/opt/hostedtoolcache/Python/3.13.5/x64/lib/python3.13/site-packages/cwl_wrapper/parser.py:3: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources

---------------------------------------------------------------------------
ValidationException                       Traceback (most recent call last)
Cell In[6], line 5
      2 cwl_dict = yaml.safe_load(StringIO(res))
      4 # baseuri just needs to not interfere
----> 5 workflow = load_document(cwl_dict, baseuri="file:///", id_="_main")

File /opt/hostedtoolcache/Python/3.13.5/x64/lib/python3.13/site-packages/cwl_utils/parser/__init__.py:297, in load_document(doc, baseuri, loadingOptions, id_, load_all)
    295 if isinstance(doc, str):
    296     return load_document_by_string(doc, baseuri, loadingOptions, id_)
--> 297 return load_document_by_yaml(doc, baseuri, loadingOptions, id_, load_all)

File /opt/hostedtoolcache/Python/3.13.5/x64/lib/python3.13/site-packages/cwl_utils/parser/__init__.py:321, in load_document_by_yaml(yaml, uri, loadingOptions, id_, load_all)
    313 def load_document_by_yaml(
    314     yaml: Any,
    315     uri: str,
   (...)    318     load_all: bool = False,
    319 ) -> Any:
    320     """Load a CWL object from a YAML object."""
--> 321     version = cwl_version(yaml)
    322     if "$graph" in yaml and not load_all:
    323         yaml = _get_id_from_graph(yaml, id_)

File /opt/hostedtoolcache/Python/3.13.5/x64/lib/python3.13/site-packages/cwl_utils/parser/__init__.py:236, in cwl_version(yaml)
    228 """
    229 Return the cwlVersion of a YAML object.
    230 
   (...)    233 :raises ValidationException: If `yaml` is not a MutableMapping.
    234 """
    235 if not isinstance(yaml, MutableMapping):
--> 236     raise ValidationException("MutableMapping is required")
    237 if "cwlVersion" not in list(yaml.keys()):
    238     return None

ValidationException: MutableMapping is required

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[7], line 3
      1 md = "## Inputs\n"
----> 3 for inp in workflow.inputs:
      5     md += f"- `{inp.id.replace("file:///#_main/", "")}`: {inp.type_}\n"
      7 display(Markdown(md))

NameError: name 'workflow' is not defined

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[8], line 3
      1 md = "## Outputs\n"
----> 3 for inp in workflow.outputs:
      5     md += f"- `{inp.id.replace("file:///#_main/", "")}`: {inp.type_}\n"
      7 display(Markdown(md))

NameError: name 'workflow' is not defined

---------------------------------------------------------------------------
GraphTargetMissingException               Traceback (most recent call last)
Cell In[9], line 7
      2     cwl_dict = yaml.safe_load(f)
      4 #cwl_dict = yaml.safe_load(StringIO(res))
      5 
      6 # baseuri just needs to not interfere
----> 7 workflow = load_document(cwl_dict, baseuri="file:///", id_="water-bodies-detection")

File /opt/hostedtoolcache/Python/3.13.5/x64/lib/python3.13/site-packages/cwl_utils/parser/__init__.py:297, in load_document(doc, baseuri, loadingOptions, id_, load_all)
    295 if isinstance(doc, str):
    296     return load_document_by_string(doc, baseuri, loadingOptions, id_)
--> 297 return load_document_by_yaml(doc, baseuri, loadingOptions, id_, load_all)

File /opt/hostedtoolcache/Python/3.13.5/x64/lib/python3.13/site-packages/cwl_utils/parser/__init__.py:323, in load_document_by_yaml(yaml, uri, loadingOptions, id_, load_all)
    321 version = cwl_version(yaml)
    322 if "$graph" in yaml and not load_all:
--> 323     yaml = _get_id_from_graph(yaml, id_)
    324     yaml["cwlVersion"] = version
    325 if version == "v1.0":

File /opt/hostedtoolcache/Python/3.13.5/x64/lib/python3.13/site-packages/cwl_utils/parser/__init__.py:221, in _get_id_from_graph(yaml, id_)
    219     if el["id"].lstrip("#") == id_:
    220         return el
--> 221 raise GraphTargetMissingException(
    222     "Tool file contains graph of multiple objects, must specify "
    223     "one of #%s" % ", #".join(el["id"] for el in yaml["$graph"])
    224 )

GraphTargetMissingException: Tool file contains graph of multiple objects, must specify one of #pattern-1, #clt

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[10], line 3
      1 md = "## Inputs\n"
----> 3 for inp in workflow.inputs:
      5     md += f"- `{inp.id.replace("file:///#water-bodies-detection/", "")}`: {inp.type_}\n"
      7 display(Markdown(md))

NameError: name 'workflow' is not defined

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[11], line 3
      1 md = "## Outputs\n"
----> 3 for inp in workflow.outputs:
      5     md += f"- `{inp.id.replace("file:///#water-bodies-detection/", "")}`: {inp.type_}\n"
      7 display(Markdown(md))

NameError: name 'workflow' is not defined