Merge pull request #601 from gregmedlock/develop

fix: biomass SBO annotation test

HISTORY.rst

@@ -7,6 +7,7 @@ Next Release
 0.9.1 (2019-01-28)
 ------------------
 * Add ``seed.reaction`` namespace to the reaction annotation databases.
+* Fix bug that would lead to biomass SBO annotations not being reported.
 
 0.9.0 (2019-01-28)
 ------------------

memote/suite/tests/test_sbo.py

@@ -418,4 +418,4 @@ def test_biomass_specific_sbo_presence(model):
         'biomass production': {}""".format(
             len(ann["data"]), ann["metric"], truncate(ann["data"])
         ))
-    assert len(ann["data"]) == len(biomass), ann["message"]
+    assert len(ann["data"]) == 0, ann["message"]

tests/test_for_support/test_for_sbo.py

@@ -53,6 +53,7 @@ def specific_sbo_term(base):
     base.add_reactions([rxn])
     return base
 
+
 @register_with(MODEL_REGISTRY)
 def multiple_sbo_terms(base):
     met = cobra.Metabolite(id='met_c', name="Met")
@@ -65,6 +66,17 @@ def multiple_sbo_terms(base):
     base.add_reactions([rxn])
     return base
 
+
+@register_with(MODEL_REGISTRY)
+def biomass_sbo_term(base):
+    met = cobra.Metabolite(id='met_c', name="Met")
+    rxn = cobra.Reaction(id='RXN', name="Rxn")
+    rxn.add_metabolites({met: -1})
+    rxn.annotation = {'sbo': 'SBO:0000629'}
+    base.add_reactions([rxn])
+    return base
+
+
 @pytest.mark.parametrize("model, num, components", [
     ("no_annotations", 2, "metabolites"),
     ("no_annotations", 1, "reactions"),
@@ -81,6 +93,7 @@ def test_find_components_without_sbo_terms(model, num, components):
     ("specific_sbo_term", 0, "metabolites", "SBO:1"),
     ("specific_sbo_term", 1, "reactions", "SBO:1"),
     ("specific_sbo_term", 1, "genes", "SBO:1"),
+    ("biomass_sbo_term", 0, "reactions", "SBO:0000629"),
     ("multiple_sbo_terms", 0, "metabolites", ["SBO:1","SBO:2","SBO:3"]),
     ("multiple_sbo_terms", 1, "reactions", ["SBO:1","SBO:2","SBO:3"]),
     ("multiple_sbo_terms", 1, "genes", ["SBO:1","SBO:2","SBO:3"])