Resolved conflict in views.py

3 files changed, 149 insertions, 132 deletions

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 8886e4bc..3f06e7f9 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -68,32 +68,36 @@ if [ "$1" = "-c" -o "$1" = "-gunicorn" ]; then
     echo "Can not use $1 switch without default settings file"
     exit 1
 fi
-# Handle settings parameter (can be .py or .json)
-if [ ! -z $1 ]; then
-    settings=$(realpath "$1")
-    if [ ! -e $settings ]; then
-        settings=$GN2_BASE_DIR/etc/default_settings.py
-    else
-        shift
-    fi
-fi
 
-ext="${settings##*.}"
-if [ "$ext" = "json" -o "$ext" = "JSON" ]; then
-    overrides=$settings
+settings=$1
+if [ -z $settings ]; then
+    settings=$GN2_BASE_DIR/etc/default_settings.py
 else
-    echo $settings
+    shift
 fi
+settings=$(realpath $settings)
+
+# ext="${settings##*.}"
+# if [ "$ext" = "json" -o "$ext" = "JSON" ]; then
+#     overrides=$settings
+# else
+#     echo $settings
+# fi
 
 if [ ! -e $settings ]; then
     echo "ERROR: can not locate settings file - pass it in the command line"
     exit 1
 fi
-export WQFLASK_SETTINGS=$settings     # Python
-export WQFLASK_OVERRIDES=$overrides   # JSON
 
