2 files changed, 123 insertions, 36 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index d3bf3299..52d3155c 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -1,44 +1,112 @@
 #! /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
+#
+# But better is to retain the defaults and override them with
+# JSON file (see the deploy docs).
+#
+#   ./bin/genenetwork2 ~/my_overrides.json
+#
+# To run a maintenance script with settings (instead of the webserver) add that with
+# a -c switch, e.g.
+#
+#   ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py
 #
 # Environment settings can be used to preconfigure as well as a
 # settings.py file.
+#
+# GN2_BASE_PATH is base directory of wqflask source code
+#
 
-# 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_BASE_DIR=$(dirname $(dirname "$SCRIPT"))
 
-GN2_GUIX_PATH=$GN2_BASE_PATH/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg
-if [ -d $GN2_GUIX_PATH ]; then
-  GN2_BASE_PATH=$GN2_GUIX_PATH
-fi
-echo $GN2_BASE_PATH
+echo GN2_BASE_DIR=$GN2_BASE_DIR
+
+GIT_HASH=$(git rev-parse HEAD)
+GIT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
+export GN_VERSION=$(cat $GN2_BASE_DIR/VERSION)-$GIT_BRANCH-${GIT_HASH:0:9}
+echo GN_VERSION=$GN_VERSION
 
-# Handle settings parameter
+# Handle settings parameter (can be .py or .json)
 settings=$1
-if [ -z $settings ]; then settings=$GN2_BASE_PATH/etc/default_settings.py ; fi
+ext="${settings##*.}"
+if [ -z "$settings" -o "$ext" = "json" -o "$ext" = "JSON" ]; then
+    overrides=$settings
+    settings=$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=$overrides   # JSON
+
+echo WQFLASK_SETTINGS=$settings
+echo WQFLASK_OVERRIDES=$overrides
+
+# ---- Checks and balances
+if [ -z $GUIX_ETC ]; then
+    if [ -z $GN2_PROFILE ] ; then
+        echo "WARNING: GN2_PROFILE has not been set - I hope you know what you are doing!"
+    else
+        export PATH=$GN2_PROFILE/bin:$PATH
+        export PYTHONPATH=$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"
+        export LC_ALL=C
+    fi
+    if [ -z $PYTHONPATH ] ; then
+        echo "WARNING PYTHONPATH has not been set - use GN2_PROFILE!"
+    fi
+    if [ ! -d $R_LIBS_SITE ] ; then
+        echo "ERROR: R_LIBS_SITE has not been set correctly (we only allow one path) - use GN2_PROFILE!"
+        echo "Paste into your shell the output of (for example)"
+        echo "guix package -p \$GN2_PROFILE --search-paths"
+        exit 1
+    fi
 fi
-export WQFLASK_SETTINGS=$settings
 
 # 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"
+# Our UNIX TMPDIR defaults to /tmp - change this on a shared server
+if [ -z $TMPDIR ]; then
+    TMPDIR="/tmp"
 fi
-                         
+
+set|grep $GN2_PROFILE
+set|grep TMPDIR
+
+# Now handle command parameter -c
+if [ "$1" = '-c' ] ; then
+    cd $GN2_BASE_DIR/wqflask
+    cmd=${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
+echo -n "dir $TMPDIR
 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
diff --git a/bin/test-website b/bin/test-website
index 2e91f364..be223d94 100755
--- a/bin/test-website
+++ b/bin/test-website
@@ -2,9 +2,9 @@
 
 
 USAGE = <<EOT
-This is Mechanical-Rob - an automated web server tester for 
-                         Genenetwork.org that uses the brilliant 
-                         mechanize gem.
+This is Mechanical-Rob - an automated web server tester for
+                         Genenetwork.org that uses the brilliant
+                         mechanize gem with minitest.
 
 To use this software you need to install mechanize. Run it from
 the root of the genenetwork2 source tree as, for example,
@@ -15,8 +15,16 @@ If you are using the small deployment database you can use
 
   ./bin/test-website --skip -n
 
+To run all tests
+
+  ./bin/test-website --all
+
+To run individual tests on localhost you can do
+
+  ruby -Itest -Itest/lib test/lib/mapping.rb --name="/Mapping/"
+
 For more information see http://genenetwork.org/
-                        
+
 EOT
 $stderr.print USAGE
 
@@ -25,7 +33,7 @@ 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
@@ -36,12 +44,20 @@ opts = OptionParser.new do |o|
       end
   end
 
+  o.on('--all', 'Run all tests') do
+    options[:all] = true
+  end
+
   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
-    options[:navigation_test] = true
+
+  o.on('--navigation', 'Check for navigation') do
+    options[:navigation] = true
+  end
+
+  o.on('--mapping', 'Check for mapping') do
+    options[:mapping] = true
   end
 
   o.on('--skip-broken', 'Skip tests that are known to be broken') do
@@ -62,7 +78,7 @@ if options[:show_help]
 end
 
 $options = options  # we are using a global here
-$host = 
+$host =
   if ARGV.size>0
     ARGV.shift
   else
@@ -80,13 +96,16 @@ require 'minitest/autorun'
 libpath = File.dirname(File.dirname(__FILE__))
 $: << File.join(libpath,'test/lib')
 
-if options[:link_checker]
+require 'main_web_functionality'
+
+if options[:all] or options[:mapping]
+  require 'mapping'
+end
+
+if options[:all] or options[:link_checker]
   require 'link_checker'
-else
-  require 'main_web_functionality'
 end
-  
-if options[:navigation_test]
+
+if options[:all] or options[:navigation]
   require 'navigation'
 end
-