diff options
| -rw-r--r-- | gn3/db/traits.py | 16 | ||||
| -rw-r--r-- | tests/unit/db/test_traits.py | 46 |
2 files changed, 52 insertions, 10 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 29c91a6..9f89510 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -341,8 +341,18 @@ def set_riset_fields(trait_info, conn): **trait_info, "risetid": riid, "riset": "BXD" if riset == "BXD300" else riset} +def build_trait_name(trait_fullname): + name_parts = trait_fullname.split("::") + assert len(name_parts) >= 2, "Name format error" + return { + "trait_db": name_parts[0], + "trait_fullname": trait_fullname, + "trait_name": name_parts[1], + "cellid": name_parts[2] if len(name_parts) == 3 else "" + } + def retrieve_trait_info( - trait_type: str, trait_name: str, trait_dataset_id: int, + trait_type: str, trait_full_name: str, trait_dataset_id: int, trait_dataset_name: str, conn: Any, qtl=None): """Retrieves the trait information. @@ -351,6 +361,7 @@ def retrieve_trait_info( This function, or the dependent functions, might be incomplete as they are currently.""" # pylint: disable=[R0913] + trait = build_trait_name(trait_full_name) trait_info_function_table = { "Publish": retrieve_publish_trait_info, "ProbeSet": retrieve_probeset_trait_info, @@ -362,6 +373,7 @@ def retrieve_trait_info( lambda ti: set_riset_fields(ti, conn), lambda ti: set_homologene_id_field(ti, conn), lambda ti: {"type": trait_type, **ti}, + lambda ti: {**ti, **trait}, set_haveinfo_field) trait_post_processing_functions_table = { @@ -377,7 +389,7 @@ def retrieve_trait_info( return retrieve_info( { - "trait_name": trait_name, + "trait_name": trait["trait_name"], "trait_dataset_id": trait_dataset_id, "trait_dataset_name":trait_dataset_name }, diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py index 1c481a2..39d7a31 100644 --- a/tests/unit/db/test_traits.py +++ b/tests/unit/db/test_traits.py @@ -1,6 +1,7 @@ """Tests for gn3/db/traits.py""" from unittest import mock, TestCase from gn3.db.traits import ( + build_trait_name, set_riset_fields, set_haveinfo_field, update_sample_data, @@ -155,18 +156,47 @@ class TestTraitsDBFunctions(TestCase): "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", + {"trait_db": "testdb", "trait_name": "testname", "cellid": "", + "trait_fullname": "testdb::testname"}], + ["testdb::testname::testcell", + {"trait_db": "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, expected in [ - ["Publish", "PublishTraitName", 1, "PublishDatasetTraitName", + ["Publish", "pubDb::PublishTraitName::pubCell", 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"}]]: + "confidential": 0, "trait_db": "pubDb", + "trait_name": "PublishTraitName", "cellid": "pubCell", + "trait_fullname": "pubDb::PublishTraitName::pubCell"}], + ["ProbeSet", "prbDb::ProbeSetTraitName::prbCell", 2, + "ProbeSetDatasetTraitName", + {"haveinfo": 0, "homologeneid": None, "type": "ProbeSet", + "trait_fullname": "prbDb::ProbeSetTraitName::prbCell", + "trait_db": "prbDb", "trait_name": "ProbeSetTraitName", + "cellid": "prbCell"}], + ["Geno", "genDb::GenoTraitName", 3, "GenoDatasetTraitName", + {"haveinfo": 0, "homologeneid": None, "type": "Geno", + "trait_fullname": "genDb::GenoTraitName", "trait_db": "genDb", + "trait_name": "GenoTraitName", "cellid": ""}], + ["Temp", "tmpDb::TempTraitName", 4, "TempDatasetTraitName", + {"haveinfo": 0, "homologeneid": None, "type": "Temp", + "trait_fullname": "tmpDb::TempTraitName", "trait_db": "tmpDb", + "trait_name": "TempTraitName", "cellid": ""}]]: db_mock = mock.MagicMock() with self.subTest(trait_type=trait_type): with db_mock.cursor() as cursor: |