Pattern 2

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[7], line 2
      1 w = WorkflowWrapper(workflow=wf.workflow, entrypoint=entrypoint)
----> 2 wrapped = w.wrap()
      3 
      4 app_cwl_file = f".{entrypoint}.cwl"
      5 

File ~/work/application-package-patterns/application-package-patterns/docs/helpers.py:121, in WorkflowWrapper.wrap(self)
    114 file_stage_in = load_cwl_from_location(
    115     path=f"{self.base_url}/templates/stage-in-file.cwl"
    116 )
    117 stage_out_cwl = load_cwl_from_location(
    118     path=f"{self.base_url}/templates/stage-out.cwl"
    119 )
--> 121 return wrap(
    122     directory_stage_in=directory_stage_in,
    123     file_stage_in=file_stage_in,
    124     workflows=self.workflow,
    125     workflow_id=self.entrypoint,
    126     stage_out=stage_out_cwl,
    127 )

TypeError: wrap() got an unexpected keyword argument 'workflows'. Did you mean 'workflow'?

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[8], line 1
----> 1 wf = WorkflowViewer(cwl_file=app_cwl_file, workflow=wrapped, entrypoint="main")
      2 
      3 wf.plot()

NameError: name 'wrapped' is not defined

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[9], line 1
----> 1 wf.display_components_diagram()

File ~/work/application-package-patterns/application-package-patterns/docs/helpers.py:72, in WorkflowViewer.display_components_diagram(self)
     70 def display_components_diagram(self):
     71     out = StringIO()
---> 72     to_puml(
     73         cwl_document=self.workflow,
     74         diagram_type=DiagramType.COMPONENT,
     75         output_stream=out,
     76     )
     78     clear_output = out.getvalue()
     79     encoded = deflate_and_encode(clear_output)

File /opt/hostedtoolcache/Python/3.14.6/x64/lib/python3.14/site-packages/cwl2puml/__init__.py:222, in to_puml(cwl_document, diagram_type, output_stream, workflow_id)
    205 def to_puml(
    206     cwl_document: Process | List[Process],
    207     diagram_type: DiagramType,
    208     output_stream: TextIO,
    209     workflow_id: str = "main",
    210 ):
    211     """
    212     Converts a CWL, given its document model, to a PlantUML diagram.
    213 
   (...)    220         `None`: none
    221     """
--> 222     assert_process_contained(process=cwl_document, process_id=workflow_id)
    224     assert_connected_graph(cwl_document)
    226     index = (
    227         to_index(cwl_document)
    228         if isinstance(cwl_document, list)
    229         else {workflow_id: cwl_document}
    230     )

File /opt/hostedtoolcache/Python/3.14.6/x64/lib/python3.14/site-packages/cwl_loader/utils.py:50, in assert_process_contained(process_id, process)
     48 def assert_process_contained(process_id: str, process: Process | List[Process]):
     49     if not contains_process(process_id=process_id, process=process):
---> 50         raise ValueError(
     51             f"Process {process_id} does not exist in input CWL document, only {list(map(lambda p: p.id, process)) if isinstance(process, list) else [process.id]} available."
     52         )

ValueError: Process main does not exist in input CWL document, only ['pattern-2', 'clt'] available.

---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
Cell In[16], line 19
     15     stdout=stream_out,
     16     stderr=stream_err,
     17 )
     18 
---> 19 assert res == 0
     20 
     21 md = f"""
     22 

AssertionError: