Only mount reference disks if requested [WX-925]

centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_mounted_only_if_requested.wdl

@@ -0,0 +1,49 @@
+version 1.0
+
+
+workflow ReferenceDiskMountedOnlyIfRequested {
+    call MentionsNirvanaReference {}
+    output {
+        Boolean disk_mounted = MentionsNirvanaReference.disk_mounted
+    }
+}
+
+
+task MentionsNirvanaReference {
+    input {
+        # Tiny 116 byte reference file, certainly not worth attaching a 55 GiB Nirvana reference disk for this.
+        File mention =
+            "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx"
+    }
+    command <<<
+        PS4='\D{+%F %T} \w $ '
+        set -o nounset -o xtrace
+
+        # Debug output
+        lsblk
+
+        CANDIDATE_MOUNT_POINT=$(lsblk | sed -E -n 's!.*(/mnt/[a-f0-9]+).*!\1!p')
+
+        if [[ ! -z ${CANDIDATE_MOUNT_POINT} ]]; then
+            echo "Found unexpected mounted disk, investigating further."
+            find ${CANDIDATE_MOUNT_POINT} -print | tee find.out
+
+            if grep -i nirvana find.out; then
+                echo "Found what appears to be a Nirvana reference disk."
+            else
+                echo "Found unknown volume mounted, see 'find.out' for manifest."
+            fi
+            echo true > disk_mounted.out
+        else
+            echo false > disk_mounted.out
+        fi
+    >>>
+    runtime {
+        docker: "ubuntu:latest"
+        backend: "Papiv2-Reference-Disk-Localization"
+    }
+    output {
+        Boolean disk_mounted = read_boolean("disk_mounted.out")
+        File? find_out = "find.out"
+    }
+}

centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_false.test

@@ -0,0 +1,14 @@
+name: reference_disk_mounted_only_if_requested_false
+testFormat: workflowsuccess
+backends: [Papiv2-Reference-Disk-Localization]
+
+files {
+  workflow: reference_disk/reference_disk_mounted_only_if_requested.wdl
+  options: reference_disk/reference_disk_test_false.options.json
+}
+
+metadata {
+  workflowName: ReferenceDiskMountedOnlyIfRequested
+  status: Succeeded
+  "outputs.ReferenceDiskMountedOnlyIfRequested.disk_mounted": false
+}

centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_true.test

@@ -0,0 +1,14 @@
+name: reference_disk_mounted_only_if_requested_true
+testFormat: workflowsuccess
+backends: [Papiv2-Reference-Disk-Localization]
+
+files {
+  workflow: reference_disk/reference_disk_mounted_only_if_requested.wdl
+  options: reference_disk/reference_disk_test_true.options.json
+}
+
+metadata {
+  workflowName: ReferenceDiskMountedOnlyIfRequested
+  status: Succeeded
+  "outputs.ReferenceDiskMountedOnlyIfRequested.disk_mounted": true
+}

centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_unspecified.test

@@ -0,0 +1,14 @@
+name: reference_disk_mounted_only_if_requested_unspecified
+testFormat: workflowsuccess
+backends: [Papiv2-Reference-Disk-Localization]
+
+files {
+  workflow: reference_disk/reference_disk_mounted_only_if_requested.wdl
+  options: reference_disk/reference_disk_test_unspecified.options.json
+}
+
+metadata {
+  workflowName: ReferenceDiskMountedOnlyIfRequested
+  status: Succeeded
+  "outputs.ReferenceDiskMountedOnlyIfRequested.disk_mounted": false
+}

supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala

@@ -452,7 +452,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
 
         val inputFilePaths = inputOutputParameters.jobInputParameters.map(_.cloudPath.pathAsString).toSet
         val referenceDisksToMount =
-          jesAttributes.referenceFileToDiskImageMappingOpt.map(getReferenceDisksToMount(_, inputFilePaths))
+          if (useReferenceDisks)
+            jesAttributes.referenceFileToDiskImageMappingOpt.map(getReferenceDisksToMount(_, inputFilePaths))
+          else None
 
         val workflowOptions = workflowDescriptor.workflowOptions