From 3cf1208708bd475e928b070d28580403dafa5519 Mon Sep 17 00:00:00 2001
From: Ilya Shlyakhter <ilya_shl@alum.mit.edu>
Date: Tue, 4 Dec 2018 13:07:52 -0500
Subject: [PATCH] Set timeouts for dx jobs launched from travis-ci . (#901)

Set timeouts for dx jobs launched from travis-ci.
---
 travis/tests-dx.sh | 33 +++++++++++++++++++++++++++++++--
 1 file changed, 31 insertions(+), 2 deletions(-)

diff --git a/travis/tests-dx.sh b/travis/tests-dx.sh
index 2a0c4134d..4e9c1089a 100755
--- a/travis/tests-dx.sh
+++ b/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