -124,7 +131,11 @@ 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 $PPart ] ; then echo "PYTHONPATH not valid "$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 @@ -157,8 +168,9 @@ 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 @@ -167,8 +179,9 @@ if [ "$1" = "-cli" ] ; then 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 |