to_bel_script() invokes a TypeError: make_knowledge_header() missing 1 required positional argument: 'name'

[djinnome]

Hi @cthoyt

When I try to run
pybel.to_bel_script() I get the following error:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-55-6e2178fff4cb> in <module>
      2 
      3 mars_graph = get_subgraph_by_pubmed( emmaa_covid_graph, pmids)
----> 4 pybel.to_bel_script(mars_graph,os.path.join(curation_dir,'mars_indra.bel'))

</Users/zuck016/.pyenv/versions/anaconda3-2019.10/lib/python3.7/site-packages/decorator.py:decorator-gen-803> in to_bel_script(graph, path, use_identifiers)

~/.pyenv/versions/anaconda3-2019.10/lib/python3.7/site-packages/networkx/utils/decorators.py in _open_file(func_to_be_decorated, *args, **kwargs)
    238         # Finally, we call the original function, making sure to close the fobj
    239         try:
--> 240             result = func_to_be_decorated(*new_args, **kwargs)
    241         finally:
    242             if close_fobj:

~/.pyenv/versions/anaconda3-2019.10/lib/python3.7/site-packages/pybel/canonicalize.py in to_bel_script(graph, path, use_identifiers)
     46     :param use_identifiers: Enables extended `BEP-0008 <http://bep.bel.bio/published/BEP-0008.html>`_ syntax
     47     """
---> 48     for line in to_bel_script_lines(graph, use_identifiers=use_identifiers):
     49         print(line, file=path)
     50 

~/.pyenv/versions/anaconda3-2019.10/lib/python3.7/site-packages/pybel/canonicalize.py in _to_bel_lines_header(graph)
    263         annotation_patterns=graph.annotation_pattern,
    264         annotation_list=graph.annotation_list,
--> 265         **graph.document,
    266     )
    267 

TypeError: make_knowledge_header() missing 1 required positional argument: 'name'

According to:
https://github.com/pybel/bel-resources/blob/master/src/bel_resources/write_document.py#L17

make_knowledge_header() requires a positional name parameter
However,

pybel/src/pybel/canonicalize.py

Lines 259 to 266 in e108252

	yield from make_knowledge_header(
	namespace_url=graph.namespace_url,
	namespace_patterns=graph.namespace_pattern,
	annotation_url=graph.annotation_url,
	annotation_patterns=graph.annotation_pattern,
	annotation_list=graph.annotation_list,
	**graph.document,
	)

attempts to call make_knowledge_header() without calling the name parameter.

[cthoyt]

It should give nicer output but to write to bel script you need to set the name of the graph. I think the version as well.

[djinnome]

Thanks! Now I am getting this error:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-59-999f6b46130e> in <module>
      4 mars_graph.name = 'MARS_Indra'
      5 mars_graph.version = emmaa_covid_graph.version
----> 6 pybel.to_bel_script(mars_graph,os.path.join(curation_dir,'mars_indra.bel'))

</Users/zuck016/.pyenv/versions/anaconda3-2019.10/lib/python3.7/site-packages/decorator.py:decorator-gen-803> in to_bel_script(graph, path, use_identifiers)

~/.pyenv/versions/anaconda3-2019.10/lib/python3.7/site-packages/networkx/utils/decorators.py in _open_file(func_to_be_decorated, *args, **kwargs)
    238         # Finally, we call the original function, making sure to close the fobj
    239         try:
--> 240             result = func_to_be_decorated(*new_args, **kwargs)
    241         finally:
    242             if close_fobj:

~/.pyenv/versions/anaconda3-2019.10/lib/python3.7/site-packages/pybel/canonicalize.py in to_bel_script(graph, path, use_identifiers)
     46     :param use_identifiers: Enables extended `BEP-0008 <http://bep.bel.bio/published/BEP-0008.html>`_ syntax
     47     """
---> 48     for line in to_bel_script_lines(graph, use_identifiers=use_identifiers):
     49         print(line, file=path)
     50 

~/.pyenv/versions/anaconda3-2019.10/lib/python3.7/site-packages/pybel/canonicalize.py in _to_bel_lines_body(graph, use_identifiers)
    296                 keys = sorted(annotations_data) if annotations_data is not None else tuple()
    297                 for key in keys:
--> 298                     yield _set_annotation_to_str(annotations_data, key)
    299 
    300                 yield graph.edge_to_bel(u, v, data, use_identifiers=use_identifiers)

~/.pyenv/versions/anaconda3-2019.10/lib/python3.7/site-packages/pybel/canonicalize.py in _set_annotation_to_str(annotation_data, key)
    233     value = annotation_data[key]
    234 
--> 235     if len(value) == 1:
    236         return 'SET {} = "{}"'.format(key, list(value)[0])
    237 

TypeError: object of type 'NoneType' has no len()

[djinnome]

Weirdly, when I try this:

from pybel.canonicalize import _set_annotation_to_str
for u,v,data in mars_graph.edges(data=True):
                annotations_data = data.get("ANNOTATIONS")

                keys = sorted(annotations_data) if annotations_data is not None else tuple()
                for key in keys:
                    print(_set_annotation_to_str(annotations_data, key))
print("No keys found")

I just get:

No keys found

So I am not sure how to reproduce this error.

[cthoyt]

Quite strange, maybe you could try and figure out for which annotation there's a None as the value (that shouldn't happen...)