support packed $graph documents

Author: mr-c

cwlupgrader/main.py

@@ -217,15 +217,14 @@ def process_imports(
 def v1_0_to_v1_1(document: CommentedMap, outdir: str) -> CommentedMap:
     """CWL v1.0.x to v1.1 transformation loop."""
     _v1_0_to_v1_1(document, outdir)
-    if isinstance(document, MutableMapping):
-        for key, value in document.items():
-            with SourceLine(document, key, Exception):
-                if isinstance(value, CommentedMap):
-                    document[key] = _v1_0_to_v1_1(value, outdir)
-                elif isinstance(value, list):
-                    for index, entry in enumerate(value):
-                        if isinstance(entry, CommentedMap):
-                            value[index] = _v1_0_to_v1_1(entry, outdir)
+    for key, value in document.items():
+        with SourceLine(document, key, Exception):
+            if isinstance(value, CommentedMap):
+                document[key] = _v1_0_to_v1_1(value, outdir)
+            elif isinstance(value, list):
+                for index, entry in enumerate(value):
+                    if isinstance(entry, CommentedMap):
+                        value[index] = _v1_0_to_v1_1(entry, outdir)
     document["cwlVersion"] = "v1.1"
     return sort_v1_0(document)
 
@@ -345,12 +344,17 @@ def _v1_0_to_v1_1(document: CommentedMap, outdir: str) -> CommentedMap:
                                 _v1_0_to_v1_1(process, outdir)
                                 if "cwlVersion" in process:
                                     del process["cwlVersion"]
-                            elif isinstance(entry["run"], str):
+                            elif (
+                                isinstance(entry["run"], str)
+                                and "#" not in entry["run"]
+                            ):
                                 path = Path(document.lc.filename).parent / entry["run"]
                                 process = v1_0_to_v1_1(
                                     load_cwl_document(str(path)), outdir
                                 )
                                 write_cwl_document(process, path.name, outdir)
+                            elif isinstance(entry["run"], str) and "#" in entry["run"]:
+                                pass  # reference to $graph entry
                             else:
                                 raise Exception(
                                     "'run' entry was neither a CWL Process nor "

testdata/v1.0/conflict-wf.cwl

@@ -0,0 +1,79 @@
+cwlVersion: v1.0
+$graph:
+- id: echo
+  class: CommandLineTool
+  hints:
+    ResourceRequirement:
+      ramMin: 8
+  inputs:
+    text:
+      type: string
+      inputBinding: {}
+
+  outputs:
+    fileout:
+      type: File
+      outputBinding:
+        glob: out.txt
+
+  baseCommand: echo
+  stdout: out.txt
+
+- id: cat
+  class: CommandLineTool
+  hints:
+    ResourceRequirement:
+      ramMin: 8
+
+  inputs:
+    file1:
+      type: File
+      inputBinding:
+        position: 1
+    file2:
+      type: File
+      inputBinding:
+        position: 2
+
+  outputs:
+    fileout:
+      type: File
+      outputBinding:
+        glob: out.txt
+
+  baseCommand: cat
+  stdout: out.txt
+
+- class: Workflow
+  id: collision
+
+  inputs:
+    input_1: string
+    input_2: string
+
+  outputs:
+    fileout:
+      type: File
+      outputSource: cat_step/fileout
+
+  steps:
+    echo_1:
+      run: "#echo"
+      in:
+        text: input_1
+      out: [fileout]
+
+    echo_2:
+      run: "#echo"
+      in:
+        text: input_2
+      out: [fileout]
+
+    cat_step:
+      run: "#cat"
+      in:
+        file1:
+          source: echo_1/fileout
+        file2:
+          source: echo_2/fileout
+      out: [fileout]

testdata/v1.1/conflict-wf.cwl

@@ -0,0 +1,88 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.1
+$graph:
+- id: echo
+  class: CommandLineTool
+  hints:
+    ResourceRequirement:
+      ramMin: 8
+    NetworkAccess:
+      networkAccess: true
+    LoadListingRequirement:
+      loadListing: deep_listing
+  inputs:
+    text:
+      type: string
+      inputBinding: {}
+
+  outputs:
+    fileout:
+      type: File
+      outputBinding:
+        glob: out.txt
+
+  baseCommand: echo
+  stdout: out.txt
+
+- id: cat
+  class: CommandLineTool
+  hints:
+    ResourceRequirement:
+      ramMin: 8
+
+    NetworkAccess:
+      networkAccess: true
+    LoadListingRequirement:
+      loadListing: deep_listing
+  inputs:
+    file1:
+      type: File
+      inputBinding:
+        position: 1
+    file2:
+      type: File
+      inputBinding:
+        position: 2
+
+  outputs:
+    fileout:
+      type: File
+      outputBinding:
+        glob: out.txt
+
+  baseCommand: cat
+  stdout: out.txt
+
+- class: Workflow
+  id: collision
+
+  inputs:
+    input_1: string
+    input_2: string
+
+  outputs:
+    fileout:
+      type: File
+      outputSource: cat_step/fileout
+
+  steps:
+    echo_1:
+      run: "#echo"
+      in:
+        text: input_1
+      out: [fileout]
+
+    echo_2:
+      run: "#echo"
+      in:
+        text: input_2
+      out: [fileout]
+
+    cat_step:
+      run: "#cat"
+      in:
+        file1:
+          source: echo_1/fileout
+        file2:
+          source: echo_2/fileout
+      out: [fileout]

tests/test_complete.py

@@ -36,3 +36,13 @@ def test_v1_1_to_v1_2(tmp_path: Path) -> None:
     doc = load_cwl_document(get_data("testdata/v1.1/listing_deep1.cwl"))
     upgraded = upgrade_document(doc, str(tmp_path), "v1.2")
     assert doc == upgraded
+
+
+def test_packed_graph(tmp_path: Path) -> None:
+    """Test packed document with $graph."""
+    main([f"--dir={tmp_path}", "--v1.1-only", get_data("testdata/v1.0/conflict-wf.cwl")])
+    assert filecmp.cmp(
+        get_data("testdata/v1.1/conflict-wf.cwl"),
+        tmp_path / "conflict-wf.cwl",
+        shallow=False,
+    )