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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Compute partial correlations against a selection of traits rather than against
an entire dataset.
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* Use `with` in place of plain `open`
* Use f-strings in place of `str.format()`
* Remove string interpolation from queries - provide data as query parameters
* other minor fixes
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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
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Test that if the endpoint is queried and not a single one of the control
traits exists in the database, then the endpoint will respond with a
404 (not-found) status code.
Summary of changes:
* gn3/computations/partial_correlations.py: Check whether any control trait is
found. If none is found, return "not-found" message.
* gn3/db/partial_correlations.py: Fix bug in Geno query.
* tests/integration/test_partial_correlations.py: Add test for non-existing
control traits. Rename function to make it clearer what it is testing
for. Remove obsoleted comments.
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The code was migrated from GN1 with a faulty assumption that all trait types
have a corresponding `*Freeze` table in the database. This assumption is not
true for the `Temp` traits.
This commit removes the buggy code.
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Test that the partial correlations endpoint responds with an appropriate
"not-found" message and the corresponding 404 status code in the case where a
request is made and the primary trait requested for does not exist in the
database.
Summary of the changes in each file:
* gn3/api/correlation.py: generalise the building of the response
* gn3/computations/partial_correlations.py: return with a "not-found" if the
primary trait does not exist in the database
* gn3/db/partial_correlations.py: Fix a number of bugs that led to exceptions
in the case that the primary trait did not exist
* pytest.ini: register a `slow` pytest marker
* tests/integration/test_partial_correlations.py: Add a new test to check for
an appropriate 404 response in case of a primary trait that does not exist
in the database.
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Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
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* Some traits have a name composed of all numerals, which leads to the names
being interpreted as numbers. This commit forces them to string to avoid
subtle bugs where the code fails.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* In an attempt to optimise the performance of the partial correlations
feature, this commit reworks some database access functions to fetch
multiple items from the database, per query, unlike their original forms
which would fetch a single item per query.
This reduces queries to the database, and should hopefully improve the
responsiveness of the partial correlations feature.
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