jenkins/run-cwl-test.sh

   1 #!/bin/bash
   2
   3 set -o pipefail
   4
   5 DEBUG=0
   6 SSH_PORT=22
   7 ACCT=ci
   8
   9 function usage {
  10     echo >&2
  11     echo >&2 "usage: $0 [options] <identifier>"
  12     echo >&2
  13     echo >&2 "   <identifier>                 Arvados cluster name"
  14     echo >&2
  15     echo >&2 "$0 options:"
  16     echo >&2 "  -p, --port <ssh port>         SSH port to use (default 22)"
  17     echo >&2 "      --acct <username>         Account to log in with"
  18     echo >&2 "  -d, --debug                   Enable debug output"
  19     echo >&2 "  -h, --help                    Display this help and exit"
  20     echo >&2
  21     echo >&2 " Required scope for the token used to run the tests:"
  22     echo >&2
  23     echo >&2 " arv api_client_authorization create_system_auth     --scopes "
  24     echo >&2 "[\"GET /arvados/v1/virtual_machines\","
  25     echo >&2 "\"GET /arvados/v1/keep_services\","
  26     echo >&2 "\"GET /arvados/v1/keep_services/\","
  27     echo >&2 "\"GET /arvados/v1/groups\","
  28     echo >&2 "\"GET /arvados/v1/groups/\","
  29     echo >&2 "\"GET /arvados/v1/links\","
  30     echo >&2 "\"GET /arvados/v1/collections\","
  31     echo >&2 "\"POST /arvados/v1/collections\","
  32     echo >&2 "\"POST /arvados/v1/links\","
  33     echo >&2 "\"GET /arvados/v1/users/current\","
  34     echo >&2 "\"POST /arvados/v1/users/current\","
  35     echo >&2 "\"GET /arvados/v1/jobs\","
  36     echo >&2 "\"POST /arvados/v1/jobs\","
  37     echo >&2 "\"GET /arvados/v1/pipeline_instances\","
  38     echo >&2 "\"GET /arvados/v1/pipeline_instances/\","
  39     echo >&2 "\"POST /arvados/v1/pipeline_instances\","
  40     echo >&2 "\"GET /arvados/v1/collections/\","
  41     echo >&2 "\"POST /arvados/v1/collections/\","
  42     echo >&2 "\"GET /arvados/v1/container_requests\","
  43     echo >&2 "\"GET /arvados/v1/container_requests/\","
  44     echo >&2 "\"POST /arvados/v1/container_requests\","
  45     echo >&2 "\"POST /arvados/v1/container_requests/\","
  46     echo >&2 "\"GET /arvados/v1/containers\","
  47     echo >&2 "\"GET /arvados/v1/containers/\","
  48     echo >&2 "\"GET /arvados/v1/logs\" ]"
  49     echo >&2
  50 }
  51
  52 # NOTE: This requires GNU getopt (part of the util-linux package on Debian-based distros).
  53 TEMP=`getopt -o hdp: \
  54     --long help,debug,port:,acct: \
  55     -n "$0" -- "$@"`
  56
  57 if [ $? != 0 ] ; then echo "Use -h for help"; exit 1 ; fi
  58 # Note the quotes around `$TEMP': they are essential!
  59 eval set -- "$TEMP"
  60
  61 while [ $# -ge 1 ]
  62 do
  63     case $1 in
  64         -p | --port)
  65             SSH_PORT="$2"; shift 2
  66             ;;
  67         --acct)
  68             ACCT="$2"; shift 2
  69             ;;
  70         -d | --debug)
  71             DEBUG=1
  72             shift
  73             ;;
  74         --)
  75             shift
  76             break
  77             ;;
  78         *)
  79             usage
  80             exit 1
  81             ;;
  82     esac
  83 done
  84
  85 IDENTIFIER=$1
  86
  87 if [[ "$IDENTIFIER" == '' ]]; then
  88   usage
  89   exit 1
  90 fi
  91
  92 EXITCODE=0
  93
  94 COLUMNS=80
  95
  96 PUPPET_AGENT='
  97 now() { date +%s; }
  98 let endtime="$(now) + 600"
  99 while [ "$endtime" -gt "$(now)" ]; do
 100     puppet agent --test --detailed-exitcodes
 101     agent_exitcode=$?
