diff options
| -rw-r--r-- | gn3/db/datasets.py | 52 | ||||
| -rw-r--r-- | gn3/db/traits.py | 16 | ||||
| -rw-r--r-- | gn3/heatmaps.py | 2 | ||||
| -rw-r--r-- | tests/unit/db/test_datasets.py | 42 |
4 files changed, 56 insertions, 56 deletions
diff --git a/gn3/db/datasets.py b/gn3/db/datasets.py index 4a05499..6c328f5 100644 --- a/gn3/db/datasets.py +++ b/gn3/db/datasets.py @@ -119,9 +119,9 @@ def retrieve_dataset_name( return fn_map[trait_type](threshold, dataset_name, conn) -def retrieve_geno_riset_fields(name, conn): +def retrieve_geno_group_fields(name, conn): """ - Retrieve the RISet, and RISetID values for various Geno trait types. + Retrieve the Group, and GroupID values for various Geno trait types. """ query = ( "SELECT InbredSet.Name, InbredSet.Id " @@ -130,12 +130,12 @@ def retrieve_geno_riset_fields(name, conn): "AND GenoFreeze.Name = %(name)s") with conn.cursor() as cursor: cursor.execute(query, {"name": name}) - return dict(zip(["riset", "risetid"], cursor.fetchone())) + return dict(zip(["group", "groupid"], cursor.fetchone())) return {} -def retrieve_publish_riset_fields(name, conn): +def retrieve_publish_group_fields(name, conn): """ - Retrieve the RISet, and RISetID values for various Publish trait types. + Retrieve the Group, and GroupID values for various Publish trait types. """ query = ( "SELECT InbredSet.Name, InbredSet.Id " @@ -144,12 +144,12 @@ def retrieve_publish_riset_fields(name, conn): "AND PublishFreeze.Name = %(name)s") with conn.cursor() as cursor: cursor.execute(query, {"name": name}) - return dict(zip(["riset", "risetid"], cursor.fetchone())) + return dict(zip(["group", "groupid"], cursor.fetchone())) return {} -def retrieve_probeset_riset_fields(name, conn): +def retrieve_probeset_group_fields(name, conn): """ - Retrieve the RISet, and RISetID values for various ProbeSet trait types. + Retrieve the Group, and GroupID values for various ProbeSet trait types. """ query = ( "SELECT InbredSet.Name, InbredSet.Id " @@ -159,12 +159,12 @@ def retrieve_probeset_riset_fields(name, conn): "AND ProbeSetFreeze.Name = %(name)s") with conn.cursor() as cursor: cursor.execute(query, {"name": name}) - return dict(zip(["riset", "risetid"], cursor.fetchone())) + return dict(zip(["group", "groupid"], cursor.fetchone())) return {} -def retrieve_temp_riset_fields(name, conn): +def retrieve_temp_group_fields(name, conn): """ - Retrieve the RISet, and RISetID values for `Temp` trait types. + Retrieve the Group, and GroupID values for `Temp` trait types. """ query = ( "SELECT InbredSet.Name, InbredSet.Id " @@ -173,30 +173,30 @@ def retrieve_temp_riset_fields(name, conn): "AND Temp.Name = %(name)s") with conn.cursor() as cursor: cursor.execute(query, {"name": name}) - return dict(zip(["riset", "risetid"], cursor.fetchone())) + return dict(zip(["group", "groupid"], cursor.fetchone())) return {} -def retrieve_riset_fields(trait_type, trait_name, dataset_info, conn): +def retrieve_group_fields(trait_type, trait_name, dataset_info, conn): """ - Retrieve the RISet, and RISetID values for various trait types. + Retrieve the Group, and GroupID values for various trait types. """ - riset_fns_map = { - "Geno": retrieve_geno_riset_fields, - "Publish": retrieve_publish_riset_fields, - "ProbeSet": retrieve_probeset_riset_fields + group_fns_map = { + "Geno": retrieve_geno_group_fields, + "Publish": retrieve_publish_group_fields, + "ProbeSet": retrieve_probeset_group_fields } if trait_type == "Temp": - riset_info = retrieve_temp_riset_fields(trait_name, conn) + group_info = retrieve_temp_group_fields(trait_name, conn) else: - riset_info = riset_fns_map[trait_type](dataset_info["dataset_name"], conn) + group_info = group_fns_map[trait_type](dataset_info["dataset_name"], conn) return { **dataset_info, - **riset_info, - "riset": ( - "BXD" if riset_info.get("riset") == "BXD300" - else riset_info.get("riset", "")) + **group_info, + "group": ( + "BXD" if group_info.get("group") == "BXD300" + else group_info.get("group", "")) } def retrieve_temp_trait_dataset(): @@ -281,11 +281,11 @@ def retrieve_trait_dataset(trait_type, trait, threshold, conn): trait_type, threshold, trait["trait_name"], trait["db"]["dataset_name"], conn) } - riset = retrieve_riset_fields( + group = retrieve_group_fields( trait_type, trait["trait_name"], dataset_name_info, conn) return { "display_name": dataset_name_info["dataset_name"], **dataset_name_info, **dataset_fns[trait_type](), - **riset + **group } diff --git a/gn3/db/traits.py b/gn3/db/traits.py index c9d05d7..f2673c8 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -226,7 +226,7 @@ def set_homologene_id_field_probeset(trait_info, conn): """ query = ( "SELECT HomologeneId FROM Homologene, Species, InbredSet" - " WHERE Homologene.GeneId = %(geneid)s AND InbredSet.Name = %(riset)s" + " WHERE Homologene.GeneId = %(geneid)s AND InbredSet.Name = %(group)s" " AND InbredSet.SpeciesId = Species.Id AND" " Species.TaxonomyId = Homologene.TaxonomyId") with conn.cursor() as cursor: @@ -234,7 +234,7 @@ def set_homologene_id_field_probeset(trait_info, conn): query, { k:v for k, v in trait_info.items() - if k in ["geneid", "riset"] + if k in ["geneid", "group"] }) res = cursor.fetchone() if res: @@ -422,7 +422,7 @@ def retrieve_trait_info( if trait_info["haveinfo"]: return { **trait_post_processing_functions_table[trait_dataset_type]( - {**trait_info, "riset": trait_dataset["riset"]}), + {**trait_info, "group": trait_dataset["group"]}), "db": {**trait["db"], **trait_dataset} } return trait_info @@ -449,14 +449,14 @@ def retrieve_temp_trait_data(trait_info: dict, conn: Any): for row in cursor.fetchall()] return [] -def retrieve_species_id(riset, conn: Any): +def retrieve_species_id(group, conn: Any): """ - Retrieve a species id given the RISet value + Retrieve a species id given the Group value """ with conn.cursor as cursor: cursor.execute( - "SELECT SpeciesId from InbredSet WHERE Name = %(riset)s", - {"riset": riset}) + "SELECT SpeciesId from InbredSet WHERE Name = %(group)s", + {"group": group}) return cursor.fetchone()[0] return None @@ -482,7 +482,7 @@ def retrieve_geno_trait_data(trait_info: Dict, conn: Any): {"trait_name": trait_info["trait_name"], "dataset_name": trait_info["db"]["dataset_name"], "species_id": retrieve_species_id( - trait_info["db"]["riset"], conn)}) + trait_info["db"]["group"], conn)}) return [dict(zip( ["sample_name", "value", "se_error", "id"], row)) for row in cursor.fetchall()] diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py index b6fc6d3..a36940d 100644 --- a/gn3/heatmaps.py +++ b/gn3/heatmaps.py @@ -164,7 +164,7 @@ def build_heatmap(traits_names, conn: Any): retrieve_trait_info(threshold, fullname, conn) for fullname in traits_names] traits_data_list = [retrieve_trait_data(t, conn) for t in traits] - genotype_filename = build_genotype_file(traits[0]["riset"]) + genotype_filename = build_genotype_file(traits[0]["group"]) samples = load_genotype_samples(genotype_filename) exported_traits_data_list = [ export_trait_data(td, samples) for td in traits_data_list] diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py