testBrowser

#!/bin/bash
set -bEu -o pipefail

# Christopher Lee
# "smoke tests" a gbib or gbic Genome Browser with a Selenium Script
# If gbic option is passed, installs a Genome Browser mirror and
#    runs a Selenium script against it

# Global vars
pyloc="/Library/Frameworks/Python.framework/Versions/3.5/bin/python3.5"
machine=""
machines=""
loc=""
urlStub="http://127.0.0.1:808"
urlList=()

function testUrl ()
{
   curl $1 &> /dev/null
}

# runs vagrant commands to setup all or specific machines
function setupVMs () 
{
   if [ $machine == "all" ]; then
      vagrant up # with no machine name this starts all machines defined in Vagrantfile
      for num in 0 1 2 3; do
          urlList[${num}]="${urlStub}${num}"
      done
      echo ${urlList[@]}
   elif [ $machine == "ubuntu" ]; then
      vagrant up ubuntu14
      vagrant up ubuntu16
      urlList=("${urlStub}0" "${urlStub}1")
      echo ${urlList[@]}
   elif [ $machine == "centos" ]; then
      vagrant up centos6
      vagrant up centos7
      urlList=("${urlStub}2" "${urlStub}3")
      echo ${urlList[@]}
   fi
}

# installs Genome Browser on specific machine
function installBrowser () 
{
# this works because browserSetup.sh is already present on the machine
# via sync defined in the Vagrantfile
   if [ $machine == "all" ]; then
      machines=("ubuntu14" "ubuntu16" "centos6" "centos7")
      for mach in "${machines[@]}"; do
         vagrant ssh $mach -- sudo bash browserSetup.sh -b install
      done
   elif [ $machine == "ubuntu" ]; then
      machines=("ubuntu14" "ubuntu16")
      for mach in "${machines[@]}"; do
         vagrant ssh $mach -- sudo bash browserSetup.sh -b install
      done
   elif [ $machine == "centos" ]; then
      machines=("centos6" "centos7")
      for mach in "${machines[@]}"; do
         vagrant ssh $mach -- sudo bash browserSetup.sh -b install
      done
   fi
}

function tearDownVMs () 
{
   vagrant destroy -f 
}

function mirrorOffline ()
{
   vagrant ssh $mach -- sudo bash browserSetup.sh -o
}

function testOfflineMirror ()
{
   # put in some offline specific testing, like making sure nothing loads when no assembly mirrored
   # after mirroring a small assembly, click into hgTracks
   # This test will take significantly longer since an assembly will be mirrored
   echo "Testing an offline mirror. These tests can take a while"
   echo ${machines[@]}
   exit 0
}

function gbibOffline ()
{
   sshpass -f .gbibpassword ssh browser@localhost -p 1235 "bash -ic gbibOffline" 2>&1 | grep -v "bash"
}

function gbibOnline ()
{
   sshpass -f .gbibpassword ssh browser@localhost -p 1235 "bash -ic gbibOnline" 2>&1 | grep -v "bash"
}

function testOfflineGbib ()
{
   # test mirroring a track
   # run a show tables hg19 and look for altLocations to be null
   # go to hgTracks and make sure no altLocations track
   # use hgMirror to download altLocations
   # altLocations should show up for hgTracks chr17
   tbl=`sshpass -f .gbibpassword ssh browser@localhost -p 1235 'mysql -Ne "show tables \
      like \"altLocations\"" hg19' 2>&1`
   if [[ "$tbl" =~ altLocations ]]; then
      # altLocations already exists abort
      echo "this gbib already contains downloaded tables, try again"
      exit 1
   else
      $pyloc genomeTest.py http://127.0.0.1:1234 offline
      if [ $? -eq 0 ]; then
         echo "selenium offline tests ran correctly"
         tbl=`sshpass -f .gbibpassword ssh browser@localhost -p 1235 'mysql -Ne "show tables \
            like \"altLocations\"" hg19' 2>&1`
         if [[ "$tbl" =~ altLocations ]]; then
            echo "altLocations table successfully downloaded, removing so test can be rerun if needed"
            sshpass -f .gbibpassword ssh browser@localhost -p 1235 'mysql -e "drop table altLocations" hg19' 2>&1
         fi
      else
         echo "selenium offline test didn't run successfully"      
         exit 1
      fi
   fi
}

function shutDownGbib ()
{
   if [[ $(VBoxManage list runningvms) =~ browserbox ]]; then
      echo "shutting off gbib because of ctrl-c"
      VBoxManage controlvm browserbox poweroff
      exit 1
   fi
}

function showHelp ()
{
   cat << EOF
Usage: $0 [-h] -w [gbic|gbib] -m [ubuntu|centos|all]

   -h          Show this help and exit
   -w website  Test which instance of the Genome Browser we are testing.
               gbib uses the url http://127.0.0.1:1234
               gbic uses the -m parameter to find url
   -m machine  Which machine to test. By default tests all machines:
                  Ubuntu 14/16
                  Centos 6/7
               If "ubuntu" or "centos" is given we test both machines of that type.
               Only applicable if -w gbic is supplied.

