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| author | Muriithi Frederick Muriuki | 2021-08-09 14:25:49 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2021-08-09 14:25:49 +0300 |
| commit | 243d76bd5cdb989ee7d3311e44aafb7e8f7da712 (patch) | |
| tree | 0869114d6207343d3c97fca597d7843aa7d8aa5e /tests/unit/db | |
| parent | 8f022ae1a31224d0526443ad9779f30206b4a770 (diff) | |
| download | genenetwork3-243d76bd5cdb989ee7d3311e44aafb7e8f7da712.tar.gz | |
Set up the trait dataset type correctly
* gn3/db/traits.py: setup `trait_dataset_type`
* tests/unit/db/test_traits.py: fix tests
The type ('Temp', 'Geno', 'Publish', and 'ProbeSet') relate to a trait's
dataset, and not the trait itself. This commit updates the code to take this
into consideration.
The dataset type is also set up from a trait's full name, therefore this
commit removes the `trait_type` argument from the `retrieve_trait_info`
function.
Diffstat (limited to 'tests/unit/db')
| -rw-r--r-- | tests/unit/db/test_traits.py | 27 |
1 files changed, 12 insertions, 15 deletions
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py index d9d7bbb..ee98893 100644 --- a/tests/unit/db/test_traits.py +++ b/tests/unit/db/test_traits.py @@ -126,11 +126,12 @@ class TestTraitsDBFunctions(TestCase): """ for fullname, expected in [ ["testdb::testname", - {"db": {"dataset_name": "testdb"}, "trait_name": "testname", - "cellid": "", "trait_fullname": "testdb::testname"}], + {"db": {"dataset_name": "testdb", "dataset_type": "ProbeSet"}, + "trait_name": "testname", "cellid": "", + "trait_fullname": "testdb::testname"}], ["testdb::testname::testcell", - {"db": {"dataset_name": "testdb"}, "trait_name": "testname", - "cellid": "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) @@ -146,22 +147,18 @@ class TestTraitsDBFunctions(TestCase): def test_retrieve_trait_info(self): """Test that information on traits is retrieved as appropriate.""" - for trait_type, threshold, trait_fullname, expected in [ - ["Publish", 9, "pubDb::PublishTraitName::pubCell", - {"haveinfo": 0}], - ["ProbeSet", 5, "prbDb::ProbeSetTraitName::prbCell", - {"haveinfo": 0}], - ["Geno", 12, "genDb::GenoTraitName", - {"haveinfo": 0}], - ["Temp", 6, "tmpDb::TempTraitName", - {"haveinfo": 0}]]: + 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_type=trait_type): + with self.subTest(trait_fullname=trait_fullname): with db_mock.cursor() as cursor: cursor.fetchone.return_value = tuple() self.assertEqual( retrieve_trait_info( - trait_type, threshold, trait_fullname, db_mock), + threshold, trait_fullname, db_mock), expected) def test_update_sample_data(self): |