Shell escape reference image files [VS-796] [WX-910]

centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs

@@ -1,4 +1,5 @@
 {
   "wf_reference_disk_test.broad_reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
-  "wf_reference_disk_test.nirvana_reference_file_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx"
+  "wf_reference_disk_test.nirvana_reference_file_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx",
+  "wf_reference_disk_test.nirvana_reference_file_metachar_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_(SV)_Phase_3_v5a.nsi"
 }

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

@@ -4,17 +4,23 @@ task check_if_localized_as_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}
+
+    # 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}
   }
   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}")
   }
   runtime {
     docker: "ubuntu:latest"
@@ -26,14 +32,17 @@ 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_as_symlink {
     input:
       broad_reference_file_input = broad_reference_file_input,
-      nirvana_reference_file_input = nirvana_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
   }
 }

supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala

@@ -179,11 +179,12 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
                                            (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
     // Generate a mapping of reference inputs to their mounted paths and a section of the localization script to
     // "faux localize" these reference inputs with symlinks to their locations on mounted reference disks.
+    import cromwell.backend.google.pipelines.common.action.ActionUtils.shellEscaped
     val referenceFilesLocalizationScript = {
       val symlinkCreationCommandsOpt = referenceInputsToMountedPathsOpt map { referenceInputsToMountedPaths =>
         referenceInputsToMountedPaths map {
           case (input, absolutePathOnRefDisk) =>
-            s"mkdir -p ${input.containerPath.parent.pathAsString} && ln -s $absolutePathOnRefDisk ${input.containerPath.pathAsString}"
+            s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(absolutePathOnRefDisk)} ${shellEscaped(input.containerPath.pathAsString)}"
         }
       }
 

supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala

@@ -192,11 +192,12 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
                                            (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
     // Generate a mapping of reference inputs to their mounted paths and a section of the localization script to
     // "faux localize" these reference inputs with symlinks to their locations on mounted reference disks.
+    import cromwell.backend.google.pipelines.common.action.ActionUtils.shellEscaped
     val referenceFilesLocalizationScript = {
       val symlinkCreationCommandsOpt = referenceInputsToMountedPathsOpt map { referenceInputsToMountedPaths =>
         referenceInputsToMountedPaths map {
           case (input, absolutePathOnRefDisk) =>
-            s"mkdir -p ${input.containerPath.parent.pathAsString} && ln -s $absolutePathOnRefDisk ${input.containerPath.pathAsString}"
+            s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(absolutePathOnRefDisk)} ${shellEscaped(input.containerPath.pathAsString)}"
         }
       }