hetionet does not work

[chaxor]

The function get_hetionet() in pybel.io.hetionet no longer works, due to the use of the key "source" in the annotations dictionary.

Here is a stacktrace:

----> 1 hetio = pybel.get_hetionet()

File /usr/local/lib/python3.10/dist-packages/pybel/io/hetionet/hetionet.py:44, in get_hetionet()
     42 """Get Hetionet from GitHub, cache, and convert to BEL."""
     43 path = pystow.ensure("bio2bel", "hetionet", url=JSON_BZ2_URL)
---> 44 return from_hetionet_gz(path.as_posix())

File /usr/local/lib/python3.10/dist-packages/pybel/io/hetionet/hetionet.py:51, in from_hetionet_gz(path)
     49 logger.info("opening %s", path)
     50 with bz2.open(path) as file:
---> 51     return from_hetionet_file(file)

File /usr/local/lib/python3.10/dist-packages/pybel/io/hetionet/hetionet.py:59, in from_hetionet_file(file)
     57 j = json.load(file)
     58 logger.info("converting hetionet dict to BEL")
---> 59 return from_hetionet_json(j)

File /usr/local/lib/python3.10/dist-packages/pybel/io/hetionet/hetionet.py:86, in from_hetionet_json(hetionet_dict, use_tqdm)
     83     it_logger = logger.info
     85 for edge in edges:
---> 86     _add_edge(graph, edge, kind_identifier_to_name, it_logger)
     88 return graph

File /usr/local/lib/python3.10/dist-packages/pybel/io/hetionet/hetionet.py:159, in _add_edge(graph, edge, kind_identifier_to_name, it_logger)
    157 rv = set()
    158 for citation in citations:
--> 159     key = f(
    160         graph,
    161         h_dsl(namespace=source_ns, identifier=source_identifier, name=source_name),
    162         t_dsl(namespace=target_ns, identifier=target_identifier, name=target_name),
    163         citation=citation,
    164         evidence="",
    165         annotations=annotations,
    166     )
    167     rv.add(key)
    168 return rv

File /usr/lib/python3.10/functools.py:388, in partialmethod._make_unbound_method.<locals>._method(cls_or_self, *args, **keywords)
    386 def _method(cls_or_self, /, *args, **keywords):
    387     keywords = {**self.keywords, **keywords}
--> 388     return self.func(cls_or_self, *self.args, *args, **keywords)

File /usr/local/lib/python3.10/dist-packages/pybel/struct/graph.py:543, in BELGraph._add_two_way_qualified_edge(self, source, target, *args, **kwargs)
    541 def _add_two_way_qualified_edge(self, source: BaseEntity, target: BaseEntity, *args, **kwargs) -> str:
    542     """Add an qualified edge both ways."""
--> 543     self.add_qualified_edge(source=target, target=source, *args, **kwargs)
    544     return self.add_qualified_edge(source=source, target=target, *args, **kwargs)

File /usr/local/lib/python3.10/dist-packages/pybel/struct/graph.py:609, in BELGraph.add_qualified_edge(self, source, target, relation, evidence, citation, annotations, source_modifier, target_modifier, **attr)
    606     warnings.warn("object_modifier has been renamed to target_modifier")
    607     target_modifier = attr.pop("object_modifier")
--> 609 attr = self._build_attr(
    610     relation=relation,
    611     evidence=evidence,
    612     citation=citation,
    613     annotations=annotations,
    614     source_modifier=source_modifier,
    615     target_modifier=target_modifier,
    616     **attr,
    617 )
    618 return self._help_add_edge(source=source, target=target, attr=attr)

File /usr/local/lib/python3.10/dist-packages/pybel/struct/graph.py:639, in BELGraph._build_attr(self, relation, evidence, citation, annotations, source_modifier, target_modifier, **attr)
    630 attr.update(
    631     {
    632         RELATION: relation,
   (...)
    635     }
    636 )
    638 if annotations:  # clean up annotations
--> 639     attr[ANNOTATIONS] = self._clean_annotations(annotations)
    641 if source_modifier:
    642     attr[SOURCE_MODIFIER] = _handle_modifier(source_modifier)

File /usr/local/lib/python3.10/dist-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 /usr/local/lib/python3.10/dist-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 /usr/local/lib/python3.10/dist-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 source?

[cthoyt]

what version of PyBEL are you using?