Merge branch 'master' into chfi

2 files changed, 42 insertions, 13 deletions

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index d3bf3299..d926d6a1 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -1,24 +1,36 @@
 #! /bin/bash
 #
-# This will run the GN2 server (with default settings if none supplied).
+# This will run the GN2 server (with default settings if none supplied). Pass in
+# your own settings file, e.g.
+#
+#   ./bin/genenetwork2 ~/my_settings.py
+#
+# To run a maintenance script with settings (instead of the webserver) add that with
+# a -c switch, e.g.
+#
+#   ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
 #
 # 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
 
 # Handle settings parameter
 settings=$1
-if [ -z $settings ]; then settings=$GN2_BASE_PATH/etc/default_settings.py ; fi
+if [ -z $settings ]; then
+    # get default
+    settings=$GN2_BASE_PATH/etc/default_settings.py
+else
+    shift
+fi
 if [ ! -e $settings ]; then
     echo "ERROR: can not locate settings file - pass it in the command line"
     exit 1
@@ -32,7 +44,17 @@ export PYTHONPATH=$GN2_BASE_PATH/wqflask:$PYTHONPATH
 if [ -z $TEMPDIR ]; then
     TEMPDIR="/tmp"
 fi
-                         
+
+# Now handle command parameter -c
+if [ $1 = '-c' ] ; then
+    cd $GN2_BASE_PATH/wqflask
+    cmd=${2#wqflask/}
+    echo PYTHONPATH=$PYTHONPATH
+    echo RUNNING COMMAND $cmd
+    /usr/bin/env python $cmd
+    exit 0
+fi
+
 echo "Starting the redis server:"
 echo -n "dir $TEMPDIR
 dbfilename gn2.rdb
diff --git a/bin/test-website b/bin/test-website
index 2e91f364..18994cc5 100755
--- a/bin/test-website
+++ b/bin/test-website
@@ -2,8 +2,8 @@
 
 
 USAGE = <<EOT
-This is Mechanical-Rob - an automated web server tester for 
-                         Genenetwork.org that uses the brilliant 
+This is Mechanical-Rob - an automated web server tester for
+                         Genenetwork.org that uses the brilliant
                          mechanize gem.
 
 To use this software you need to install mechanize. Run it from
@@ -16,7 +16,7 @@ If you are using the small deployment database you can use
   ./bin/test-website --skip -n
 
 For more information see http://genenetwork.org/
-                        
+
 EOT
 $stderr.print USAGE
 
@@ -25,7 +25,7 @@ require 'optparse'
 options = { database: :small, link_checker: false}
 opts = OptionParser.new do |o|
   o.banner = "Usage: #{File.basename($0)} [options] URL"
-  
+
   o.on('-d','--database', String, 'Use database (default db_webqtl_s)') do |s|
     options[:database] =
       case s
@@ -39,11 +39,15 @@ opts = OptionParser.new do |o|
   o.on('-l','--link-checker', 'Check for dead links') do
     options[:link_checker] = true
   end
-  
-  o.on('-n','--navigation-test', 'Check for navigation test results') do
+
+  o.on('--navigation-test', 'Check for navigation') do
     options[:navigation_test] = true
   end
 
+  o.on('--mapping-test', 'Check for mapping') do
+    options[:mapping_test] = true
+  end
+
   o.on('--skip-broken', 'Skip tests that are known to be broken') do
     options[:skip_broken] = true
   end
@@ -62,7 +66,7 @@ if options[:show_help]
 end
 
 $options = options  # we are using a global here
-$host = 
+$host =
   if ARGV.size>0
     ARGV.shift
   else
@@ -85,8 +89,11 @@ if options[:link_checker]
 else
   require 'main_web_functionality'
 end
-  
+
 if options[:navigation_test]
   require 'navigation'
 end
 
+if options[:mapping_test]
+  require 'mapping'
+end