def test_interaction_id_id_must_be_int(self, mock_json_retriever):
mock_json_retriever.return_value = [
self.interaction_json, self.interaction_json
]
target = Target(self.target_json)
with self.assertRaises(TypeError):
target.get_interaction_by_id("1")
def test_can_get_interactions(self, mock_json_retriever):
mock_json_retriever.return_value = [self.interaction_json, self.interaction_json]
target = Target(self.target_json)
interactions = target.interactions()
self.assertIsInstance(interactions, list)
self.assertEqual(len(interactions), 2)
for interaction in interactions:
self.assertIsInstance(interaction, Interaction)
def test_can_get_interaction_by_id(self, mock_json_retriever):
mock_json_retriever.return_value = [
self.interaction_json, self.interaction_json
]
target = Target(self.target_json)
interaction = target.get_interaction_by_id(
self.interaction_json["interactionId"])
self.assertIsInstance(interaction, Interaction)
def test_can_get_subunits(self, mock_json_retriever):
mock_json_retriever.return_value = self.target_json
target = Target(self.target_json)
subunits = target.subunits()
self.assertIsInstance(subunits, list)
self.assertEqual(len(subunits), len(self.target_json["subunitIds"]))
for subunit in subunits:
self.assertIsInstance(subunit, Target)
def test_can_get_complexes(self, mock_json_retriever):
mock_json_retriever.return_value = self.target_json
target = Target(self.target_json)
complexes = target.complexes()
self.assertIsInstance(complexes, list)
self.assertEqual(len(complexes), len(self.target_json["complexIds"]))
for complex_ in complexes:
self.assertIsInstance(complex_, Target)
def test_can_get_subunits(self, mock_json_retriever):
mock_json_retriever.return_value = self.target_json
target = Target(self.target_json)
subunits = target.subunits()
self.assertIsInstance(subunits, list)
self.assertEqual(len(subunits), len(self.target_json["subunitIds"]))
for subunit in subunits:
self.assertIsInstance(subunit, Target)
def test_can_get_complexes(self, mock_json_retriever):
mock_json_retriever.return_value = self.target_json
target = Target(self.target_json)
complexes = target.complexes()
self.assertIsInstance(complexes, list)
self.assertEqual(len(complexes), len(self.target_json["complexIds"]))
for complex_ in complexes:
self.assertIsInstance(complex_, Target)
def test_synonym_properties(self, mock_json_retriever):
mock_json_retriever.return_value = [
{"name": "ADRBRL1", "refs": []},
{"name": "5-HT1A", "refs": []}
]
target = Target(self.target_json)
self.assertEqual(target.synonyms(), ["ADRBRL1", "5-HT1A"])
def test_can_get_uniprot_pdbs_when_no_results(self, mock_xml_retriever, mock_json_retriever):
mock_json_retriever.return_value = [
{"accession": "10576", "database": "UniProtKB", "species": "Human", "url":"http"}
]
mock_xml_retriever.return_value = None
target = Target(self.target_json)
pdbs = target.uniprot_pdbs()
self.assertEqual(pdbs, [])
def test_species_gene_properties(self, mock_json_retriever):
mock_json_retriever.return_value = self.gene_json
target = Target(self.target_json)
genes = target.genes(species="mouse")
self.assertEqual(len(genes), 1)
self.assertIsInstance(genes[0], Gene)
self.assertEqual(genes[0].gene_symbol(), "Kcnma1")
self.assertEqual(genes[0].species(), "Mouse")
def test_species_database_properties(self, mock_json_retriever):
mock_json_retriever.return_value = self.database_json
target = Target(self.target_json)
links = target.database_links(species="mouse")
self.assertEqual(len(links), 1)
self.assertIsInstance(links[0], DatabaseLink)
self.assertEqual(links[0].accession(), "11863")
self.assertEqual(links[0].species(), "Mouse")
def test_can_get_uniprot_pdbs_by_species(self, mock_xml_retriever, mock_json_retriever):
mock_json_retriever.return_value = [
