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Keep edge provenance #94

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merged 5 commits into from
Jan 4, 2024
Merged

Keep edge provenance #94

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b3383e0
Update kgx.py
YaphetKG Nov 29, 2023
94984ce
Update kgx.py
YaphetKG Nov 30, 2023
e51ddc4
Update kgx.py
YaphetKG Nov 30, 2023
ad975e0
just collect then update
YaphetKG Nov 30, 2023
a0ea087
Update requirements.txt (#93)
YaphetKG Dec 21, 2023
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7 changes: 7 additions & 0 deletions dags/roger/models/kgx.py
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Original file line number Diff line number Diff line change
Expand Up @@ -478,6 +478,13 @@ def merge(self):
edges['subject'] + edges['predicate'] +
edges['object'] +
edges.get("biolink:primary_knowledge_source", ""))
keys_to_del = set()
for key in edges:
if key.startswith('biolink:'):
keys_to_del.add(key)
for k in keys_to_del:
edges[k.replace('biolink:', '')] = edges[k]
del edges[k]
stream.write(json.dumps(edges).decode('utf-8') + '\n')

write_merge_metric['edges_writing_time'] = time.time() - start_edge_jsonl
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4 changes: 2 additions & 2 deletions requirements.txt
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Expand Up @@ -6,8 +6,8 @@ flatten-dict
redisgraph-bulk-loader==0.12.3
pytest
PyYAML
git+https://github.com/helxplatform/dug@cde-links-2
git+https://github.com/helxplatform/dug@patch-nrslv-resp
orjson
kg-utils==0.0.6
bmt==1.1.0
linkml-runtime==1.6.0
linkml-runtime==1.6.0