expand stdin shortcut even when an ID is preset

Author: mr-c

cwltool/load_tool.py

@@ -207,7 +207,7 @@ def _convert_stdstreams_to_files(
                     else:
                         workflowobj["stdin"] = (
                             "$(inputs.%s.path)"
-                            % cast(str, inp["id"]).rpartition("#")[2]
+                            % cast(str, inp["id"]).rpartition("#")[2].split("/")[-1]
                         )
                         inp["type"] = "File"
         else:

tests/test_examples.py

@@ -1303,6 +1303,18 @@ def test_bad_stdout_expr_error() -> None:
     )
 
 
+def test_stdin_with_id_preset() -> None:
+    """Confirm that a type: stdin with a preset id does not give an error."""
+    error_code, _, stderr = get_main_output(
+        [
+            get_data("tests/wf/1590.cwl"),
+            "--file1",
+            get_data("tests/wf/whale.txt"),
+        ]
+    )
+    assert error_code == 0
+
+
 @needs_docker
 @pytest.mark.parametrize("factor", test_factors)
 def test_no_compute_chcksum(tmp_path: Path, factor: str) -> None:

tests/wf/1590.cwl

@@ -0,0 +1,30 @@
+{
+  "baseCommand": [
+    "cat"
+  ],
+  "class": "CommandLineTool",
+  "cwlVersion": "v1.2",
+  "id": "cat-tool-shortcut.cwl",
+  "inputs": [
+    {
+      "id": "file1",
+      "type": "stdin"
+    }
+  ],
+  "outputs": [
+    {
+      "id": "output",
+      "outputBinding": {
+        "glob": "output"
+      },
+      "type": "File"
+    }
+  ],
+  "requirements": [
+    {
+      "class": "DockerRequirement",
+      "dockerPull": "debian:stretch-slim"
+    }
+  ],
+  "stdout": "output"
+}