diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/unit/db/test_datasets.py | 133 | ||||
| -rw-r--r-- | tests/unit/db/test_traits.py | 200 |
2 files changed, 277 insertions, 56 deletions
diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py new file mode 100644 index 0000000..34fe7f0 --- /dev/null +++ b/tests/unit/db/test_datasets.py @@ -0,0 +1,133 @@ +from unittest import mock, TestCase + +class TestDatasetsDBFunctions(TestCase): + + 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_set_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( + set_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_set_riset_fields(self): + """ + Test that the riset fields are set up correctly for the different trait + types. + """ + for trait_info, expected in [ + [{}, {}], + [{"haveinfo": 0, "type": "Publish"}, + {"haveinfo": 0, "type": "Publish"}], + [{"haveinfo": 0, "type": "ProbeSet"}, + {"haveinfo": 0, "type": "ProbeSet"}], + [{"haveinfo": 0, "type": "Geno"}, + {"haveinfo": 0, "type": "Geno"}], + [{"haveinfo": 0, "type": "Temp"}, + {"haveinfo": 0, "type": "Temp"}], + [{"haveinfo": 1, "type": "Publish", "name": "test"}, + {"haveinfo": 1, "type": "Publish", "name": "test", + "riset": "riset_name", "risetid": 0}], + [{"haveinfo": 1, "type": "ProbeSet", "name": "test"}, + {"haveinfo": 1, "type": "ProbeSet", "name": "test", + "riset": "riset_name", "risetid": 0}], + [{"haveinfo": 1, "type": "Geno", "name": "test"}, + {"haveinfo": 1, "type": "Geno", "name": "test", + "riset": "riset_name", "risetid": 0}], + [{"haveinfo": 1, "type": "Temp", "name": "test"}, + {"haveinfo": 1, "type": "Temp", "name": "test", "riset": None, + "risetid": None}] + ]: + db_mock = mock.MagicMock() + with self.subTest(trait_info=trait_info, expected=expected): + with db_mock.cursor() as cursor: + cursor.execute.return_value = ("riset_name", 0) + self.assertEqual( + set_riset_fields(trait_info, db_mock), expected) + + def test_set_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( + set_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_set_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( + set_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 index c8f28b5..7d161bf 100644 --- a/tests/unit/db/test_traits.py +++ b/tests/unit/db/test_traits.py @@ -1,51 +1,20 @@ """Tests for gn3/db/traits.py""" from unittest import mock, TestCase from gn3.db.traits import ( - GENO_TRAIT_INFO_QUERY, - TEMP_TRAIT_INFO_QUERY, - PUBLISH_TRAIT_INFO_QUERY, - PROBESET_TRAIT_INFO_QUERY) -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_trait_dataset_name, retrieve_publish_trait_info, - retrieve_probeset_trait_info, - update_sample_data) - + retrieve_probeset_trait_info) 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 in [ - ["ProbeSet", 9, "testName", - "Id, Name, FullName, ShortName, DataScale"], - ["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName"], - ["Publish", 6, "publishTraitName", - "Id, Name, FullName, ShortName"], - ["Temp", 4, "tempTraitName", "Id, Name, FullName, ShortName"]]: - 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 {cols} " - "FROM {ttype}Freeze " - "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}) - def test_retrieve_publish_trait_info(self): """Test retrieval of type `Publish` traits.""" db_mock = mock.MagicMock() @@ -54,12 +23,32 @@ class TestTraitsDBFunctions(TestCase): trait_source = { "trait_name": "PublishTraitName", "trait_dataset_id": 1} self.assertEqual( - retrieve_publish_trait_info( - trait_source, - db_mock), - tuple()) + retrieve_publish_trait_info(trait_source, db_mock), {}) cursor.execute.assert_called_once_with( - PUBLISH_TRAIT_INFO_QUERY, trait_source) + ("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.""" @@ -70,9 +59,31 @@ class TestTraitsDBFunctions(TestCase): "trait_name": "ProbeSetTraitName", "trait_dataset_name": "ProbeSetDatasetTraitName"} self.assertEqual( - retrieve_probeset_trait_info(trait_source, db_mock), tuple()) + retrieve_probeset_trait_info(trait_source, db_mock), {}) cursor.execute.assert_called_once_with( - PROBESET_TRAIT_INFO_QUERY, trait_source) + ( + "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.""" @@ -83,9 +94,19 @@ class TestTraitsDBFunctions(TestCase): "trait_name": "GenoTraitName", "trait_dataset_name": "GenoDatasetTraitName"} self.assertEqual( - retrieve_geno_trait_info(trait_source, db_mock), tuple()) + retrieve_geno_trait_info(trait_source, db_mock), {}) cursor.execute.assert_called_once_with( - GENO_TRAIT_INFO_QUERY, trait_source) + ( + "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.""" @@ -94,26 +115,60 @@ class TestTraitsDBFunctions(TestCase): cursor.fetchone.return_value = tuple() trait_source = {"trait_name": "TempTraitName"} self.assertEqual( - retrieve_temp_trait_info(trait_source, db_mock), tuple()) + retrieve_temp_trait_info(trait_source, db_mock), {}) cursor.execute.assert_called_once_with( - TEMP_TRAIT_INFO_QUERY, trait_source) + "SELECT name, description FROM Temp WHERE Name = %(trait_name)s", + trait_source) + + def test_build_trait_name_with_good_fullnames(self): + 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): + 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, trait_name, trait_dataset_id, trait_dataset_name, in [ - ["Publish", "PublishTraitName", 1, "PublishDatasetTraitName"], - ["ProbeSet", "ProbeSetTraitName", 2, "ProbeSetDatasetTraitName"], - ["Geno", "GenoTraitName", 3, "GenoDatasetTraitName"], - ["Temp", "TempTraitName", 4, "TempDatasetTraitName"]]: + for trait_type, threshold, trait_fullname, expected in [ + ["Publish", 9, "pubDb::PublishTraitName::pubCell", + {"haveinfo": 0, "homologeneid": None, "type": "Publish", + "confidential": 0, "db": {"dataset_name": "pubDb"}, + "trait_name": "PublishTraitName", "cellid": "pubCell", + "trait_fullname": "pubDb::PublishTraitName::pubCell"}], + ["ProbeSet", 5, "prbDb::ProbeSetTraitName::prbCell", + {"haveinfo": 0, "homologeneid": None, "type": "ProbeSet", + "trait_fullname": "prbDb::ProbeSetTraitName::prbCell", + "db": {"dataset_name": "prbDb"}, + "trait_name": "ProbeSetTraitName", "cellid": "prbCell"}], + ["Geno", 12, "genDb::GenoTraitName", + {"haveinfo": 0, "homologeneid": None, "type": "Geno", + "trait_fullname": "genDb::GenoTraitName", + "db": {"dataset_name": "genDb"}, + "trait_name": "GenoTraitName", "cellid": ""}], + ["Temp", 6, "tmpDb::TempTraitName", + {"haveinfo": 0, "homologeneid": None, "type": "Temp", + "trait_fullname": "tmpDb::TempTraitName", + "db": {"dataset_name": "tmpDb"}, + "trait_name": "TempTraitName", "cellid": ""}]]: 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), - tuple()) + 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 @@ -143,3 +198,36 @@ class TestTraitsDBFunctions(TestCase): 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) |