--print-targets: support embedded step processess

Author: mr-c

cwltool/main.py

@@ -929,9 +929,11 @@ def print_targets(
         _logger.info("%s steps targets:", prefix[:-1])
         for t in tool.tool["steps"]:
             stdout.write(f"  {prefix}{shortname(t['id'])}\n")
-            run: Union[str, Process] = t["run"]
+            run: Union[str, Process, Dict[str, Any]] = t["run"]
             if isinstance(run, str):
                 process = make_tool(run, loading_context)
+            elif isinstance(run, dict):
+                process = make_tool(cast(CommentedMap, cmap(run)), loading_context)
             else:
                 process = run
             print_targets(process, stdout, loading_context, shortname(t["id"]) + "/")

tests/subgraph/timelimit2-wf.cwl

@@ -0,0 +1,49 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.2
+
+requirements:
+  ToolTimeLimit:
+    timelimit: 5
+  InlineJavascriptRequirement: {}
+
+inputs:
+  i:
+    type: string?
+
+outputs:
+  o:
+    type: string?
+    outputSource: step2/o
+
+steps:
+  step1:
+    in:
+      i: i
+    out: [o]
+    run:
+      class: CommandLineTool
+      baseCommand: ["sleep", "3"]
+      inputs:
+        i:
+          type: string?
+      outputs:
+        o:
+          type: string?
+          outputBinding:
+            outputEval: $("time passed")
+  step2:
+    in:
+      i: step1/o
+    out: [o]
+    run:
+      class: CommandLineTool
+      baseCommand: ["sleep", "3"]
+      inputs:
+        i:
+          type: string?
+      outputs:
+        o:
+          type: string?
+          outputBinding:
+            outputEval: $("time passed")

tests/test_subgraph.py

@@ -240,3 +240,14 @@ def test_single_step_packed_subwf_step() -> None:
         json.loads(stdout)["out"]["checksum"]
         == "sha1$7608e5669ba454c61fab01c9b133b52a9a7de68c"
     )
+
+
+def test_print_targets_embedded_step() -> None:
+    """Confirm that --print-targets works when a Workflow has embedded Processes."""
+    err_code, stdout, stderr = get_main_output(
+        [
+            "--print-targets",
+            get_data("tests/subgraph/timelimit2-wf.cwl"),
+        ]
+    )
+    assert err_code == 0