"""Tests for gn3/db/traits.py""" from unittest import mock, TestCase from gn3.db.traits import ( build_trait_name, set_haveinfo_field, update_sample_data, retrieve_trait_info, set_confidential_field, set_homologene_id_field, retrieve_geno_trait_info, retrieve_temp_trait_info, retrieve_publish_trait_info, retrieve_probeset_trait_info) class TestTraitsDBFunctions(TestCase): "Test cases for traits functions" def test_retrieve_publish_trait_info(self): """Test retrieval of type `Publish` traits.""" db_mock = mock.MagicMock() with db_mock.cursor() as cursor: cursor.fetchone.return_value = tuple() trait_source = { "trait_name": "PublishTraitName", "trait_dataset_id": 1} self.assertEqual( retrieve_publish_trait_info(trait_source, db_mock), {}) cursor.execute.assert_called_once_with( ("SELECT " "PublishXRef.Id, Publication.PubMed_ID," " Phenotype.Pre_publication_description," " Phenotype.Post_publication_description," " Phenotype.Original_description," " Phenotype.Pre_publication_abbreviation," " Phenotype.Post_publication_abbreviation," " Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner," " Phenotype.Authorized_Users," " CAST(Publication.Authors AS BINARY)," " Publication.Title, Publication.Abstract," " Publication.Journal," " Publication.Volume, Publication.Pages, Publication.Month," " Publication.Year, PublishXRef.Sequence, Phenotype.Units," " PublishXRef.comments" " FROM" " PublishXRef, Publication, Phenotype, PublishFreeze" " WHERE" " PublishXRef.Id = %(trait_name)s" " AND Phenotype.Id = PublishXRef.PhenotypeId" " AND Publication.Id = PublishXRef.PublicationId" " AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId" " AND PublishFreeze.Id =%(trait_dataset_id)s"), trait_source) def test_retrieve_probeset_trait_info(self): """Test retrieval of type `Probeset` traits.""" db_mock = mock.MagicMock() with db_mock.cursor() as cursor: cursor.fetchone.return_value = tuple() trait_source = { "trait_name": "ProbeSetTraitName", "trait_dataset_name": "ProbeSetDatasetTraitName"} self.assertEqual( retrieve_probeset_trait_info(trait_source, db_mock), {}) cursor.execute.assert_called_once_with( ( "SELECT " "ProbeSet.name, ProbeSet.symbol, ProbeSet.description, " "ProbeSet.probe_target_description, ProbeSet.chr, " "ProbeSet.mb, ProbeSet.alias, ProbeSet.geneid, " "ProbeSet.genbankid, ProbeSet.unigeneid, ProbeSet.omim, " "ProbeSet.refseq_transcriptid, ProbeSet.blatseq, " "ProbeSet.targetseq, ProbeSet.chipid, ProbeSet.comments, " "ProbeSet.strand_probe, ProbeSet.strand_gene, " "ProbeSet.probe_set_target_region, ProbeSet.proteinid, " "ProbeSet.probe_set_specificity, " "ProbeSet.probe_set_blat_score, " "ProbeSet.probe_set_blat_mb_start, " "ProbeSet.probe_set_blat_mb_end, " "ProbeSet.probe_set_strand, ProbeSet.probe_set_note_by_rw, " "ProbeSet.flag " "FROM " "ProbeSet, ProbeSetFreeze, ProbeSetXRef " "WHERE " "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id " "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id " "AND ProbeSetFreeze.Name = %(trait_dataset_name)s " "AND ProbeSet.Name = %(trait_name)s"), trait_source) def test_retrieve_geno_trait_info(self): """Test retrieval of type `Geno` traits.""" db_mock = mock.MagicMock() with db_mock.cursor() as cursor: cursor.fetchone.return_value = tuple() trait_source = { "trait_name": "GenoTraitName", "trait_dataset_name": "GenoDatasetTraitName"} self.assertEqual( retrieve_geno_trait_info(trait_source, db_mock), {}) cursor.execute.assert_called_once_with( ( "SELECT " "Geno.name, Geno.chr, Geno.mb, Geno.source2, Geno.sequence " "FROM " "Geno, GenoFreeze, GenoXRef " "WHERE " "GenoXRef.GenoFreezeId = GenoFreeze.Id " "AND GenoXRef.GenoId = Geno.Id " "AND GenoFreeze.Name = %(trait_dataset_name)s " "AND Geno.Name = %(trait_name)s"), trait_source) def test_retrieve_temp_trait_info(self): """Test retrieval of type `Temp` traits.""" db_mock = mock.MagicMock() with db_mock.cursor() as cursor: cursor.fetchone.return_value = tuple() trait_source = {"trait_name": "TempTraitName"} self.assertEqual( retrieve_temp_trait_info(trait_source, db_mock), {}) cursor.execute.assert_called_once_with( "SELECT name, description FROM Temp WHERE Name = %(trait_name)s", trait_source) def test_build_trait_name_with_good_fullnames(self): """ Check that the name is built correctly. """ for fullname, expected in [ ["testdb::testname", {"db": {"dataset_name": "testdb"}, "trait_name": "testname", "cellid": "", "trait_fullname": "testdb::testname"}], ["testdb::testname::testcell", {"db": {"dataset_name": "testdb"}, "trait_name": "testname", "cellid": "testcell", "trait_fullname": "testdb::testname::testcell"}]]: with self.subTest(fullname=fullname): self.assertEqual(build_trait_name(fullname), expected) def test_build_trait_name_with_bad_fullnames(self): """ Check that an exception is raised if the full name format is wrong. """ for fullname in ["", "test", "test:test"]: with self.subTest(fullname=fullname): with self.assertRaises(AssertionError, msg="Name format error"): build_trait_name(fullname) def test_retrieve_trait_info(self): """Test that information on traits is retrieved as appropriate.""" for trait_type, threshold, trait_fullname, expected in [ ["Publish", 9, "pubDb::PublishTraitName::pubCell", {"haveinfo": 0}], ["ProbeSet", 5, "prbDb::ProbeSetTraitName::prbCell", {"haveinfo": 0}], ["Geno", 12, "genDb::GenoTraitName", {"haveinfo": 0}], ["Temp", 6, "tmpDb::TempTraitName", {"haveinfo": 0}]]: db_mock = mock.MagicMock() with self.subTest(trait_type=trait_type): with db_mock.cursor() as cursor: cursor.fetchone.return_value = tuple() self.assertEqual( retrieve_trait_info( trait_type, threshold, trait_fullname, db_mock), expected) def test_update_sample_data(self): """Test that the SQL queries when calling update_sample_data are called with the right calls. """ db_mock = mock.MagicMock() STRAIN_ID_SQL: str = "UPDATE Strain SET Name = %s WHERE Id = %s" PUBLISH_DATA_SQL: str = ("UPDATE PublishData SET value = %s " "WHERE StrainId = %s AND Id = %s") PUBLISH_SE_SQL: str = ("UPDATE PublishSE SET error = %s " "WHERE StrainId = %s AND DataId = %s") N_STRAIN_SQL: str = ("UPDATE NStrain SET count = %s " "WHERE StrainId = %s AND DataId = %s") with db_mock.cursor() as cursor: type(cursor).rowcount = 1 self.assertEqual(update_sample_data( conn=db_mock, strain_name="BXD11", strain_id=10, publish_data_id=8967049, value=18.7, error=2.3, count=2), (1, 1, 1, 1)) cursor.execute.assert_has_calls( [mock.call(STRAIN_ID_SQL, ('BXD11', 10)), mock.call(PUBLISH_DATA_SQL, (18.7, 10, 8967049)), mock.call(PUBLISH_SE_SQL, (2.3, 10, 8967049)), mock.call(N_STRAIN_SQL, (2, 10, 8967049))] ) def test_set_haveinfo_field(self): """Test that the `haveinfo` field is set up correctly""" for trait_info, expected in [ [{}, {"haveinfo": 0}], [{"k1": "v1"}, {"k1": "v1", "haveinfo": 1}]]: with self.subTest(trait_info=trait_info, expected=expected): self.assertEqual(set_haveinfo_field(trait_info), expected) def test_set_homologene_id_field(self): """Test that the `homologene_id` field is set up correctly""" for trait_type, trait_info, expected in [ ["Publish", {}, {"homologeneid": None}], ["ProbeSet", {}, {"homologeneid": None}], ["Geno", {}, {"homologeneid": None}], ["Temp", {}, {"homologeneid": None}]]: db_mock = mock.MagicMock() with self.subTest(trait_info=trait_info, expected=expected): with db_mock.cursor() as cursor: cursor.fetchone.return_value = () self.assertEqual( set_homologene_id_field(trait_type, trait_info, db_mock), expected) def test_set_confidential_field(self): """Test that the `confidential` field is set up correctly""" for trait_type, trait_info, expected in [ ["Publish", {}, {"confidential": 0}], ["ProbeSet", {}, {}], ["Geno", {}, {}], ["Temp", {}, {}]]: with self.subTest(trait_info=trait_info, expected=expected): self.assertEqual( set_confidential_field(trait_type, trait_info), expected)