{"accession": "10576", "database": "UniProtKB", "species": "Human", "url":"http"},
{"accession": "10576", "database": "UniProtKB", "species": "Rat", "url":"http"}
]
mock_xml_retriever.side_effect = [["2XG3", "3A1I"], ["1xxx"]]
target = Target(self.target_json)
pdbs = target.uniprot_pdbs(species="rat")
self.assertEqual(pdbs, ["2XG3", "3A1I"])
def test_species_database_properties(self, mock_json_retriever):
mock_json_retriever.return_value = self.database_json
target = Target(self.target_json)
links = target.database_links(species="mouse")
self.assertEqual(len(links), 1)
self.assertIsInstance(links[0], DatabaseLink)
self.assertEqual(links[0].accession(), "11863")
self.assertEqual(links[0].species(), "Mouse")
def test_species_gene_properties(self, mock_json_retriever):
mock_json_retriever.return_value = self.gene_json
target = Target(self.target_json)
genes = target.genes(species="mouse")
self.assertEqual(len(genes), 1)
self.assertIsInstance(genes[0], Gene)
self.assertEqual(genes[0].gene_symbol(), "Kcnma1")
self.assertEqual(genes[0].species(), "Mouse")
def test_can_get_ligands(self, mock_json_retriever):
mock_json_retriever.side_effect = [[
self.interaction_json, self.interaction_json
], self.ligand_json, self.ligand_json]
target = Target(self.target_json)
ligands = target.ligands()
self.assertIsInstance(ligands, list)
self.assertEqual(len(ligands), 2)
for ligand in ligands:
self.assertIsInstance(ligand, Ligand)
def test_can_get_ligands(self, mock_json_retriever):
mock_json_retriever.side_effect = [
[self.interaction_json, self.interaction_json], self.ligand_json, self.ligand_json
]
target = Target(self.target_json)
ligands = target.ligands()
self.assertIsInstance(ligands, list)
self.assertEqual(len(ligands), 2)
for ligand in ligands:
self.assertIsInstance(ligand, Ligand)
def test_basic_property_methods(self):
target = Target(self.target_json)
self.assertIs(target._target_id, target.target_id())
self.assertIs(target._name, target.name())
self.assertIs(target._abbreviation, target.abbreviation())
self.assertIs(target._systematic_name, target.systematic_name())
self.assertIs(target._target_type, target.target_type())
self.assertIs(target._family_ids, target.family_ids())
self.assertIs(target._subunit_ids, target.subunit_ids())
self.assertIs(target._complex_ids, target.complex_ids())
def test_can_get_interactions(self, mock_json_retriever):
mock_json_retriever.return_value = [
self.interaction_json, self.interaction_json
]
target = Target(self.target_json)
interactions = target.interactions()
self.assertIsInstance(interactions, list)
self.assertEqual(len(interactions), 2)
for interaction in interactions:
self.assertIsInstance(interaction, Interaction)
def test_database_properties(self, mock_json_retriever):
mock_json_retriever.return_value = self.database_json
target = Target(self.target_json)
self.assertEqual(len(target.database_links()), 2)
self.assertIsInstance(target.database_links()[0], DatabaseLink)
self.assertIsInstance(target.database_links()[1], DatabaseLink)
self.assertEqual(target.database_links()[0].accession(), "10576")
self.assertEqual(target.database_links()[1].accession(), "11863")
self.assertEqual(target.database_links()[0].species(), "Rat")
self.assertEqual(target.database_links()[1].species(), "Mouse")
def test_can_get_all_pdbs(self, mock_xml_retriever, mock_json_retriever):
mock_json_retriever.side_effect = [
self.pdb_json,
[{"accession": "10576", "database": "UniProtKB", "species": "Human", "url":"http"}]
]
mock_xml_retriever.return_value = ["2XG3", "3A1I"]
target = Target(self.target_json)
pdbs = target.all_pdbs()
self.assertEqual(len(pdbs), 4)
for code in ["4IAQ", "4IAR", "2XG3", "3A1I"]:
self.assertIn(code, pdbs)
def test_synonym_properties(self, mock_json_retriever):
mock_json_retriever.return_value = [{
"name": "ADRBRL1",
"refs": []
