"""Tests for gn3/db/traits.py""" from unittest import mock, TestCase from gn3.db.traits import ( retrieve_trait_info, retrieve_geno_trait_info, retrieve_temp_trait_info, retrieve_trait_dataset_name, retrieve_publish_trait_info, retrieve_probeset_trait_info, update_sample_data) class TestTraitsDBFunctions(TestCase): "Test cases for traits functions" def test_retrieve_trait_dataset_name(self): """Test that the function is called correctly.""" for trait_type, thresh, trait_dataset_name, columns, table in [ ["ProbeSet", 9, "testName", "Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze"], ["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName", "GenoFreeze"], ["Publish", 6, "publishTraitName", "Id, Name, FullName, ShortName", "PublishFreeze"], ["Temp", 4, "tempTraitName", "Id, Name, FullName, ShortName", "TempFreeze"]]: db_mock = mock.MagicMock() with self.subTest(trait_type=trait_type): with db_mock.cursor() as cursor: cursor.fetchone.return_value = ( "testName", "testNameFull", "testNameShort", "dataScale") self.assertEqual( retrieve_trait_dataset_name( trait_type, thresh, trait_dataset_name, db_mock), ("testName", "testNameFull", "testNameShort", "dataScale")) cursor.execute.assert_called_once_with( "SELECT %(columns)s " "FROM %(table)s " "WHERE public > %(threshold)s AND " "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)".format( cols=columns, ttype=trait_type), {"threshold": thresh, "name": trait_dataset_name, "table": table, "columns": columns}) 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_retrieve_trait_info(self): """Test that information on traits is retrieved as appropriate.""" for trait_type, trait_name, trait_dataset_id, trait_dataset_name, expected in [ ["Publish", "PublishTraitName", 1, "PublishDatasetTraitName", {"haveinfo": 0, "homologeneid": None, "type": "Publish", "confidential": 0}], ["ProbeSet", "ProbeSetTraitName", 2, "ProbeSetDatasetTraitName", {"haveinfo": 0, "homologeneid": None, "type": "ProbeSet"}], ["Geno", "GenoTraitName", 3, "GenoDatasetTraitName", {"haveinfo": 0, "homologeneid": None, "type": "Geno"}], ["Temp", "TempTraitName", 4, "TempDatasetTraitName", {"haveinfo": 0, "homologeneid": None, "type": "Temp"}]]: 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, trait_name, trait_dataset_id, trait_dataset_name, 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))] )