diff options
Diffstat (limited to 'bin')
| -rwxr-xr-x | bin/genenetwork2 | 81 | ||||
| -rwxr-xr-x | bin/test-website | 114 |
2 files changed, 54 insertions, 141 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 8886e4bc..b3a8d8c2 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -15,20 +15,29 @@ # installation path of genenetwork). Say your profile is in # ~/opt/gn-latest-guix # -# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 # # You can pass in your own settings file, e.g. # -# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_settings.py +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ~/my_settings.py # -# To run a maintenance script with settings (instead of the webserver) add that with -# a -c switch, e.g. +# To run a maintenance python script with settings (instead of the +# webserver) run from the base-dir with settings file and add that +# script with a -c switch, e.g. # -# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ./maintenance/gen_select_dataset.py +# +# To run any script in the environment +# +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD" +# +# To get a python REPL(!) +# +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -cli python # # For development you may want to run # -# env GN2_PROFILE=~/opt/gn-latest-guix WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG ./bin/genenetwork2 +# env GN2_PROFILE=~/opt/gn-latest WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG ./bin/genenetwork2 # # For staging and production we use gunicorn. Run with something like # (note you have to provide the server port). Provide a settings file! @@ -68,32 +77,36 @@ 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!" @@ -108,9 +121,8 @@ 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 export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0" export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0" @@ -124,9 +136,12 @@ 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 if [ -z $PYTHONPATH ] ; then echo "ERROR PYTHONPATH has not been set - use GN2_PROFILE!" @@ -157,18 +172,20 @@ 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 if [ "$1" = "-cli" ] ; then - echo "HERE" 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 [ "$1" = '-gunicorn' ] ; then diff --git a/bin/test-website b/bin/test-website index be223d94..5935f016 100755 --- a/bin/test-website +++ b/bin/test-website @@ -1,111 +1,7 @@ -#!/usr/bin/env ruby +#! /bin/bash - -USAGE = <<EOT -This is Mechanical-Rob - an automated web server tester for - Genenetwork.org that uses the brilliant - mechanize gem with minitest. - -To use this software you need to install mechanize. Run it from -the root of the genenetwork2 source tree as, for example, - - ./bin/test-website http://localhost:5003/ (default) - -If you are using the small deployment database you can use - - ./bin/test-website --skip -n - -To run all tests - - ./bin/test-website --all - -To run individual tests on localhost you can do - - ruby -Itest -Itest/lib test/lib/mapping.rb --name="/Mapping/" - -For more information see http://genenetwork.org/ - -EOT -$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 |