Support more methods of WDL task disk specification

src/toil/provisioners/node.py

@@ -13,7 +13,7 @@
 # limitations under the License.
 import datetime
 import logging
-import shlex
+from shlex import quote
 import socket
 import subprocess
 import time
@@ -279,7 +279,7 @@ def coreSSH(self, *args, **kwargs):
             commandTokens += ['docker', 'exec', '-i', ttyFlag, 'toil_leader']
 
         logger.debug('Node %s: %s', self.effectiveIP, ' '.join(args))
-        args = list(map(shlex.quote, args))
+        args = list(map(quote, args))
         commandTokens += args
         logger.debug('Full command %s', ' '.join(commandTokens))
         process = subprocess.Popen(commandTokens, **kwargs)

src/toil/test/wdl/md5sum/md5sum.1.0.wdl

@@ -4,16 +4,17 @@ task md5 {
   input {
     File inputFile
   }
-  command {
-    /bin/my_md5sum ${inputFile}
-  }
+  command <<<
+    set -euf -o pipefail
+    md5sum ~{inputFile} | awk '{print $1}' > md5sum.txt
+  >>>
 
  output {
     File value = "md5sum.txt"
  }
 
  runtime {
-   docker: "quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4"
+   docker: "ubuntu:22.04"
    cpu: 1
    memory: "512 MB"
    disks: "local-disk 10 HDD"

src/toil/test/wdl/wdltoil_test.py

@@ -24,7 +24,7 @@
                        needs_wdl,
                        slow, integrative)
 from toil.version import exactPython
-from toil.wdl.wdltoil import WDLSectionJob, WDLWorkflowGraph, remove_common_leading_whitespace
+from toil.wdl.wdltoil import WDLSectionJob, WDLWorkflowGraph, remove_common_leading_whitespace, parse_disks
 
 import WDL.Expr
 import WDL.Error
@@ -733,6 +733,42 @@ def test_uri_packing(self):
 
         self.assertEqual(unpacked[3], file_basename)
 
+    def test_disk_parse(self):
+        """
+        Test to make sure the disk parsing is correct
+        """
+        # Test cromwell compatibility
+        spec = "local-disk 5 SSD"
+        specified_mount_point, part_size, part_suffix = parse_disks(spec, spec)
+        self.assertEqual(specified_mount_point, None)
+        self.assertEqual(part_size, 5)
+        self.assertEqual(part_suffix, "GB")
+
+        # Test spec conformance
+        # https://github.com/openwdl/wdl/blob/e43e042104b728df1f1ad6e6145945d2b32331a6/SPEC.md?plain=1#L5072-L5082
+        spec = "10"
+        specified_mount_point, part_size, part_suffix = parse_disks(spec, spec)
+        self.assertEqual(specified_mount_point, None)
+        self.assertEqual(part_size, 10)
+        self.assertEqual(part_suffix, "GiB")  # WDL spec default
+
+        spec = "1 MB"
+        specified_mount_point, part_size, part_suffix = parse_disks(spec, spec)
+        self.assertEqual(specified_mount_point, None)
+        self.assertEqual(part_size, 1)
+        self.assertEqual(part_suffix, "MB")
+
+        spec = "MOUNT_POINT 3"
+        specified_mount_point, part_size, part_suffix = parse_disks(spec, spec)
+        self.assertEqual(specified_mount_point, "MOUNT_POINT")
+        self.assertEqual(part_size, 3)
+        self.assertEqual(part_suffix, "GiB")
+
+        spec = "MOUNT_POINT 2 MB"
+        specified_mount_point, part_size, part_suffix = parse_disks(spec, spec)
+        self.assertEqual(specified_mount_point, "MOUNT_POINT")
+        self.assertEqual(part_size, 2)
+        self.assertEqual(part_suffix, "MB")
 
 
 if __name__ == "__main__":