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| author | Frederick Muriuki Muriithi | 2022-02-21 09:07:31 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2022-02-21 09:18:39 +0300 |
| commit | f914dc21577253f293b50b890ea0ac4bd2fd5d1b (patch) | |
| tree | e51406a86ac63ff59724baa9dc7b6cdf72976387 /gn3/db | |
| parent | 058f6592d8815a64544f6721a9984b89ea92522a (diff) | |
| download | genenetwork3-f914dc21577253f293b50b890ea0ac4bd2fd5d1b.tar.gz | |
Test partial corrs API with mix of existing and non-existing control traits
Test that the partial correlations endpoint handles a mix of existing and
non-existing control traits gracefully and issues a warning to the user.
Summary of changes:
* gn3/computations/partial_correlations.py: Issue a warning for all
non-existing control traits
* gn3/db/partial_correlations.py: update queries - use `INNER JOIN` for tables
instead of comma-separated list of tables
* tests/integration/conftest.py: Add `db_conn` fixture to provide a database
connection to the tests. This will probably be changed in the future to
connect to a temporary database for tests.
* tests/integration/test_partial_correlations.py: Add test to check for
correct behaviour with a mix of existing and non-existing control traits
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/partial_correlations.py | 18 |
1 files changed, 9 insertions, 9 deletions
diff --git a/gn3/db/partial_correlations.py b/gn3/db/partial_correlations.py index 0931f09..0075cad 100644 --- a/gn3/db/partial_correlations.py +++ b/gn3/db/partial_correlations.py @@ -347,10 +347,11 @@ def probeset_traits_info( "probe_set_note_by_rw", "flag") query = ( "SELECT ProbeSet.Name AS trait_name, {columns} " - "FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef " - "WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id " - "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id " - "AND ProbeSetFreeze.Name IN ({dataset_names}) " + "FROM ProbeSet INNER JOIN ProbeSetXRef " + "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id " + "INNER JOIN ProbeSetFreeze " + "ON ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId " + "WHERE ProbeSetFreeze.Name IN ({dataset_names}) " "AND ProbeSet.Name IN ({trait_names})").format( columns=", ".join(["ProbeSet.{}".format(x) for x in keys]), dataset_names=", ".join(["%s"] * len(dataset_names)), @@ -376,11 +377,10 @@ def geno_traits_info( "SELECT " "Geno.Name AS trait_name, {columns} " "FROM " - "Geno, GenoFreeze, GenoXRef " - "WHERE " - "GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoXRef.GenoId = Geno.Id AND " - "GenoFreeze.Name IN ({dataset_names}) AND " - "Geno.Name IN ({trait_names})").format( + "Geno INNER JOIN GenoXRef ON GenoXRef.GenoId = Geno.Id " + "INNER JOIN GenoFreeze ON GenoFreeze.Id = GenoXRef.GenoFreezeId " + "WHERE GenoFreeze.Name IN ({dataset_names}) " + "AND Geno.Name IN ({trait_names})").format( columns=", ".join(["Geno.{}".format(x) for x in keys]), dataset_names=", ".join(["%s"] * len(dataset_names)), trait_names=", ".join(["%s"] * len(traits))) |