diff options
Diffstat (limited to 'bin')
| -rwxr-xr-x | bin/genenetwork2 | 30 | ||||
| -rwxr-xr-x | bin/mechnical-rob | 111 | ||||
| -rwxr-xr-x | bin/test-website | 114 |
3 files changed, 135 insertions, 120 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 145ce395..2a83a1cd 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -45,6 +45,7 @@ SCRIPT=$(realpath "$0") echo SCRIPT=$SCRIPT +echo GN2_PROFILE=$GN2_PROFILE GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT")) GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR) @@ -94,11 +95,13 @@ export WQFLASK_OVERRIDES=$overrides # JSON echo WQFLASK_SETTINGS=$settings echo WQFLASK_OVERRIDES=$overrides -if [ -z $ELASTICSEARCH_PROFILE ]; then - echo -e "\033[1;33mWARNING: Elastic Search profile has not been set - use ELASTICSEARCH_PROFILE\033[0m"; -else - PYTHONPATH="$PYTHONPATH${PYTHONPATH:+:}$ELASTICSEARCH_PROFILE/lib/python2.7/site-packages" -fi +# 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 $GN2_PROFILE ] ; then echo "WARNING: GN2_PROFILE has not been set - you need the environment, so I hope you know what you are doing!" export GN2_PROFILE=$(dirname $(dirname $(which genenetwork2))) @@ -125,7 +128,9 @@ else export PLINK_COMMAND="$GN2_PROFILE/bin/plink2" export PYLMM_COMMAND="$GN2_PROFILE/bin/pylmm_redis" export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma" - export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper" + if [ -z $GEMMA_WRAPPER_COMMAND ]; then + export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper" + fi while IFS=":" read -ra PPATH; do for PPart in "${PPATH[@]}"; do if [ ! -d $PPart ] ; then echo "PYTHONPATH not valid "$PYTHONPATH ; exit 1 ; fi @@ -163,8 +168,9 @@ 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 @@ -173,8 +179,9 @@ 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 @@ -198,7 +205,8 @@ if [ "$1" = '-gunicorn-prod' ] ; then cd $GN2_BASE_DIR/wqflask echo PYTHONPATH=$PYTHONPATH if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi - cmd="--bind 0.0.0.0:$SERVER_PORT --workers=32 --max-requests 1000 --timeout 1200 wsgi" + PID=$TMPDIR/gunicorn.$USER.pid + cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID -k eventlet --workers 20 --keep-alive 1200 --max-requests 1000 --timeout 1200 wsgi" echo RUNNING gunicorn $cmd gunicorn $cmd exit $? diff --git a/bin/mechnical-rob b/bin/mechnical-rob new file mode 100755 index 00000000..be223d94 --- /dev/null +++ b/bin/mechnical-rob @@ -0,0 +1,111 @@ +#!/usr/bin/env ruby + + +USAGE = <<EOT +This is Mechanical-Rob - an automated web server tester for + Genenetwork.org that uses the brilliant + mechanize gem with minitest. + +To use this software you need to install mechanize. Run it from +the root of the genenetwork2 source tree as, for example, + + ./bin/test-website http://localhost:5003/ (default) + +If you are using the small deployment database you can use + + ./bin/test-website --skip -n + +To run all tests + + ./bin/test-website --all + +To run individual tests on localhost you can do + + ruby -Itest -Itest/lib test/lib/mapping.rb --name="/Mapping/" + +For more information see http://genenetwork.org/ + +EOT +$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 |