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Bug fixes for DKG build #187

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merged 2 commits into from
Jul 5, 2023
Merged

Bug fixes for DKG build #187

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2e45c92
Update construct.py
cthoyt Jul 5, 2023
e87de50
Fix predicate curie reference
cthoyt Jul 5, 2023
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22 changes: 14 additions & 8 deletions mira/dkg/construct.py
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Original file line number Diff line number Diff line change
Expand Up @@ -464,7 +464,8 @@ def construct(
property_values="",
xref_types="", # TODO
synonym_types=";".join(
synonym.type.curie for synonym in term.synonyms or []
synonym.type.curie if synonym.type is not None else "skos:exactMatch"
for synonym in term.synonyms or []
),
)
for parent in term.parents:
Expand Down Expand Up @@ -761,7 +762,11 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str:
# intfmt=",",
)
)
edge_counter = Counter(edge.pred for edge in graph.edges)
edge_counter = Counter(
edge.predicate.curie
for edge in graph.edges
if edge.predicate is not None
)
tqdm.write(
"\n"
+ tabulate(
Expand All @@ -778,7 +783,7 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str:

unstandardized_nodes.extend(node.id for node in graph.nodes if not node.reference)
unstandardized_edges.extend(
edge.pred for edge in graph.edges if edge.pred.startswith("http")
edge.pred for edge in graph.edges if edge.predicate is None
)

clean_edges = (
Expand All @@ -793,10 +798,10 @@ def _get_edge_name(curie_: str, strict: bool = False) -> str:
)
edges.extend(
(
edge.sub,
edge.obj,
_get_edge_name(edge.pred).lower().replace(" ", "_").replace("-", "_"),
edge.pred,
edge.subject.curie,
edge.object.curie,
_get_edge_name(edge.predicate.curie).lower().replace(" ", "_").replace("-", "_"),
edge.predicate.curie,
prefix,
graph_id,
version or "",
Expand Down Expand Up @@ -979,7 +984,8 @@ def get_node_info(term: pyobo.Term, type: EntityType = "class"):
property_values="",
xref_types="",
synonym_types=";".join(
synonym.type.curie for synonym in term.synonyms or []
synonym.type.curie if synonym.type is not None else "skos:exactMatch"
for synonym in term.synonyms or []
),
)

Expand Down