diff options
Diffstat (limited to 'tests/unit/db')
| -rw-r--r-- | tests/unit/db/test_datasets.py | 133 | ||||
| -rw-r--r-- | tests/unit/db/test_traits.py | 224 |
2 files changed, 357 insertions, 0 deletions
diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py new file mode 100644 index 0000000..38de0e2 --- /dev/null +++ b/tests/unit/db/test_datasets.py @@ -0,0 +1,133 @@ +"""Tests for gn3/db/datasets.py""" + +from unittest import mock, TestCase +from gn3.db.datasets import ( + retrieve_dataset_name, + retrieve_riset_fields, + retrieve_geno_riset_fields, + retrieve_publish_riset_fields, + retrieve_probeset_riset_fields) + +class TestDatasetsDBFunctions(TestCase): + """Test cases for datasets functions.""" + + def test_retrieve_dataset_name(self): + """Test that the function is called correctly.""" + for trait_type, thresh, trait_name, dataset_name, columns, table in [ + ["ProbeSet", 9, "probesetTraitName", "probesetDatasetName", + "Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze"], + ["Geno", 3, "genoTraitName", "genoDatasetName", + "Id, Name, FullName, ShortName", "GenoFreeze"], + ["Publish", 6, "publishTraitName", "publishDatasetName", + "Id, Name, FullName, ShortName", "PublishFreeze"], + ["Temp", 4, "tempTraitName", "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 = {} + self.assertEqual( + retrieve_dataset_name( + trait_type, thresh, trait_name, dataset_name, db_mock), + {}) + cursor.execute.assert_called_once_with( + "SELECT {cols} " + "FROM {table} " + "WHERE public > %(threshold)s AND " + "(Name = %(name)s " + "OR FullName = %(name)s " + "OR ShortName = %(name)s)".format( + table=table, cols=columns), + {"threshold": thresh, "name": dataset_name}) + + def test_retrieve_probeset_riset_fields(self): + """ + Test that the `riset` and `riset_id` fields are retrieved appropriately + for the 'ProbeSet' trait type. + """ + for trait_name, expected in [ + ["testProbeSetName", {}]]: + db_mock = mock.MagicMock() + with self.subTest(trait_name=trait_name, expected=expected): + with db_mock.cursor() as cursor: + cursor.execute.return_value = () + self.assertEqual( + retrieve_probeset_riset_fields(trait_name, db_mock), + expected) + cursor.execute.assert_called_once_with( + ( + "SELECT InbredSet.Name, InbredSet.Id" + " FROM InbredSet, ProbeSetFreeze, ProbeFreeze" + " WHERE ProbeFreeze.InbredSetId = InbredSet.Id" + " AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId" + " AND ProbeSetFreeze.Name = %(name)s"), + {"name": trait_name}) + + def test_retrieve_riset_fields(self): + """ + Test that the riset fields are set up correctly for the different trait + types. + """ + for trait_type, trait_name, dataset_info, expected in [ + ["Publish", "pubTraitName01", {"dataset_name": "pubDBName01"}, + {"dataset_name": "pubDBName01", "riset": ""}], + ["ProbeSet", "prbTraitName01", {"dataset_name": "prbDBName01"}, + {"dataset_name": "prbDBName01", "riset": ""}], + ["Geno", "genoTraitName01", {"dataset_name": "genoDBName01"}, + {"dataset_name": "genoDBName01", "riset": ""}], + ["Temp", "tempTraitName01", {}, {"riset": ""}], + ]: + db_mock = mock.MagicMock() + with self.subTest( + trait_type=trait_type, trait_name=trait_name, + dataset_info=dataset_info): + with db_mock.cursor() as cursor: + cursor.execute.return_value = ("riset_name", 0) + self.assertEqual( + retrieve_riset_fields( + trait_type, trait_name, dataset_info, db_mock), + expected) + + def test_retrieve_publish_riset_fields(self): + """ + Test that the `riset` and `riset_id` fields are retrieved appropriately + for the 'Publish' trait type. + """ + for trait_name, expected in [ + ["testPublishName", {}]]: + db_mock = mock.MagicMock() + with self.subTest(trait_name=trait_name, expected=expected): + with db_mock.cursor() as cursor: + cursor.execute.return_value = () + self.assertEqual( + retrieve_publish_riset_fields(trait_name, db_mock), + expected) + cursor.execute.assert_called_once_with( + ( + "SELECT InbredSet.Name, InbredSet.Id" + " FROM InbredSet, PublishFreeze" + " WHERE PublishFreeze.InbredSetId = InbredSet.Id" + " AND PublishFreeze.Name = %(name)s"), + {"name": trait_name}) + + def test_retrieve_geno_riset_fields(self): + """ + Test that the `riset` and `riset_id` fields are retrieved appropriately + for the 'Geno' trait type. + """ + for trait_name, expected in [ + ["testGenoName", {}]]: + db_mock = mock.MagicMock() + with self.subTest(trait_name=trait_name, expected=expected): + with db_mock.cursor() as cursor: + cursor.execute.return_value = () + self.assertEqual( + retrieve_geno_riset_fields(trait_name, db_mock), + expected) + cursor.execute.assert_called_once_with( + ( + "SELECT InbredSet.Name, InbredSet.Id" + " FROM InbredSet, GenoFreeze" + " WHERE GenoFreeze.InbredSetId = InbredSet.Id" + " AND GenoFreeze.Name = %(name)s"), + {"name": trait_name}) diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py new file mode 100644 index 0000000..ee98893 --- /dev/null +++ b/tests/unit/db/test_traits.py @@ -0,0 +1,224 @@ +"""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", "dataset_type": "ProbeSet"}, + "trait_name": "testname", "cellid": "", + "trait_fullname": "testdb::testname"}], + ["testdb::testname::testcell", + {"db": {"dataset_name": "testdb", "dataset_type": "ProbeSet"}, + "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 threshold, trait_fullname, expected in [ + [9, "pubDb::PublishTraitName::pubCell", {"haveinfo": 0}], + [5, "prbDb::ProbeSetTraitName::prbCell", {"haveinfo": 0}], + [12, "genDb::GenoTraitName", {"haveinfo": 0}], + [6, "tmpDb::TempTraitName", {"haveinfo": 0}]]: + db_mock = mock.MagicMock() + with self.subTest(trait_fullname=trait_fullname): + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = tuple() + self.assertEqual( + retrieve_trait_info( + 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) |