Cannot parse graph of full file

[kkaris]

Using pybel to parse human_2.0.bel.nodelink.json in this repository errors with NotImplementedError: where is key cbn_pathway?. Looking into the file itself, it seems like the key cbn_pathway does exist, I'm wondering if the generated data files might be out of date with respect to pybel?

The following code reproduces the error:

import pybel
import requests
full_res = requests.get('https://raw.githubusercontent.com/pybel/cbn-bel/master/bel/human_2.0.bel.nodelink.json')
full_graph = pybel.from_nodelink(full_res.json())

Python version 3.11.4
OS: Ubuntu 20.04.6
pybel version: 0.15.5

The traceback I get:

---------------------------------------------------------------------------
NotImplementedError                       Traceback (most recent call last)
Cell In[13], line 1
----> 1 full_graph = pybel.from_nodelink(full_res.json())

File ~/.virtualenvs/py3114/lib/python3.11/site-packages/pybel/io/nodelink.py:100, in from_nodelink(graph_json_dict, check_version)
     98 if pybel_version[1] < 14:  # if minor version is less than 14
     99     raise ValueError("Invalid NodeLink JSON from old version of PyBEL (v{}.{}.{})".format(*pybel_version))
--> 100 graph = _from_nodelink_json_helper(graph_json_dict)
    101 return ensure_version(graph, check_version=check_version)

File ~/.virtualenvs/py3114/lib/python3.11/site-packages/pybel/io/nodelink.py:204, in _from_nodelink_json_helper(data)
    201         edge_data[CITATION] = citation_dict(**edge_data[CITATION])
    203     if ANNOTATIONS in edge_data:
--> 204         edge_data[ANNOTATIONS] = graph._clean_annotations(edge_data[ANNOTATIONS])
    206     graph.add_edge(u, v, key=hash_edge(u, v, edge_data), **edge_data)
    208 return graph

File ~/.virtualenvs/py3114/lib/python3.11/site-packages/pybel/struct/graph.py:1011, in BELGraph._clean_annotations(self, annotations_dict)
    994 def _clean_annotations(self, annotations_dict: AnnotationsHint) -> AnnotationsDict:
    995     """Fix the formatting of annotation dict.
    996 
    997     .. seealso:: https://github.com/vtoure/bep/blob/master/docs/published/BEP-0013.md
   (...)
   1009        ``{'ECO': dict(namespace='ECO', identifier='0007682', name='reporter gene assay...')}``
   1010     """
-> 1011     return {
   1012         key: sorted(
   1013             self._clean_value(key, values),
   1014             key=lambda e: (e.namespace, e.identifier, e.name),
   1015         )
   1016         for key, values in annotations_dict.items()
   1017     }

File ~/.virtualenvs/py3114/lib/python3.11/site-packages/pybel/struct/graph.py:1013, in <dictcomp>(.0)
    994 def _clean_annotations(self, annotations_dict: AnnotationsHint) -> AnnotationsDict:
    995     """Fix the formatting of annotation dict.
    996 
    997     .. seealso:: https://github.com/vtoure/bep/blob/master/docs/published/BEP-0013.md
   (...)
   1009        ``{'ECO': dict(namespace='ECO', identifier='0007682', name='reporter gene assay...')}``
   1010     """
   1011     return {
   1012         key: sorted(
-> 1013             self._clean_value(key, values),
   1014             key=lambda e: (e.namespace, e.identifier, e.name),
   1015         )
   1016         for key, values in annotations_dict.items()
   1017     }

File ~/.virtualenvs/py3114/lib/python3.11/site-packages/pybel/struct/graph.py:1052, in BELGraph._clean_value(self, key, values)
   1049     return self._clean_value_helper(key=key, namespace=key, values=values)
   1051 if self.raise_on_missing_annotations:
-> 1052     raise NotImplementedError(f"where is key {key}?")
   1054 return self._clean_value_helper(key=key, namespace=key, values=values)

NotImplementedError: where is key cbn_pathway?