From 63a5c8a42ad02e9126bb207465ff5eca98f6515d Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Fri, 19 Jan 2018 10:36:19 +0300
Subject: Add elasticsearch module to the path

* Add some code to set up the path for the python-elasticsearch module.
---
 bin/genenetwork2 | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

(limited to 'bin')

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index a7edb1c2..ccd9b1d9 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -61,6 +61,11 @@ export WQFLASK_OVERRIDES=$overrides   # JSON
 echo WQFLASK_SETTINGS=$settings
 echo WQFLASK_OVERRIDES=$overrides
 
+if [ -z $ELASTICSEARCH_PROFILE ]; then
+    echo -e "\033[1;33mWARNING: Elastic Search profile has not been set - use ELASTICSEARCH_PROFILE\033[0m";
+else
+    PYTHONPATH="$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)))
@@ -72,7 +77,7 @@ 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
-- 
cgit 1.4.1


From 6ec9dcc365b899f7f4aaab739103f4559c2c1620 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Mon, 5 Feb 2018 16:19:13 +0300
Subject: Check each part of the PYTHONPATH

* PYTHONPATH may be composed of multiple locations in the filesystem,
  thus the need to test that each location exists and is a directory.
---
 bin/genenetwork2 | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

(limited to 'bin')

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 34fbc72e..145ce395 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -126,7 +126,11 @@ else
     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 [ ! -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
-- 
cgit 1.4.1