increase coverage of API lib tests

datanator/api/lib/search/manager.py

@@ -49,7 +49,6 @@ def search(self, string):
         subunit = subunit_manager._search_simple(string)
 
         rxns = []
-        print(metabolite[:METABOLITE_REACTION_LIMIT])
         for _metabolite in metabolite[:METABOLITE_REACTION_LIMIT]:
             rxn_list = reaction_manager.get_reaction_by_metabolite(_metabolite)
             if rxn_list:

datanator/api/lib/subunit/manager.py

@@ -204,19 +204,19 @@ def get_abundance_by_sequence(self, sequence, select=models.AbundanceData):
         condition = models.ProteinSubunit.canonical_sequence == sequence
         return q.filter(condition)
 
-    def get_abundance_by_entrez(self, entrez_id, select=models.AbundanceData):
-        """ Find the abundance from uniprot
-
-        Args:
-            entrez_id (:obj:`str`): NCBI entrez id for a given protein
-
-        Returns:
-            :obj:`sqlalchemy.orm.query.Query`: query for matching abundance rows
-        """
-        q = self.data_source.session.query(select).join(
-            models.ProteinSubunit, models.AbundanceData.subunit)
-        condition = models.ProteinSubunit.entrez_id == entrez_id
-        return q.filter(condition)
+    # def get_abundance_by_entrez(self, entrez_id, select=models.AbundanceData):
+    #     """ Find the abundance from uniprot
+    #
+    #     Args:
+    #         entrez_id (:obj:`str`): NCBI entrez id for a given protein
+    #
+    #     Returns:
+    #         :obj:`sqlalchemy.orm.query.Query`: query for matching abundance rows
+    #     """
+    #     q = self.data_source.session.query(select).join(
+    #         models.ProteinSubunit, models.AbundanceData.subunit)
+    #     condition = models.ProteinSubunit.entrez_id == entrez_id
+    #     return q.filter(condition)
 
     def get_abundance_by_mass(self, mass, select=models.AbundanceData):
         """ Find the abundance from uniprot

tests/api/lib/test_complex_manager.py

@@ -16,6 +16,9 @@ class TestProteinComplexManager(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         cls.signal_peptidase = complex_manager.data_source.session.query(models.ProteinComplex).filter_by(complex_name = 'signal peptidase I').first()
+        cls.rhino_complex = complex_manager.data_source.session.query(models.ProteinComplex).filter_by(complex_name = 'Rhino-Deadlock-Cutoff Complex').first()
+
+
 
     def test_get_complex_by_id(self):
         prot = complex_manager.get_complex_by_id(self.signal_peptidase.id)
@@ -29,3 +32,19 @@ def test__port(self):
         ported_prot = complex_manager._port(self.signal_peptidase)
         self.assertEqual(ported_prot.name, 'signal peptidase I')
         self.assertEqual(ported_prot.cross_references, [])
+
+
+    def test_get_observable_subunits(self):
+        observed_subunits = complex_manager.get_observable_subunits(self.rhino_complex)
+        self.assertEqual(set(['Q9VIF5', 'Q9V629', 'Q7JXA8']), set([subunit.specie.uniprot_id for subunit in observed_subunits]))
+
+    def test_get_subunits_by_known_complex(self):
+        subunits = complex_manager.get_subunits_by_known_complex(self.rhino_complex.complex_name)
+        self.assertEqual(set(['Q9VIF5', 'Q9V629', 'Q7JXA8']), set([subunit.uniprot_id for subunit in subunits]))
+
+    def test_get_known_complex_by_subunit(self):
+        complex = complex_manager.get_known_complex_by_subunit('Q9CWF2').all()
+
+        self.assertEqual(len(complex), 1)
+        self.assertEqual(complex[0].complex_name, 'Profilin 1 complex')
+        self.assertEqual(complex[0].go_id, 'GO:0006461;GO:0006897;GO:0030036')

tests/api/lib/test_metabolite_manager.py

@@ -78,3 +78,11 @@ def test__port(self):
         self.assertEqual(ported_specie.name, self.proline.metabolite_name)
         self.assertEqual(ported_specie.structure, self.proline.structure._value_inchi)
         self.assertGreater(len(ported_specie.cross_references), 0)
+
+
+    def test_get_metabolite_by_structure(self):
+        metabolites = metabolite_manager.get_metabolite_by_structure(self.proline.structure._value_inchi)
+        self.assertIn(self.proline, metabolites)
+
+        metabolites = metabolite_manager.get_metabolite_by_structure(self.proline.structure._value_inchi, only_formula_and_connectivity=True)
+        self.assertIn(self.proline, metabolites)

tests/api/lib/test_search_manager.py

@@ -17,3 +17,7 @@ def test_search(self):
         self.assertGreater(len(dict['Reaction']), 0)
         self.assertEqual(len(dict['ProteinSubunit']), 0)
         self.assertEqual(len(dict['ProteinComplex']), 0)
+
+    def test_get_object_by_id(self):
+        obj = search_manager.get_object_by_id(5)
+        self.assertTrue(obj)

tests/api/lib/test_subunit_manager.py

@@ -17,6 +17,8 @@ class TestProteinSubunitManager(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         cls.protein_P00323 = subunit_manager.data_source.session.query(models.ProteinSubunit).filter_by(uniprot_id = 'P00323').first()
+        cls.protein_P49418 = subunit_manager.data_source.session.query(models.ProteinSubunit).filter_by(uniprot_id = 'P49418').first()
+        cls.protein_O15169 = subunit_manager.data_source.session.query(models.ProteinSubunit).filter_by(uniprot_id = 'O15169').first()
 
     def test_get_abundance_by_uniprot(self):
         uniprot = self.protein_P00323.uniprot_id
@@ -61,3 +63,12 @@ def test_get_abundance_by_length(self):
             models.AbundanceData.pax_load.in_([1, 2])).all()
         self.assertEqual(set(c.abundance for c in abundances),
                          set([1003.0, 1336.0, 1027.0, 1861.0]))
+
+
+    def test_get_observable_interactions(self):
+        interactions = subunit_manager.get_observable_interactions(self.protein_P49418)
+        self.assertGreater(len(interactions), 0)
+
+    def test_get_observable_complex(self):
+        complexes = subunit_manager.get_observable_complex(self.protein_O15169)
+        self.assertGreater(len(complexes), 0)