Merge pull request #181 from pjotrp/zsloan

Run scripts from ./wqflask - just like the webserver

3 files changed, 8 insertions, 7 deletions

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 3a8c3ff4..d926d6a1 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -13,13 +13,12 @@
 # Environment settings can be used to preconfigure as well as a
 # settings.py file.
 
-# Absolute path to this script, e.g. /home/user/bin/foo.sh
 SCRIPT=$(readlink -f "$0")
-# Absolute path this script is in, thus /home/user/bin
 GN2_BASE_PATH=$(dirname $(dirname "$SCRIPT"))
 
 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
@@ -48,9 +47,11 @@ fi
 
 # Now handle command parameter -c
 if [ $1 = '-c' ] ; then
+    cd $GN2_BASE_PATH/wqflask
+    cmd=${2#wqflask/}
     echo PYTHONPATH=$PYTHONPATH
-    echo RUNNING COMMAND $2
-    /usr/bin/env python $2
+    echo RUNNING COMMAND $cmd
+    /usr/bin/env python $cmd
     exit 0
 fi
 
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 6cd3c8e6..1b4e1195 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -91,7 +91,7 @@ Publish or ProbeSet. E.g.
         if USE_GN_SERVER:
             data = menu_main()
         else:
-            file_name = "wqflask/wqflask/static/new/javascript/dataset_menu_structure.json"
+            file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
             with open(file_name, 'r') as fh:
                 data = json.load(fh)
 
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index f2f0830f..23adc4f9 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -40,8 +40,8 @@ from __future__ import print_function, division
 
 import sys
 
-# NEW: Note we prepend the current path - otherwise a guix instance of GN2 is used instead
-sys.path.insert(0,'./wqflask')
+# NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
+sys.path.insert(0,'./')
 # NEW: import app to avoid a circular dependency on utility.tools
 from wqflask import app