17801: Handle glob capture of keep URI with a trailing slash

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 1e339d5bb7d4ab20f90438ed5670f3d67d51e548..4da8f855692aed44f212739d5e515af3fef2ceb0 100644 (file)
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -129,7 +129,7 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
 
     def glob(self, pattern):
         collection, rest = self.get_collection(pattern)
-        if collection is not None and not rest:
+        if collection is not None and rest in (None, "", "."):
             return [pattern]
         patternsegments = rest.split("/")
         return sorted(self._match(collection, patternsegments, "keep:" + collection.manifest_locator()))

diff --git a/sdk/cwl/tests/17801-runtime-outdir.cwl b/sdk/cwl/tests/17801-runtime-outdir.cwl
new file mode 100644 (file)
index 0000000..c01ef05
--- /dev/null
+++ b/sdk/cwl/tests/17801-runtime-outdir.cwl
@@ -0,0 +1,15 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+cwlVersion: v1.2
+class: CommandLineTool
+inputs: []
+outputs:
+  stuff:
+    type: Directory
+    outputBinding:
+      glob: $(runtime.outdir)
+requirements:
+  ShellCommandRequirement: {}
+arguments: [{shellQuote: false, valueFrom: "mkdir -p foo && touch baz.txt && touch foo/bar.txt"}]

diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index 41feb7796baf4301af1bb6316952c3c3020f1b45..b22c9aaa27684084ef088f95f119badf1d04e598 100644 (file)
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -393,3 +393,37 @@
   }
   tool: 10380-trailing-slash-dir.cwl
   doc: "Test issue 10380 - bug with trailing slash when capturing an output directory"
+
+- job: null
+  output: {
+    "stuff": {
+        "basename": "78f3957c41d044352303a3fa326dff1e+102",
+        "class": "Directory",
+        "listing": [
+            {
+                "basename": "baz.txt",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "class": "File",
+                "location": "78f3957c41d044352303a3fa326dff1e+102/baz.txt",
+                "size": 0
+            },
+            {
+                "basename": "foo",
+                "class": "Directory",
+                "listing": [
+                    {
+                        "basename": "bar.txt",
+                        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                        "class": "File",
+                        "location": "78f3957c41d044352303a3fa326dff1e+102/foo/bar.txt",
+                        "size": 0
+                    }
+                ],
+                "location": "78f3957c41d044352303a3fa326dff1e+102/foo"
+            }
+        ],
+        "location": "78f3957c41d044352303a3fa326dff1e+102"
+    }
+  }
+  tool: 17801-runtime-outdir.cwl
+  doc: "Test issue 17801 - bug using $(runtime.outdir) to capture the output directory"