enable loading all parts of a $graph document

Fixes: #200

Author: mr-c

cwl_utils/parser/__init__.py

@@ -134,6 +134,7 @@ def cwl_version(yaml: Any) -> Optional[str]:
 def load_document_by_uri(
     path: Union[str, Path],
     loadingOptions: Optional[LoadingOptions] = None,
+    load_all: bool = False,
 ) -> Any:
     """Load a CWL object from a URI or a path."""
     if isinstance(path, str):
@@ -153,44 +154,47 @@ def load_document_by_uri(
         loadingOptions = cwl_v1_2.LoadingOptions(fileuri=baseuri)
 
     doc = loadingOptions.fetcher.fetch_text(real_path)
-    return load_document_by_string(doc, baseuri, loadingOptions, id_)
+    return load_document_by_string(doc, baseuri, loadingOptions, id_, load_all)
 
 
 def load_document(
     doc: Any,
     baseuri: Optional[str] = None,
     loadingOptions: Optional[LoadingOptions] = None,
     id_: Optional[str] = None,
+    load_all: bool = False,
 ) -> Any:
     """Load a CWL object from a serialized YAML string or a YAML object."""
     if baseuri is None:
         baseuri = cwl_v1_0.file_uri(os.getcwd()) + "/"
     if isinstance(doc, str):
         return load_document_by_string(doc, baseuri, loadingOptions, id_)
-    return load_document_by_yaml(doc, baseuri, loadingOptions, id_)
+    return load_document_by_yaml(doc, baseuri, loadingOptions, id_, load_all)
 
 
 def load_document_by_string(
     string: str,
     uri: str,
     loadingOptions: Optional[LoadingOptions] = None,
     id_: Optional[str] = None,
+    load_all: bool = False,
 ) -> Any:
     """Load a CWL object from a serialized YAML string."""
     yaml = yaml_no_ts()
     result = yaml.load(string)
-    return load_document_by_yaml(result, uri, loadingOptions, id_)
+    return load_document_by_yaml(result, uri, loadingOptions, id_, load_all)
 
 
 def load_document_by_yaml(
     yaml: Any,
     uri: str,
     loadingOptions: Optional[LoadingOptions] = None,
     id_: Optional[str] = None,
+    load_all: bool = False,
 ) -> Any:
     """Load a CWL object from a YAML object."""
     version = cwl_version(yaml)
-    if "$graph" in yaml:
+    if "$graph" in yaml and not load_all:
         yaml = _get_id_from_graph(yaml, id_)
         yaml["cwlVersion"] = version
     if version == "v1.0":

tests/test_parser.py

@@ -114,3 +114,10 @@ def test_get_default_id_from_graph_without_main() -> None:
     with raises(GraphTargetMissingException):
         uri = Path(get_data("testdata/js-expr-req-wf.cwl")).resolve().as_uri()
         load_document_by_uri(uri)
+
+
+def test_graph_load_all() -> None:
+    """Test that we can get all object in a $graph file."""
+    uri = Path(get_data("testdata/js-expr-req-wf.cwl")).resolve().as_uri()
+    cwl_objs = load_document_by_uri(uri, load_all=True)
+    assert len(cwl_objs) == 2