From 3df145309159efd18dadc537ac7eebafef5b4595 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 3 Oct 2016 10:40:21 +0000
Subject: Use of GN2_PROFILE

---
 bin/genenetwork2 | 56 +++++++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 43 insertions(+), 13 deletions(-)

(limited to 'bin')

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 30a4dc95..889401fd 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -17,29 +17,33 @@
 #
 # 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"))
+
+echo GN2_BASE_DIR=$GN2_BASE_DIR
 
-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
 
 # Handle settings parameter (can be .py or .json)
 settings=$1
 ext="${settings##*.}"
 if [ -z "$settings" -o "$ext" = "json" -o "$ext" = "JSON" ]; then
     overrides=$settings
-    settings=$GN2_BASE_PATH/etc/default_settings.py
+    settings=$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=$overrides   # JSON
@@ -47,17 +51,43 @@ export WQFLASK_OVERRIDES=$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 $R_LIBS_SITE ] ; then
+        echo "ERROR: R_LIBS_SITE has not been set correctly (we only allow one path)"
+        echo "Paste in the output of, for example,"
+        echo "guix package -p /usr/local/guix-profiles/gn2-staging --search-paths"
+        exit 1
+    fi
+fi
+
 # We may change this one:
-export PYTHONPATH=$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
+    cd $GN2_BASE_DIR/wqflask
     cmd=${2#wqflask/}
     echo PYTHONPATH=$PYTHONPATH
     echo RUNNING COMMAND $cmd
@@ -71,6 +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
-- 
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