cwl inline runtag functionality

src/sophios/cli.py

@@ -27,6 +27,8 @@
                     help='Do not use the --provenance feature of CWL. (You should only disable provenance if absolutely necessary.)')
 parser.add_argument('--copy_output_files', default=False, action="store_true",
                     help='Copies output files from the cachedir to outdir/ (automatically enabled with --run_local)')
+parser.add_argument('--inline_cwl_runtag', default=False, action="store_true",
+                    help='Copies cwl adapter file contents inline into the final .cwl in autogenerated/')
 
 parser.add_argument('--parallel', default=False, action="store_true",
                     help='''When running locally, execute independent steps in parallel.

src/sophios/main.py

@@ -161,6 +161,12 @@ def main() -> None:
 
     io.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
 
+    # this has to happen after at least one write
+    # so we can copy from local cwl_dapters in autogenerated/
+    if args.inline_cwl_runtag:
+        rose_tree = plugins.cwl_update_inline_runtag_rosetree(rose_tree, Path('autogenerated/'), True)
+        io.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
+
     if args.graphviz:
         if shutil.which('dot'):
             # Render the GraphViz diagram

src/sophios/plugins.py

@@ -169,6 +169,32 @@ def cwl_update_outputs_optional(cwl: Cwl) -> Cwl:
     return cwl_mod
 
 
+def cwl_update_inline_runtag(cwl: Cwl, path: Path, relative_run_path: bool) -> Cwl:
+    """Updates 'run' tag with inline content
+
+    Args:
+        cwl (Cwl): A CWL Workflow
+        path (Path): The directory in which to read files from
+        relative_run_path (bool): Controls whether to use subdirectories or just one directory
+    Returns:
+        Cwl: A CWL Workflow with inline run (if any)
+    """
+    cwl_mod = copy.deepcopy(cwl)
+    for step in cwl_mod['steps']:
+        runtag_orig = step.get('run', '')
+        if isinstance(runtag_orig, str) and runtag_orig.endswith('.cwl'):
+            if relative_run_path:
+                yml_path = Path.cwd() / path / runtag_orig
+            else:
+                yml_path = Path(runtag_orig)  # Assume absolute path in the runtag
+            with open(yml_path, mode='r', encoding='utf-8') as f:
+                runtag_raw = yaml.safe_load(f.read())
+                step['run'] = runtag_raw
+        else:
+            pass  # We only care if the runtag is a cwl filepath
+    return cwl_mod
+
+
 Client = Union[docker.DockerClient, podman.PodmanClient]  # type: ignore
 
 
@@ -238,6 +264,30 @@ def remove_entrypoints_podman() -> None:
         remove_entrypoints(client, podman.domain.images_build.BuildMixin())
 
 
+def cwl_update_inline_runtag_rosetree(rose_tree: RoseTree, path: Path, relative_run_path: bool) -> RoseTree:
+    """Inlines the compiled CWL files runtag
+
+    Args:
+        rose_tree (RoseTree): The data associated with compiled subworkflows
+        path (Path): The directory in which to read files from
+        relative_run_path (bool): Controls whether to use subdirectories or just one directory.
+    Returns:
+        RoseTree: rose_tree with inline cwl runtag
+    """
+    n_d: NodeData = rose_tree.data
+    if n_d.compiled_cwl['class'] == 'Workflow':
+        outputs_inline_cwl_runtag = cwl_update_inline_runtag(n_d.compiled_cwl, path, relative_run_path)
+    else:
+        outputs_inline_cwl_runtag = n_d.compiled_cwl
+
+    sub_trees_path = [cwl_update_inline_runtag_rosetree(sub_rose_tree, path, relative_run_path) for
+                      sub_rose_tree in rose_tree.sub_trees]
+    node_data_path = NodeData(n_d.namespaces, n_d.name, n_d.yml, outputs_inline_cwl_runtag, n_d.tool,
+                              n_d.workflow_inputs_file, n_d.explicit_edge_defs, n_d.explicit_edge_calls,
+                              n_d.graph, n_d.inputs_workflow, n_d.step_name_1)
+    return RoseTree(node_data_path, sub_trees_path)
+
+
 def cwl_update_outputs_optional_rosetree(rose_tree: RoseTree) -> RoseTree:
     """Updates outputs optional for every CWL CommandLineTool