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-rwxr-xr-xbin/genenetwork225
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