fix: require that finding of transp rxns relies on compartments. (#531)

* fix: require that finding of transp rxns relies on compartments.

* fix: make all test cases include compartments.

* fix: ye olde flake8

* fix: remove duplicated lines

* test: extend transport rxn test cases by the test model from #528

* chore: update History.rst

HISTORY.rst

@@ -3,6 +3,7 @@ History
 
 Next Release
 ------------
+* Fix bug which involved find_transport_reactions to ignore compartments.
 * Internal change to use model context rather than copy.
 * Internal changes to JSON structure.
 * Remove tests for metabolite inconsistency with closed bounds. The results 

memote/support/helpers.py

@@ -158,6 +158,9 @@ def find_transport_reactions(model):
     transport_reactions = []
     transport_rxn_candidates = set(model.reactions) - set(model.boundary) \
         - set(find_biomass_reaction(model))
+    transport_rxn_candidates = set(
+        [rxn for rxn in transport_rxn_candidates if len(rxn.compartments) >= 2]
+    )
     # Add all labeled transport reactions
     sbo_matches = set([rxn for rxn in transport_rxn_candidates if
                        rxn.annotation is not None and

tests/test_for_support/test_for_helpers.py

@@ -219,8 +219,8 @@ def energy_transfer_annotations(base):
 @register_with(MODEL_REGISTRY)
 def labeled_reaction(base):
     """Provide a model with a labeled transport reaction."""
-    a = cobra.Metabolite("a")
-    b = cobra.Metabolite("b")
+    a = cobra.Metabolite("a", compartment="c")
+    b = cobra.Metabolite("b", compartment="p")
     rxn = cobra.Reaction("rxn")
     rxn.annotation["sbo"] = "SBO:0000655"
     rxn.add_metabolites({a: -1, b: 1})
@@ -239,6 +239,59 @@ def unlabeled_reaction(base):
     return base
 
 
+@register_with(MODEL_REGISTRY)
+def ndpk1_annotation(base):
+    """Provide a model with a reportedly false positive."""
+    a = cobra.Metabolite("atp_c", compartment="c")
+    b = cobra.Metabolite("adp_c", compartment="c")
+    c = cobra.Metabolite("gtp_c", compartment="c")
+    d = cobra.Metabolite("gdp_c", compartment="c")
+    b.charge = -3
+    b.formula = "C10H12N5O10P2"
+    b.annotation = {
+        "chebi": "45626",
+        "kegg.compound": "cpd00008",
+        "biocyc": "ADP",
+        "seed.compound": "cpd00008",
+        "pubchem": "6022",
+        "fc_source": "MetaCyc"
+    }
+    a.charge = -4
+    a.formula = "C10H12N5O13P3"
+    a.annotation = {
+        "chebi": "30616",
+        "kegg.compound": "C00002",
+        "biocyc": "ATP",
+        "seed.compound": "cpd00002",
+        "pubchem": "5957",
+        "fc_source": "MetaCyc"
+    }
+    c.charge = -4
+    c.formula = "C10H12N5O14P3"
+    c.annotation = {
+        "chebi": "57600",
+        "kegg.compound": "C00044",
+        "biocyc": "GTP",
+        "seed.compound": "cpd00038",
+        "pubchem": "6830",
+        "fc_source": "MetaCyc"
+    }
+    d.charge = -3
+    d.formula = "C10H12N5O11P2"
+    d.annotation = {
+        "chebi": "58189",
+        "kegg.compound": "C00035",
+        "biocyc": "GDP",
+        "seed.compound": "cpd00031",
+        "pubchem": "8977",
+        "fc_source": "MetaCyc"
+    }
+    rxn = cobra.Reaction("NDPK1")
+    rxn.add_metabolites({a: -1, d: -1, b: 1, c: 1})
+    base.add_reactions([rxn])
+    return base
+
+
 @register_with(MODEL_REGISTRY)
 def converting_reactions(base):
     """Provide a model with a couple of converting reaction."""
@@ -290,11 +343,11 @@ def find_met_id(base):
     g = cobra.Metabolite("cpd00010", compartment='c')
     # ADP - Cryptic ID - MNX ID in the annotation
     h = cobra.Metabolite("OVER9000_c0", compartment='c')
-    h.annotation = {"metanetx.chemical":"MNXM7"}
+    h.annotation = {"metanetx.chemical": "MNXM7"}
     # Proton - Cryptic ID - Chebi array in the annotation
     i = cobra.Metabolite("x12", compartment='c')
-    i.annotation = {"chebi":["15378", "10744", "13357", "5584",
-                             "24636", "29233", "29234"]}
+    i.annotation = {"chebi": ["15378", "10744", "13357", "5584",
+                              "24636", "29233", "29234"]}
     base.add_metabolites([a, b, c, d, e, f, g, h, i])
     return base
 
@@ -416,6 +469,7 @@ def biomass_metabolite(base):
     base.add_reactions([rxn1, rxn2])
     return base
 
+
 @register_with(REACTION_REGISTRY)
 def transport_reaction_true():
     """Provide a transport reaction identifiable through met annotations"""
@@ -427,6 +481,7 @@ def transport_reaction_true():
     r.add_metabolites({a: -1, b: 1})
     return r
 
+
 @register_with(REACTION_REGISTRY)
 def transport_reaction_missing_annotation():
     """Provide a transport reaction identifiable through met annotations"""
@@ -436,6 +491,7 @@ def transport_reaction_missing_annotation():
     r.add_metabolites({a: -1, b: 1})
     return r
 
+
 @register_with(REACTION_REGISTRY)
 def transport_reaction_missing_values():
     """Provide a transport reaction identifiable through met annotations"""
@@ -447,6 +503,7 @@ def transport_reaction_missing_values():
     r.add_metabolites({a: -1, b: 1})
     return r
 
+
 @register_with(REACTION_REGISTRY)
 def transport_reaction_false():
     """Provide a fake transport reaction that uses SBO terms"""
@@ -462,6 +519,7 @@ def transport_reaction_false():
     r.add_metabolites({a: -1, b: 1, c: -1, d: 1})
     return r
 
+
 @pytest.mark.parametrize("model, num", [
     ("uni_anti_symport_formulae", 3),
     ("uni_anti_symport_annotations", 3),
@@ -474,7 +532,8 @@ def transport_reaction_false():
     ("phosphotransferase_system_formulae", 1),
     ("phosphotransferase_system_annotations", 0),
     ("labeled_reaction", 1),
-    ("unlabeled_reaction", 0)
+    ("unlabeled_reaction", 0),
+    ("ndpk1_annotation", 0)
 ], indirect=["model"])
 def test_find_transport_reactions(model, num):
     """Expect amount of transporters to be identified correctly."""
@@ -601,6 +660,7 @@ def test_find_biomass_reaction(model, expected):
     """
     assert len(helpers.find_biomass_reaction(model)) == expected
 
+
 @pytest.mark.parametrize("reaction, boolean", [
     ("transport_reaction_true", True),
     ("transport_reaction_false", None),