-echo WQFLASK_SETTINGS=$settings
-echo WQFLASK_OVERRIDES=$overrides
+export GN2_SETTINGS=$settings     # Python
+echo GN2_SETTINGS=$settings
+
+# This is a temporary hack to inject ES - should have added python2-elasticsearch package to guix instead
+# if [ -z $ELASTICSEARCH_PROFILE ]; then
+#     echo -e "WARNING: Elastic Search profile has not been set - use ELASTICSEARCH_PROFILE";
+# else
+#     PYTHONPATH="$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!"
@@ -108,7 +112,7 @@ 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="$GN2_PROFILE/lib/python2.7/site-packages" # never inject another PYTHONPATH!!
     export R_LIBS_SITE=$GN2_PROFILE/site-library
     export GEM_PATH=$GN2_PROFILE/lib/ruby/gems/2.4.0
     export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript
@@ -124,7 +128,11 @@ else
     if [ -z $GEMMA_WRAPPER_COMMAND ]; then
         export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper"
     fi
-    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 $PPART ] ; then echo "$PPART in 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
@@ -157,8 +165,9 @@ if [ "$1" = '-c' ] ; then
     cd $GN2_BASE_DIR/wqflask
     cmd=${2#wqflask/}
     echo PYTHONPATH=$PYTHONPATH
-    echo RUNNING COMMAND $cmd
-    python $cmd
+    shift ; shift
+    echo RUNNING COMMAND $cmd $*
+    python $cmd $*
     exit $?
 fi
 # Now handle command parameter -cli which runs in bash
@@ -167,8 +176,9 @@ if [ "$1" = "-cli" ] ; then
     cd $GN2_BASE_DIR/wqflask
     cmd=$2
     echo PYTHONPATH=$PYTHONPATH
-    echo RUNNING COMMAND $cmd
-    $cmd
+    shift ; shift
+    echo RUNNING COMMAND $cmd $*
+    $cmd $*
     exit $?
 fi
 if [ "$1" = '-gunicorn' ] ; then
diff --git a/bin/mechnical-rob b/bin/mechnical-rob
new file mode 100755
index 00000000..be223d94
--- /dev/null
+++ b/bin/mechnical-rob
@@ -0,0 +1,111 @@
+#!/usr/bin/env ruby
+
+
+USAGE = <<EOT
+This is Mechanical-Rob - an automated web server tester for
+                         Genenetwork.org that uses the brilliant
+                         mechanize gem with minitest.
+
+To use this software you need to install mechanize. Run it from
+the root of the genenetwork2 source tree as, for example,
+
+  ./bin/test-website http://localhost:5003/ (default)
+
+If you are using the small deployment database you can use
+
+  ./bin/test-website --skip -n
+
+To run all tests
+
+  ./bin/test-website --all
+
+To run individual tests on localhost you can do
+
+  ruby -Itest -Itest/lib test/lib/mapping.rb --name="/Mapping/"
+
+For more information see http://genenetwork.org/
+
+EOT
+$stderr.print USAGE
+
+require 'optparse'
+
+options = { database: :small, link_checker: false}
+opts = OptionParser.new do |o|
+  o.banner = "Usage: #{File.basename($0)} [options] URL"
+
+  o.on('-d','--database', String, 'Use database (default db_webqtl_s)') do |s|
+    options[:database] =
+      case s
+      when 'xx'
+        :unknown
+      else
+        :small
+      end
+  end
+
+  o.on('--all', 'Run all tests') do
+    options[:all] = true
+  end
+
+  o.on('-l','--link-checker', 'Check for dead links') do
+    options[:link_checker] = true
+  end
+
+  o.on('--navigation', 'Check for navigation') do
+    options[:navigation] = true
+  end
+
+  o.on('--mapping', 'Check for mapping') do
+    options[:mapping] = true
+  end
+
+  o.on('--skip-broken', 'Skip tests that are known to be broken') do
+    options[:skip_broken] = true
+  end
+
+  o.separator ""
+  o.on_tail('-h', '--help', 'display this help and exit') do
+    options[:show_help] = true
+  end
+end
+
+opts.parse!(ARGV)
+
+if options[:show_help]
+  print opts
+  exit 1
+end
+
+$options = options  # we are using a global here
+$host =
+  if ARGV.size>0
+    ARGV.shift
+  else
+    "http://localhost:5003"
+  end
+
+$stderr.print "Testing <",$host,">\n"
+
+require 'mechanize'
+require 'minitest/spec'
+require 'minitest/autorun'
+
+# These are the actual testing modules
+
+libpath = File.dirname(File.dirname(__FILE__))
+$: << File.join(libpath,'test/lib')
+
+require 'main_web_functionality'
+
+if options[:all] or options[:mapping]
+  require 'mapping'
+end
+
+if options[:all] or options[:link_checker]
+  require 'link_checker'
+end
+
+if options[:all] or options[:navigation]
+  require 'navigation'
+end
diff --git a/bin/test-website b/bin/test-website
index be223d94..5935f016 100755
--- a/bin/test-website
+++ b/bin/test-website
@@ -1,111 +1,7 @@
-#!/usr/bin/env ruby
+#! /bin/bash
 
-
-USAGE = <<EOT
-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,
-
-  ./bin/test-website http://localhost:5003/ (default)
-
-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
-
-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
-      when 'xx'
-        :unknown
-      else
-        :small
-      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('--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
-    options[:skip_broken] = true
-  end
-
-  o.separator ""
-  o.on_tail('-h', '--help', 'display this help and exit') do
-    options[:show_help] = true
-  end
-end
-
-opts.parse!(ARGV)
-
-if options[:show_help]
-  print opts
+if [ -z $GN2_PROFILE ]; then
+  echo "Run request tests with something like"
+  echo env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py http://localhost:5003
   exit 1
-end
-
-$options = options  # we are using a global here
-$host =
-  if ARGV.size>0
-    ARGV.shift
-  else
-    "http://localhost:5003"
-  end
-
-$stderr.print "Testing <",$host,">\n"
-
-require 'mechanize'
-require 'minitest/spec'
-require 'minitest/autorun'
-
-# These are the actual testing modules
-
-libpath = File.dirname(File.dirname(__FILE__))
-$: << File.join(libpath,'test/lib')
-
-require 'main_web_functionality'
-
-if options[:all] or options[:mapping]
-  require 'mapping'
-end
-
-if options[:all] or options[:link_checker]
-  require 'link_checker'
-end
-
-if options[:all] or options[:navigation]
-  require 'navigation'
-end
+fi