Reference disks in GCP Batch [WX-1819]

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

@@ -0,0 +1,17 @@
+name: gcpbatch_reference_disk_test_true_option
+testFormat: workflowsuccess
+backends: [GCPBATCH-Reference-Disk-Localization]
+
+files {
+  workflow: reference_disk/gcpbatch/reference_disk_test.wdl
+  inputs: reference_disk/reference_disk_test.inputs
+  options: reference_disk/reference_disk_test_true.options.json
+}
+
+metadata {
+  workflowName: wf_reference_disk_test
+  status: Succeeded
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": true
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": true
+  "outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": true
+}

centaur/src/main/resources/standardTestCases/reference_disk/gcpbatch/reference_disk_test.wdl

@@ -0,0 +1,60 @@
+version 1.0
+
+task check_if_localized_with_valid_symlink {
+  input {
+    File broad_reference_file_input
+    File nirvana_reference_file_input
+    File nirvana_reference_file_metachar_input
+  }
+  String broad_input_valid_symlink = "broad_input_valid_symlink.txt"
+  String nirvana_input_valid_symlink = "nirvana_input_valid_symlink.txt"
+  String nirvana_metachar_input_valid_symlink = "nirvana_metachar_input_valid_symlink.txt"
+  command <<<
+      PS4='\D{+%F %T} \w $ '
+      set -o nounset -o pipefail -o xtrace
+
+      # Echo true to stdout if the argument is a symlink pointing to an extant file, otherwise echo false.
+      check_if_valid_symlink() {
+          local reference_input="$1"
+
+          if [[ -h "${reference_input}" && -f $(readlink "${reference_input}") ]]; then
+              echo true
+          else
+              echo false
+          fi
+      }
+
+      check_if_valid_symlink "~{broad_reference_file_input}" > ~{broad_input_valid_symlink}
+      check_if_valid_symlink "~{nirvana_reference_file_input}" > ~{nirvana_input_valid_symlink}
+      check_if_valid_symlink "~{nirvana_reference_file_metachar_input}" > ~{nirvana_metachar_input_valid_symlink}
+
+  >>>
+  output {
+    Boolean is_broad_input_valid_symlink = read_boolean("~{broad_input_valid_symlink}")
+    Boolean is_nirvana_input_valid_symlink = read_boolean("~{nirvana_input_valid_symlink}")
+    Boolean is_nirvana_metachar_input_valid_symlink = read_boolean("~{nirvana_metachar_input_valid_symlink}")
+  }
+  runtime {
+    docker: "ubuntu:latest"
+    backend: "GCPBATCH-Reference-Disk-Localization"
+  }
+}
+
+workflow wf_reference_disk_test {
+  input {
+    File broad_reference_file_input
+    File nirvana_reference_file_input
+    File nirvana_reference_file_metachar_input
+  }
+  call check_if_localized_with_valid_symlink {
+    input:
+      broad_reference_file_input = broad_reference_file_input,
+      nirvana_reference_file_input = nirvana_reference_file_input,
+      nirvana_reference_file_metachar_input = nirvana_reference_file_metachar_input
+  }
+  output {
+    Boolean is_broad_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_broad_input_valid_symlink
+    Boolean is_nirvana_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_nirvana_input_valid_symlink
+    Boolean is_nirvana_metachar_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_nirvana_metachar_input_valid_symlink
+  }
+}

src/ci/resources/gcp_batch_application.conf

@@ -8,5 +8,11 @@ backend {
         include "gcp_batch_provider_config.inc.conf"
       }
     }
+    GCPBATCH-Reference-Disk-Localization {
+      actor-factory = "cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory"
+      config {
+        include "gcp_batch_provider_config.inc.conf"
+      }
+    }
   }
 }

src/ci/resources/gcp_batch_shared_application.inc.conf

@@ -12,7 +12,7 @@ services {
 
 backend {
   default = "GCPBATCH"
-  enabled = ["GCPBATCH"]
+  enabled = ["GCPBATCH", "GCPBATCH-Reference-Disk-Localization"]
   providers {
     # Default gcp batch backend
     GCPBATCH {
@@ -30,5 +30,23 @@ backend {
         filesystems.http {}
       }
     }
+    GCPBATCH-Reference-Disk-Localization {
+      actor-factory = "cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory"
+      config {
+        # When importing: Remember to also include an appropriate provider_config.inc.conf here.
+
+        # TODO: Should not need because already included.  testing.
+        include "gcp_batch_provider_config.inc.conf"
+
+        include "dockerhub_provider_config_v2.inc.conf"
+        # This SA does not have permission to bill this project when accessing RP buckets.
+        # This is on purpose so that we can assert the failure (see requester_pays_localization_negative)
+        batch.compute-service-account = "centaur@broad-dsde-cromwell-dev.iam.gserviceaccount.com"
+        filesystems.http {}
+
+        # Cromwell 57+ reference disk manifest specification included here.
+        include "papi_v2_reference_image_manifest.conf"
+      }
+    }
   }
 }