diff options
Diffstat (limited to 'tests/unit/db/test_traits.py')
| -rw-r--r-- | tests/unit/db/test_traits.py | 83 |
1 files changed, 65 insertions, 18 deletions
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py index c8f28b5..393983d 100644 --- a/tests/unit/db/test_traits.py +++ b/tests/unit/db/test_traits.py @@ -1,11 +1,6 @@ """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 ( retrieve_trait_info, retrieve_geno_trait_info, retrieve_temp_trait_info, @@ -14,7 +9,6 @@ from gn3.db.traits import ( retrieve_probeset_trait_info, update_sample_data) - class TestTraitsDBFunctions(TestCase): "Test cases for traits functions" @@ -54,12 +48,32 @@ 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 +84,31 @@ 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 +119,19 @@ 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.""" @@ -94,9 +140,10 @@ 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_retrieve_trait_info(self): """Test that information on traits is retrieved as appropriate.""" @@ -113,7 +160,7 @@ class TestTraitsDBFunctions(TestCase): retrieve_trait_info( trait_type, trait_name, trait_dataset_id, trait_dataset_name, db_mock), - tuple()) + {}) def test_update_sample_data(self): """Test that the SQL queries when calling update_sample_data are called with |