Centaur reference image test should validate symlinks [VS-796] (#6996)

broadinstitute · Feb 9, 2023 · 1795391 · 1795391
1 parent 417adfa
commit 1795391
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Showing 5 changed files with 40 additions and 25 deletions.
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
@@ -1,26 +1,38 @@
 version 1.0
 
-task check_if_localized_as_symlink {
+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_symlink = "broad_input_symlink.txt"
-  String nirvana_input_symlink = "nirvana_input_symlink.txt"
-  String nirvana_metachar_input_symlink = "nirvana_metachar_input_symlink.txt"
-  command {
-    # Print true if input is a symlink, otherwise print false.
-    if test -h ~{broad_reference_file_input}; then echo true; else echo false; fi > ~{broad_input_symlink}
-    if test -h ~{nirvana_reference_file_input}; then echo true; else echo false; fi > ~{nirvana_input_symlink}
+  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
 
-    # Quotes added here due to the metachar in the filename.
-    if test -h "~{nirvana_reference_file_metachar_input}"; then echo true; else echo false; fi > ~{nirvana_metachar_input_symlink}
-  }
+      # 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_symlink = read_boolean("~{broad_input_symlink}")
-    Boolean is_nirvana_input_symlink = read_boolean("~{nirvana_input_symlink}")
-    Boolean is_nirvana_metachar_input_symlink = read_boolean("~{nirvana_metachar_input_symlink}")
+    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"
@@ -34,15 +46,15 @@ workflow wf_reference_disk_test {
     File nirvana_reference_file_input
     File nirvana_reference_file_metachar_input
   }
-  call check_if_localized_as_symlink {
+  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_symlink = check_if_localized_as_symlink.is_broad_input_symlink
-    Boolean is_nirvana_input_file_a_symlink = check_if_localized_as_symlink.is_nirvana_input_symlink
-    Boolean is_nirvana_metachar_input_file_a_symlink = check_if_localized_as_symlink.is_nirvana_metachar_input_symlink
+    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
   }
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
@@ -11,6 +11,7 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": false
-  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": false
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
@@ -11,6 +11,7 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": true
-  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": true
+  "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
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
@@ -11,6 +11,7 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": false
-  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": false
 }
diff --git a/src/ci/resources/papi_v2_reference_image_manifest.conf b/src/ci/resources/papi_v2_reference_image_manifest.conf
@@ -192,7 +192,7 @@ reference-disk-localization-manifests = [
     ]
   },
   {
-    "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/nirvana-3-18-1-references-2023-01-03",
+    "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/nirvana-3-18-1-references-2023-02-01",
     "diskSizeGb" : 55,
     "files" : [ {
       "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd",