Merge pull request #650 from opencobra/fix-duplicates

fix: ignore any falsy genes attribute
opencobra · Apr 11, 2019 · 1ea453b · 1ea453b
2 parents 955b308 + ee45daa
commit 1ea453b
Show file tree

Hide file tree

Showing 3 changed files with 11 additions and 8 deletions.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -3,6 +3,8 @@ History
 
 Next Release
 ------------
+* Fix the reactions with identical genes test case to not group all reactions
+  without any GPR together.
 
 0.9.8 (2019-04-01)
 ------------------

diff --git a/memote/suite/reporting/history.py b/memote/suite/reporting/history.py
@@ -116,11 +116,11 @@ def format_data(data):
                                     "data": format_data(data.get(param)),
                                     "result": res.get(param)})
                     else:
-                        tests[test].setdefault("history", list())
-                        tests[test]["history"].append({
+                        tests[test].setdefault("history", list()).append({
                             "branch": branch,
                             "commit": commit,
                             "metric": metric,
                             "data": format_data(data),
-                            "result": res})
+                            "result": res
+                        })
         return base
diff --git a/memote/support/basic.py b/memote/support/basic.py
@@ -343,8 +343,8 @@ def find_reactions_with_partially_identical_annotations(model):
     for (rxn_a, ann_a), (rxn_b, ann_b) in combinations(ann_rxns, 2):
         mutual_pair = tuple(ann_a & ann_b)
         if len(mutual_pair) > 0:
-            duplicates.setdefault(mutual_pair, set())
-            duplicates[mutual_pair].update([rxn_a.id, rxn_b.id])
+            duplicates.setdefault(mutual_pair, set()).update(
+                [rxn_a.id, rxn_b.id])
     # Transform the object for JSON compatibility
     num_duplicated = set()
     duplicated = {}
@@ -508,12 +508,13 @@ def find_reactions_with_identical_genes(model):
     """
     duplicates = dict()
     for rxn_a, rxn_b in combinations(model.reactions, 2):
-        if rxn_a.genes is None or rxn_b.genes is None:
+        if not (rxn_a.genes and rxn_b.genes):
             continue
         if rxn_a.genes == rxn_b.genes:
+            # This works because the `genes` are frozen sets.
             identifiers = rxn_a.genes
-            duplicates.setdefault(identifiers, set())
-            duplicates[identifiers].update([rxn_a.id, rxn_b.id])
+            duplicates.setdefault(identifiers, set()).update(
+                [rxn_a.id, rxn_b.id])
     # Transform the object for JSON compatibility
     num_duplicated = set()
     duplicated = {}