Fix load_document_by_uri method

This commit adjusts the `load_document_by_uri` method, ensuring that the
`LoadingOptions` object used to parse the document contains the correct
values for `fileuri` and `baseuri`.

Author: GlassOfWhiskey

cwl_utils/parser/__init__.py

@@ -46,6 +46,8 @@
     cwl_v1_2.InputRecordSchema,
 ]
 """Type union for a CWL v1.x InputRecordSchema object."""
+InputSchema = Union[cwl_v1_0.InputSchema, cwl_v1_1.InputSchema, cwl_v1_2.InputSchema]
+"""Type union for a CWL v1.x InputSchema object."""
 OutputParameter = Union[
     cwl_v1_0.OutputParameter, cwl_v1_1.OutputParameter, cwl_v1_2.OutputParameter
 ]
@@ -232,8 +234,6 @@ def load_document_by_uri(
     load_all: bool = False,
 ) -> Any:
     """Load a CWL object from a URI or a path."""
-    base_uri = ""
-    real_uri = ""
     if isinstance(path, str):
         uri = urlparse(path)
         id_ = uri.fragment or None
@@ -248,8 +248,24 @@ def load_document_by_uri(
         base_uri = path.resolve().parent.as_uri()
         id_ = path.resolve().name.split("#")[1] if "#" in path.resolve().name else None
 
-    if loadingOptions is None:
+    if isinstance(loadingOptions, cwl_v1_0.LoadingOptions):
+        loadingOptions = cwl_v1_0.LoadingOptions(
+            fileuri=real_uri, baseuri=base_uri, copyfrom=loadingOptions
+        )
+    elif isinstance(loadingOptions, cwl_v1_1.LoadingOptions):
+        loadingOptions = cwl_v1_1.LoadingOptions(
+            fileuri=real_uri, baseuri=base_uri, copyfrom=loadingOptions
+        )
+    elif isinstance(loadingOptions, cwl_v1_2.LoadingOptions):
+        loadingOptions = cwl_v1_2.LoadingOptions(
+            fileuri=real_uri, baseuri=base_uri, copyfrom=loadingOptions
+        )
+    elif loadingOptions is None:
         loadingOptions = cwl_v1_2.LoadingOptions(fileuri=real_uri, baseuri=base_uri)
+    else:
+        raise ValidationException(
+            f"Unsupported loadingOptions type: {type(loadingOptions)}"
+        )
 
     doc = loadingOptions.fetcher.fetch_text(real_uri)
     return load_document_by_string(doc, real_uri, loadingOptions, id_, load_all)

testdata/remote-cwl/tool1.cwl

@@ -2,7 +2,7 @@
 # We have this tool to test both local and remote packing
 
 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.2
 inputs:
   in1: 
     type: string

testdata/remote-cwl/tool2.cwl

@@ -2,7 +2,7 @@
 # We have this tool to test both local and remote packing
 
 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.2
 inputs:
   in1:
     type: ../types/testtypes.yml#my_boolean_array

testdata/remote-cwl/wf1.cwl

@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.2
 inputs:
   - id: in1
     type: ../types/testtypes.yml#my_boolean_array

testdata/wf2.cwl

@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.2
 inputs:
   in1: types/testtypes.yml#my_boolean_array
   in2: 

testdata/workflows/wf5.cwl

@@ -2,7 +2,7 @@
 # Checks symbolic links on github
 
 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.2
 inputs:
   in1:
     type: ../types/recursive.yml#file_with_sample_meta

tests/test_parser_utils.py

@@ -105,6 +105,7 @@ def test_static_checker_success(cwlVersion: str) -> None:
                 "testdata/cond-single-source-wf-005.1.cwl",
                 "testdata/extensions/all-output-loop_v1_2.cwl",
                 "testdata/extensions/single-var-loop_v1_2.cwl",
+                "testdata/wf2.cwl",
             ]
         )
     for test_file in test_files: