diff options
| 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/computations | |
| 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/computations')
| -rw-r--r-- | gn3/computations/partial_correlations.py | 6 |
1 files changed, 6 insertions, 0 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index 1cc969c..3633a59 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -628,6 +628,12 @@ def partial_correlations_entry(# pylint: disable=[R0913, R0914, R0911] return { "status": "not-found", "message": "None of the requested control traits were found."} + for trait in cntrl_traits: + if trait["haveinfo"] == False: + warnings.warn( + (f"Control traits {trait['trait_fullname']} was not found " + "- continuing without it."), + category=UserWarning) group = primary_trait["db"]["group"] primary_trait_data = all_traits_data[primary_trait["trait_name"]] |