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

@@ -232,8 +232,6 @@ 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 +246,9 @@ 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:
-        loadingOptions = cwl_v1_2.LoadingOptions(fileuri=real_uri, baseuri=base_uri)
+    loadingOptions = cwl_v1_2.LoadingOptions(
+        fileuri=real_uri, baseuri=base_uri, copyfrom=loadingOptions
+    )
 
     doc = loadingOptions.fetcher.fetch_text(real_uri)
     return load_document_by_string(doc, real_uri, loadingOptions, id_, load_all)