Further fixes for evidence list references

Author: bgyori

indra/preassembler/grounding_mapper/adeft.py

@@ -48,7 +48,8 @@ def run_adeft_disambiguation(stmt, agent, idx):
         return
     # Initialize annotations if needed so Adeft predicted
     # probabilities can be added to Agent annotations
-    annots = stmt.evidence[0].annotations
+    ev = stmt.evidence[0]
+    annots = ev.annotations
     agent_txt = agent.db_refs['TEXT']
     if 'agents' in annots:
         if 'adeft' not in annots['agents']:
@@ -78,6 +79,7 @@ def run_adeft_disambiguation(stmt, agent, idx):
             GroundingMapper.standardize_agent_name(agent,
                                                    standardize_refs=True)
             annots['agents']['adeft'][idx] = disamb_scores
+    stmt.evidence[0] = ev
 
 
 def _get_text_for_grounding(stmt, agent_text):

indra/sources/sparser/processor.py

@@ -168,8 +168,10 @@ def set_statements_pmid(self, pmid):
                 ev['pmid'] = pmid
         # Replace PMID value in extracted Statements next
         for stmt in self.statements:
-            for ev in stmt.evidence:
+            evs = stmt.evidence
+            for ev in evs:
                 ev.pmid = pmid
+            stmt.evidence = evs
 
 
 def _fix_agent(agent):

indra/tests/test_assemble_corpus.py

@@ -588,11 +588,13 @@ def test_merge_groundings():
 
 def test_merge_deltas():
     def add_annots(stmt):
-        for ev in stmt.evidence:
+        evs = stmt.evidence
+        for ev in evs:
             ev.annotations['subj_adjectives'] = stmt.subj.delta.adjectives
             ev.annotations['obj_adjectives'] = stmt.obj.delta.adjectives
             ev.annotations['subj_polarity'] = stmt.subj.delta.polarity
             ev.annotations['obj_polarity'] = stmt.obj.delta.polarity
+        stmt.evidence = evs
         return stmt
     # d1 = {'adjectives': ['a', 'b', 'c'], 'polarity': 1}
     # d2 = {'adjectives': [], 'polarity': -1}

indra/tests/test_medscan.py

@@ -157,8 +157,8 @@ def test_evidence():
     coords = s0.evidence[0].annotations['agents']['coords']
     assert isinstance(coords, list), type(coords)
     assert len(coords) == 2, len(coords)
-    assert coords[0] == (90, 97), coords[0]
-    assert coords[1] == (106, 120), coords[1]
+    assert tuple(coords[0]) == (90, 97), tuple(coords[0])
+    assert tuple(coords[1]) == (106, 120), tuple(coords[1])
 
 
 def test_molsynthesis_positive():

indra/tests/test_preassembler.py

@@ -510,7 +510,9 @@ def test_flatten_evidence_hierarchy():
     supporting_stmt = top_stmt.supported_by[0]
     assert len(supporting_stmt.evidence) == 1
     assert supporting_stmt.evidence[0].text == 'foo'
-    supporting_stmt.evidence[0].text = 'changed_foo'
+    evs = supporting_stmt.evidence
+    evs[0].text = 'changed_foo'
+    supporting_stmt.evidence = evs
     assert supporting_stmt.evidence[0].text == 'changed_foo'
     assert 'changed_foo' not in [e.text for e in top_stmt.evidence]
     assert 'foo' in [e.text for e in top_stmt.evidence]
@@ -915,8 +917,10 @@ def test_agent_coordinates():
     evidence_list = unique_stmt.evidence
     agent_annots = [ev.annotations['agents'] for ev in unique_stmt.evidence]
     assert all(a['raw_text'] == ['MEK1', 'ERK2'] for a in agent_annots)
-    assert {tuple(a['coords']) for a in agent_annots} == {((21, 25), (0, 4)),
-                                                          ((0, 4), (15, 19))}
+    expected_coords = {((21, 25), (0, 4)), ((0, 4), (15, 19))}
+    for annot in agent_annots:
+        coords = tuple(tuple(a) for a in annot['coords'])
+        assert coords in expected_coords
 
 
 def test_association_duplicate():

indra/tools/assemble_corpus.py

@@ -244,9 +244,11 @@ def merge_deltas(stmts_in):
             for info in ('polarity', 'adjectives'):
                 key = (role, info)
                 deltas[key] = []
+                evs = stmt.evidence
                 for ev in stmt.evidence:
                     entry = ev.annotations.get('%s_%s' % key)
                     deltas[key].append(entry if entry else None)
+                stmt.evidence = evs
         # POLARITY
         # For polarity we need to work in pairs
         polarity_pairs = list(zip(deltas[('subj', 'polarity')],