}, {
"name": "5-HT1A",
"refs": []
}]
target = Target(self.target_json)
self.assertEqual(target.synonyms(), ["ADRBRL1", "5-HT1A"])
def test_can_get_uniprot_pdbs_when_no_results(self, mock_xml_retriever,
mock_json_retriever):
mock_json_retriever.return_value = [{
"accession": "10576",
"database": "UniProtKB",
"species": "Human",
"url": "http"
}]
mock_xml_retriever.return_value = None
target = Target(self.target_json)
pdbs = target.uniprot_pdbs()
self.assertEqual(pdbs, [])
def test_basic_property_methods(self):
target = Target(self.target_json)
self.assertIs(target._target_id, target.target_id())
self.assertIs(target._name, target.name())
self.assertIs(target._abbreviation, target.abbreviation())
self.assertIs(target._systematic_name, target.systematic_name())
self.assertIs(target._target_type, target.target_type())
self.assertIs(target._family_ids, target.family_ids())
self.assertIs(target._subunit_ids, target.subunit_ids())
self.assertIs(target._complex_ids, target.complex_ids())
def test_can_get_families(self, mock_json_retriever):
mock_json_retriever.return_value = {
"familyId": 1,
"name": "5-Hydroxytryptamine receptors",
"targetIds": [1, 2, 5],
"parentFamilyIds": [694],
"subFamilyIds": [9]
}
target = Target(self.target_json)
families = target.families()
self.assertIsInstance(families, list)
self.assertEqual(len(families), len(self.target_json["familyIds"]))
for family in families:
self.assertIsInstance(family, TargetFamily)
def test_can_get_families(self, mock_json_retriever):
mock_json_retriever.return_value = {
"familyId": 1,
"name": "5-Hydroxytryptamine receptors",
"targetIds": [1, 2, 5],
"parentFamilyIds": [694],
"subFamilyIds": [9]
}
target = Target(self.target_json)
families = target.families()
self.assertIsInstance(families, list)
self.assertEqual(len(families), len(self.target_json["familyIds"]))
for family in families:
self.assertIsInstance(family, TargetFamily)
def test_can_get_all_pdbs(self, mock_xml_retriever, mock_json_retriever):
mock_json_retriever.side_effect = [
self.pdb_json,
[{
"accession": "10576",
"database": "UniProtKB",
"species": "Human",
"url": "http"
}]
]
mock_xml_retriever.return_value = ["2XG3", "3A1I"]
target = Target(self.target_json)
pdbs = target.all_pdbs()
self.assertEqual(len(pdbs), 4)
for code in ["4IAQ", "4IAR", "2XG3", "3A1I"]:
self.assertIn(code, pdbs)
def test_can_get_uniprot_pdbs_by_species(self, mock_xml_retriever,
mock_json_retriever):
mock_json_retriever.return_value = [{
"accession": "10576",
"database": "UniProtKB",
"species": "Human",
"url": "http"
}, {
"accession": "10576",
"database": "UniProtKB",
"species": "Rat",
"url": "http"
}]
mock_xml_retriever.side_effect = [["2XG3", "3A1I"], ["1xxx"]]
target = Target(self.target_json)
pdbs = target.uniprot_pdbs(species="rat")
self.assertEqual(pdbs, ["2XG3", "3A1I"])
def test_can_create_target(self):
target = Target(self.target_json)
self.assertEqual(target.json_data, self.target_json)
self.assertEqual(target._target_id, 1)
self.assertEqual(target._name, "5-HT<sub>1A</sub> receptor")
self.assertEqual(target._abbreviation, "5-HT")
self.assertEqual(target._systematic_name, None)
self.assertEqual(target._target_type, "GPCR")
self.assertEqual(target._family_ids, [1])
self.assertEqual(target._subunit_ids, [2, 3])
self.assertEqual(target._complex_ids, [4])
def test_gene_properties(self, mock_json_retriever):
mock_json_retriever.return_value = self.gene_json
target = Target(self.target_json)
self.assertEqual(len(target.genes()), 3)
self.assertIsInstance(target.genes()[0], Gene)
self.assertIsInstance(target.genes()[1], Gene)
self.assertIsInstance(target.genes()[2], Gene)
self.assertEqual(target.genes()[0].gene_symbol(), "KCNMA1")
self.assertEqual(target.genes()[1].gene_symbol(), "Kcnma1")
self.assertEqual(target.genes()[2].gene_symbol(), "Kcnma2")