index 38de0e2..39f4af9 100644 --- a/tests/unit/db/test_datasets.py +++ b/tests/unit/db/test_datasets.py @@ -3,10 +3,10 @@ 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) + retrieve_group_fields, + retrieve_geno_group_fields, + retrieve_publish_group_fields, + retrieve_probeset_group_fields) class TestDatasetsDBFunctions(TestCase): """Test cases for datasets functions.""" @@ -40,9 +40,9 @@ class TestDatasetsDBFunctions(TestCase): table=table, cols=columns), {"threshold": thresh, "name": dataset_name}) - def test_retrieve_probeset_riset_fields(self): + def test_retrieve_probeset_group_fields(self): """ - Test that the `riset` and `riset_id` fields are retrieved appropriately + Test that the `group` and `group_id` fields are retrieved appropriately for the 'ProbeSet' trait type. """ for trait_name, expected in [ @@ -52,7 +52,7 @@ class TestDatasetsDBFunctions(TestCase): with db_mock.cursor() as cursor: cursor.execute.return_value = () self.assertEqual( - retrieve_probeset_riset_fields(trait_name, db_mock), + retrieve_probeset_group_fields(trait_name, db_mock), expected) cursor.execute.assert_called_once_with( ( @@ -63,34 +63,34 @@ class TestDatasetsDBFunctions(TestCase): " AND ProbeSetFreeze.Name = %(name)s"), {"name": trait_name}) - def test_retrieve_riset_fields(self): + def test_retrieve_group_fields(self): """ - Test that the riset fields are set up correctly for the different trait + Test that the group 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": ""}], + {"dataset_name": "pubDBName01", "group": ""}], ["ProbeSet", "prbTraitName01", {"dataset_name": "prbDBName01"}, - {"dataset_name": "prbDBName01", "riset": ""}], + {"dataset_name": "prbDBName01", "group": ""}], ["Geno", "genoTraitName01", {"dataset_name": "genoDBName01"}, - {"dataset_name": "genoDBName01", "riset": ""}], - ["Temp", "tempTraitName01", {}, {"riset": ""}], + {"dataset_name": "genoDBName01", "group": ""}], + ["Temp", "tempTraitName01", {}, {"group": ""}], ]: 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) + cursor.execute.return_value = ("group_name", 0) self.assertEqual( - retrieve_riset_fields( + retrieve_group_fields( trait_type, trait_name, dataset_info, db_mock), expected) - def test_retrieve_publish_riset_fields(self): + def test_retrieve_publish_group_fields(self): """ - Test that the `riset` and `riset_id` fields are retrieved appropriately + Test that the `group` and `group_id` fields are retrieved appropriately for the 'Publish' trait type. """ for trait_name, expected in [ @@ -100,7 +100,7 @@ class TestDatasetsDBFunctions(TestCase): with db_mock.cursor() as cursor: cursor.execute.return_value = () self.assertEqual( - retrieve_publish_riset_fields(trait_name, db_mock), + retrieve_publish_group_fields(trait_name, db_mock), expected) cursor.execute.assert_called_once_with( ( @@ -110,9 +110,9 @@ class TestDatasetsDBFunctions(TestCase): " AND PublishFreeze.Name = %(name)s"), {"name": trait_name}) - def test_retrieve_geno_riset_fields(self): + def test_retrieve_geno_group_fields(self): """ - Test that the `riset` and `riset_id` fields are retrieved appropriately + Test that the `group` and `group_id` fields are retrieved appropriately for the 'Geno' trait type. """ for trait_name, expected in [ @@ -122,7 +122,7 @@ class TestDatasetsDBFunctions(TestCase): with db_mock.cursor() as cursor: cursor.execute.return_value = () self.assertEqual( - retrieve_geno_riset_fields(trait_name, db_mock), + retrieve_geno_group_fields(trait_name, db_mock), expected) cursor.execute.assert_called_once_with( ( |