Performs basic automated test of Genome Browser instance:
   Loads hgTracks and click into hgGene for Human and Mouse.
   Loads an hg19 custom track and checks that hgTracks loads.
   Loads a track hub and checks that hgTracks loads.
   Runs a blat against hg19.
   Runs an isPCR against hg19.
   Tests hgConvert and hgLiftOver.

These tests should run reasonably quickly so you can watch that they are running
and completing correcly.
EOF
}

# parse command line
OPTIND=1
while getopts "hw:m:" opt
do 
   case $opt in
      h)
         showHelp
         exit 0
         ;;
      w)
         loc=$OPTARG
         ;;
      m)
         machine=$OPTARG
         ;;
      '?')
         showHelp >&2
         exit 1
         ;;
   esac
done

if [ $OPTIND -eq 1 ]; then
   showHelp >&2
   exit 1
fi

### MAIN ###

# parse command line for errors and set machines var
if [ "$loc" != "gbib" -a "$loc" != "gbic" ]; then
   echo "Wrong -w option. Please use either \"gbib\" or \"gbic\"."
   showHelp >&2
   exit 1
fi

if [ "$loc" == "gbic" -a "$machine" != "ubuntu" -a "$machine" != "centos" -a "$machine" != "all" ]; then
      echo "Wrong machine name specified. Please use either \"all\" \"ubuntu\" or \"centos\"."
      showHelp >&2
      exit 1
fi 

if [ $loc == "gbib" ]; then
   # gbib already on for some other purpose
   testUrl "http://127.0.0.1:1234"
   if [ $? -eq 0 ]; then
      echo "gbib already running, starting tests"
      # first make sure we can run online test:
      gbibOnline
      $pyloc genomeTest.py http://127.0.0.1:1234
      gbibOffline
      testOfflineGbib
      gbibOnline
      # if gbib was already on we shouldn't turn it off
      #VBoxManage controlvm browserbox poweroff
   else
      trap shutDownGbib SIGINT
      # gbib is powered off
      if [[ $(VBoxManage list vms) =~ browserbox ]]; then
         echo "starting up gbib"
         VBoxManage guestproperty set browserbox gbibAutoUpdateOff yes 
         VBoxManage startvm browserbox --type=headless
      else # fresh gbib download
         echo "Test of newly downloaded gbib"
         wget http://hgwdev.soe.ucsc.edu/gbib/gbib.zip 
         ditto -xk `pwd`/gbib.zip gbib
         VBoxManage registervm `pwd`/gbib/browserbox.vbox
         VBoxManage sharedfolder add "browserbox" --name "testHub" --hostpath "`pwd`/testHub" --readonly --automount
         VBoxManage guestproperty set browserbox gbibAutoUpdateOff yes 
         VBoxManage startvm browserbox --type=headless
      fi
      while true; do
         # just wait for gbib to get running
         testUrl http://127.0.0.1:1234
         if [ $? -eq 0 ]; then
            $pyloc genomeTest.py http://127.0.0.1:1234
            # offline testing stub
            # run a show tables hg19 and look for altLocations to be null
            # go to hgTracks and make sure no altLocations track
            # use hgMirror to download altLocations
            # altLocations should show up for hgTracks chr17
            gbibOffline
            testOfflineGbib
            gbibOnline
            VBoxManage controlvm browserbox poweroff
            break
         fi
      done
   fi
   exit 0
elif [ $loc == "gbic" ]; then # currently for testing purposes
   trap tearDownVMs SIGINT
   setupVMs
   installBrowser 
   if [ $? -eq 0 ]; then # browser install didn't fail
      for url in "${urlList[@]}"; do
         testUrl $url
         if [ $? -eq 0 ]; then
            $pyloc genomeTest.py $url
            # offline testing stub
            echo
         else
            echo "$url does not have a browser installed yet. Install one first"
            exit 1
         fi
      done
   else
      echo "install failed. login to VM and run install with bash -x to see what happened"
      exit 1
   fi
fi