def test_gene_properties(self, mock_json_retriever):
mock_json_retriever.return_value = self.gene_json
target = Target(self.target_json)
self.assertEqual(len(target.genes()), 3)
self.assertIsInstance(target.genes()[0], Gene)
self.assertIsInstance(target.genes()[1], Gene)
self.assertIsInstance(target.genes()[2], Gene)
self.assertEqual(target.genes()[0].gene_symbol(), "KCNMA1")
self.assertEqual(target.genes()[1].gene_symbol(), "Kcnma1")
self.assertEqual(target.genes()[2].gene_symbol(), "Kcnma2")
def test_database_properties(self, mock_json_retriever):
mock_json_retriever.return_value = self.database_json
target = Target(self.target_json)
self.assertEqual(len(target.database_links()), 2)
self.assertIsInstance(target.database_links()[0], DatabaseLink)
self.assertIsInstance(target.database_links()[1], DatabaseLink)
self.assertEqual(target.database_links()[0].accession(), "10576")
self.assertEqual(target.database_links()[1].accession(), "11863")
self.assertEqual(target.database_links()[0].species(), "Rat")
self.assertEqual(target.database_links()[1].species(), "Mouse")
def test_can_get_gtop_pdbs_by_species(self, mock_json_retriever):
mock_json_retriever.return_value = self.pdb_json
target = Target(self.target_json)
pdbs = target.gtop_pdbs(species="rat")
self.assertEqual(pdbs, ["4IAR"])
def test_gtop_pdbs_when_no_json(self, mock_json_retriever):
mock_json_retriever.return_value = None
target = Target(self.target_json)
self.assertEqual(target.gtop_pdbs(), [])
def test_gene_properties_when_no_json(self, mock_json_retriever):
mock_json_retriever.return_value = None
target = Target(self.target_json)
self.assertEqual(target.genes(), [])
def test_interactions_when_no_json(self, mock_json_retriever):
mock_json_retriever.return_value = None
target = Target(self.target_json)
self.assertEqual(target.interactions(), [])
def test_cannot_get_interaction_by_invalid_id(self, mock_json_retriever):
mock_json_retriever.return_value = None
target = Target(self.target_json)
with self.assertRaises(exceptions.NoSuchInteractionError):
interaction = target.get_interaction_by_id(0)
def test_interactions_when_no_json(self, mock_json_retriever):
mock_json_retriever.return_value = None
target = Target(self.target_json)
self.assertEqual(target.interactions(), [])
def test_cannot_get_interaction_by_invalid_id(self, mock_json_retriever):
mock_json_retriever.return_value = None
target = Target(self.target_json)
with self.assertRaises(exceptions.NoSuchInteractionError):
interaction = target.get_interaction_by_id(0)
def test_interaction_id_id_must_be_int(self, mock_json_retriever):
mock_json_retriever.return_value =[self.interaction_json, self.interaction_json]
target = Target(self.target_json)
with self.assertRaises(TypeError):
target.get_interaction_by_id("1")
def test_gtop_pdbs_when_no_json(self, mock_json_retriever):
mock_json_retriever.return_value = None
target = Target(self.target_json)
self.assertEqual(target.gtop_pdbs(), [])
def test_can_get_gtop_pdbs_by_species(self, mock_json_retriever):
mock_json_retriever.return_value = self.pdb_json
target = Target(self.target_json)
pdbs = target.gtop_pdbs(species="rat")
self.assertEqual(pdbs, ["4IAR"])
def test_gene_properties_when_no_json(self, mock_json_retriever):
mock_json_retriever.return_value = None
target = Target(self.target_json)
self.assertEqual(target.genes(), [])
def test_target_repr(self):
target = Target(self.target_json)
self.assertEqual(str(target),
"<Target 1 (5-HT<sub>1A</sub> receptor)>")
def test_can_get_interaction_by_id(self, mock_json_retriever):
mock_json_retriever.return_value = [self.interaction_json, self.interaction_json]
target = Target(self.target_json)
interaction = target.get_interaction_by_id(self.interaction_json["interactionId"])
self.assertIsInstance(interaction, Interaction)