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Use correct source_counts for indra net #1478

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Merged
merged 2 commits into from
Oct 22, 2025
Merged

Use correct source_counts for indra net #1478

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5a2a35d
Use source count dict to get the evidence count in INDRA net
haohangyan Jul 22, 2025
6c8d9a7
Add test for source_count in test_stmt_to_rows
haohangyan Oct 21, 2025
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15 changes: 11 additions & 4 deletions indra/assemblers/indranet/assembler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -518,7 +518,7 @@ def _store_edge_data(stmts, extra_columns=None):


def statement_to_rows(stmt, exclude_stmts=None, complex_members=3,
extra_columns=None, keep_self_loops=True):
extra_columns=None, keep_self_loops=True, source_counts=None):
rows = []
if exclude_stmts:
exclude_types = tuple(
Expand Down Expand Up @@ -592,6 +592,13 @@ def statement_to_rows(stmt, exclude_stmts=None, complex_members=3,
pos = None
# Create a simple flat list of just the values instead
# of a dict with keys
statemet_hash = stmt.get_hash(refresh=True)
if source_counts:
evidence_count = sum(source_counts.get(statemet_hash, {}).values())
source_count = source_counts.get(statemet_hash, {})
else:
evidence_count = len(stmt.evidence)
source_count = _get_source_counts(stmt)
row = [
agA.name,
agB.name,
Expand All @@ -602,10 +609,10 @@ def statement_to_rows(stmt, exclude_stmts=None, complex_members=3,
res,
pos,
stmt_type,
len(stmt.evidence),
stmt.get_hash(refresh=True),
evidence_count,
statemet_hash,
stmt.belief,
_get_source_counts(stmt),
source_count,
sign
]
if extra_columns:
Expand Down
6 changes: 6 additions & 0 deletions indra/tests/test_indranet_assembler.py
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Expand Up @@ -337,3 +337,9 @@ def test_stmt_to_rows():
assert len(rows) == 1
assert rows[0] == ['a', 'b', 'HGNC', '1', 'TEXT', 'b', None, None,
'Activation', 1, 8197018847132618, 1, {None: 1}, None]

source_count = {-25125767941752990: {'db1': 1}}
rows = statement_to_rows(st2, source_counts=source_count)
assert rows[0] == ['a', 'c', 'HGNC', '1', 'TEXT', 'c', None, None,
'Inhibition', 1, -25125767941752990, 0.76, {'db1': 1}, None]