Set timeouts for dx jobs launched from travis-ci . (#901)

Set timeouts for dx jobs launched from travis-ci.

travis/tests-dx.sh

@@ -16,6 +16,28 @@ if [ ! -f $COMPILE_SUCCESS ]; then
  dx download --no-progress /build/$VERSION/$COMPILE_SUCCESS
 fi
 
+function dx_run_timeout_args {
+ #
+ # Construct command-line arguments for 'dx run' command
+ # to set a timeout on the applets it runs
+ #
+
+ local dx_workflow_id="$1"
+ local dx_extra_applet_id="$2"
+
+ local dx_workflow_applet_ids=$(dx describe $dx_workflow_id | grep applet- | awk '{print $2;}')
+ local dx_applet_ids="$dx_workflow_applet_ids $dx_extra_applet_id"
+ local comma=""
+ local timeout_args="{\"timeoutPolicyByExecutable\":{"
+ for dx_applet_id in $dx_applet_ids
+ do
+ timeout_args="${timeout_args}${comma}\"$dx_applet_id\":{\"*\":{\"hours\":3}}"
+ comma=","
+ done
+ timeout_args="$timeout_args}}"
+ echo $timeout_args
+}
+
 TEST_LAUNCH_ALL="dxWDL-execute_all-launched.txt"
 touch $TEST_LAUNCH_ALL
 for workflow in pipes/WDL/workflows/*.wdl; do
@@ -27,11 +49,14 @@ for workflow in pipes/WDL/workflows/*.wdl; do
  if [ -f $input_json ]; then
  # launch simple test cases on DNAnexus CI project
  dx_workflow_id=$(grep -w "^$workflow_name" $COMPILE_SUCCESS | cut -f 2)
+ timeout_args=$(dx_run_timeout_args $dx_workflow_id)
  dx_job_id=$(dx run \
  $dx_workflow_id -y --brief \
  -f $input_json \
  --name "$VERSION $workflow_name" \
- --destination /tests/$VERSION/$workflow_name)
+ --destination /tests/$VERSION/$workflow_name \
+ --extra-args $timeout_args \
+ )
  if [ $? -eq 0 ]; then
  echo "Launched $workflow_name as $dx_job_id"
  else
@@ -46,11 +71,15 @@ done
 # Special case: run test for the demux_launcher native applet (which invokes
 # the demux_plus WDL workflow)
 demux_launcher_id=$(grep demux_launcher $COMPILE_SUCCESS | cut -f 2)
+demux_plus_workflow_id=$(grep demux_plus $COMPILE_SUCCESS | cut -f 2)
+timeout_args=$(dx_run_timeout_args $demux_plus_workflow_id $demux_launcher_id)
 dx_job_id=$(dx run \
  $demux_launcher_id -y --brief \
  -i upload_sentinel_record=record-Bv8qkgQ0jy198GK0QVz2PV8Y \
  --name "$VERSION demux_launcher" \
- -i folder=/tests/$VERSION/demux_launcher)
+ -i folder=/tests/$VERSION/demux_launcher \
+ --extra-args $timeout_args \
+ )
 echo "Launched demux_launcher as $dx_job_id"
 echo -e "demux_launcher\t$demux_launcher_id\t$dx_job_id" >> $TEST_LAUNCH_ALL