 102     if [ 0 = "$agent_exitcode" ] || [ 2 = "$agent_exitcode" ]; then
 103         break
 104     else
 105         sleep 10s
 106     fi
 107 done
 108 exit ${agent_exitcode:-99}
 109 '
 110
 111 title () {
 112   date=`date +'%Y-%m-%d %H:%M:%S'`
 113   printf "%s\n" "$date $1"
 114 }
 115
 116 function run_command() {
 117   node=$1
 118   return_var=$2
 119   command=$3
 120
 121   title "Running '${command/ARVADOS_API_TOKEN=*/ARVADOS_API_TOKEN=suppressed}' on $node"
 122   TMP_FILE=`mktemp`
 123   if [[ "$DEBUG" != "0" ]]; then
 124     ssh -t -p$SSH_PORT -o "StrictHostKeyChecking no" -o "ConnectTimeout 125" $ACCT@$node -C "$command" | tee $TMP_FILE
 125     ECODE=$?
 126   else
 127     ssh -t -p$SSH_PORT -o "StrictHostKeyChecking no" -o "ConnectTimeout 125" $ACCT@$node -C "$command" > $TMP_FILE 2>&1
 128     ECODE=$?
 129   fi
 130
 131   if [[ "$ECODE" != "255" && "$ECODE" != "0"  ]]; then
 132     # Ssh exists 255 if the connection timed out. Just ignore that, it's possible that this node is
 133     #   a shell node that is down.
 134     title "ERROR running command on $node: exit code $ECODE"
 135     if [[ "$DEBUG" == "0" ]]; then
 136       title "Command output follows:"
 137       cat $TMP_FILE
 138     fi
 139   fi
 140   if [[ "$ECODE" == "255" ]]; then
 141     title "Connection denied or timed out"
 142   fi
 143   rm -f $TMP_FILE
 144   eval "$return_var=$ECODE"
 145 }
 146
 147 title "Loading ARVADOS_API_HOST and ARVADOS_API_TOKEN"
 148 if [[ -f "$HOME/.config/arvados/$IDENTIFIER.arvadosapi.com.conf" ]]; then
 149   . $HOME/.config/arvados/$IDENTIFIER.arvadosapi.com.conf
 150 else
 151   title "WARNING: $HOME/.config/arvados/$IDENTIFIER.arvadosapi.com.conf not found."
 152 fi
 153 if [[ "$ARVADOS_API_HOST" == "" ]] || [[ "$ARVADOS_API_TOKEN" == "" ]]; then
 154   title "ERROR: ARVADOS_API_HOST and/or ARVADOS_API_TOKEN environment variables are not set."
 155   exit 1
 156 fi
 157
 158 run_command shell.$IDENTIFIER ECODE "if [[ ! -e common-workflow-language ]]; then git clone https://github.com/common-workflow-language/common-workflow-language.git; fi"
 159
 160 if [[ "$ECODE" != "0" ]]; then
 161   echo "Failed to git clone https://github.com/common-workflow-language/common-workflow-language.git"
 162   exit $ECODE
 163 fi
 164
 165 run_command shell.$IDENTIFIER ECODE "if [[ ! -e arvados-cwl-runner-with-checksum.sh ]]; then printf \"%s\n%s\n\" '#!/bin/sh' 'exec arvados-cwl-runner --compute-checksum \"\$@\"' > arvados-cwl-runner-with-checksum.sh; chmod 755 arvados-cwl-runner-with-checksum.sh; fi"
 166
 167 if [[ "$ECODE" != "0" ]]; then
 168   echo "Failed to create ~$ACCT/arvados-cwl-runner-with-checksum.sh"
 169   exit $ECODE
 170 fi
 171
 172 run_command shell.$IDENTIFIER ECODE "cd common-workflow-language; git pull; ARVADOS_API_HOST=$ARVADOS_API_HOST ARVADOS_API_TOKEN=$ARVADOS_API_TOKEN ./run_test.sh RUNNER=/home/$ACCT/arvados-cwl-runner-with-checksum.sh "
 173
 174 exit $ECODE