Merge pull request #1478 from haohangyan/depmap

Use correct source_counts for indra net

Author: bgyori

indra/assemblers/indranet/assembler.py

@@ -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(
@@ -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,
@@ -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:

indra/tests/test_indranet_assembler.py

@@ -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]
+