Age | Commit message (Collapse) | Author |
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* gn3/db/correlations.py (__fetch_data__): Ignore "Too many args" [R0913]
error.
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* gn3/db/correlations.py (__build_query__): Ignore the "sample_ids" and
"joins" types when calling build_query_sgo_lit_corr
(fetch_all_database_data): Ignore the return type.
TODO: Ping Alex/Arun to fix this.
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ATM, it's very difficult to work the correct type that is returned. Ignore
this for now and fix this later.
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Extract the utility functions to help with understanding the what the
`fetch_all_database_data` function is doing. This helps with maintenance.
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* gn3/db/sample_data.py: Remove "collections" import. Add "Optional" import.
(get_case_attributes): Return the results of "fetchall" from the case
attributes.
* tests/unit/db/test_sample_data.py (test_get_case_attributes): Update failing
test.
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Compute partial correlations against a selection of traits rather than against
an entire dataset.
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* gn3/db/sample_data.py (get_trait_csv_sample_data): Strip out "\n", "\t", or
"\r" from the sample data. See:
<https://issues.genenetwork.org/issues/csv-error-ITP_10001-longevity-data-set.html>
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* gn3/db/sample_data.py (delete_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_delete_sample_data): Update tests to
capture the above.
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* gn3/db/sample_data.py (insert_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_insert_sample_data): Update tests to
capture the above.
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* gn3/db/sample_data.py: Import "parse_csv_column".
(update_sample_data): If an id is present in the column header, use it.
* tests/unit/db/test_sample_data.py (test_update_sample_data): Update tests to
capture the above.
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* gn3/db/sample_data.py (get_case_attributes): New function.
* tests/unit/db/test_sample_data.py (test_get_case_attributes): Test case for
the above.
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* gn3/db/sample_data.py: Run "python black -l 79 ..."
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* gn3/db/sample_data.py (__extract_actions): During updates, make sure that
the strain name is part of the returned string when extracting "actions".
* tests/unit/db/test_sample_data.py: Add test cases for the above.
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* tests/unit/db/test_sample_data.py (delete_sample_data): Add missing return
type for type annotations.
(insert_sample_data): Ditto.
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* gn3/db/sample_data.py (get_sample_data_ids): Re-use "delete_sample_data" and
"insert_sample_data" when updating data; and also add logic for updating
modified data.
* tests/unit/db/test_sample_data.py: Add tests for the above.
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* gn3/db/sample_data.py (__extract_actions): An update on a vector of data can
contain: inserts, deletes and updates. This functions extracts these actions
during an update.
* tests/unit/db/test_sample_data.py (test_extract_actions): Add test-case for
the above.
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* gn3/db/sample_data.py (insert_sample_data)[__insert_data]: Move check to the
main body. With this check here, you have 3 redundant checks. For a successful
insert, it will insert the first value to the `PublishData` table and ignore the
rest of the inserts.
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* gn3/db/sample_data.py: Now constant, `_MAP`.
(delete_sample_data)[__delete_data]: Replace `_map` with `_MAP`.
(insert_sample_data)[__insert_data]: Ditto.
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* gn3/db/sample_data.py (insert_sample_data): Use correct query string. Also,
use CaseAttributeId to determine whether case-attributes were inserted. If so,
do not attempt an insert.
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* gn3/db/sample_data.py (insert_sample_data)[__insert_case_attribute]: Remove
extra parameters.
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* gn3/db/sample_data.py (insert_sample_data): If data already exists in the
table, do not attempt an insert; otherwise, an error will be generated.
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* gn3/db/sample_data (get_sample_data_ids): Add an extra condition that caters
for inserts: during inserts, joins won't work when fetching the strain_id,
publishdata_id, and strain_name. In this case, just create 2 separate queries
to do that work.
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* gn3/csvcmp.py (extract_strain_name): New function.
* gn3/db/sample_data (delete_sample_data): Use the aforementioned function.
(insert_sample_data): Ditto.
* tests/unit/test_csvcmp: Test cases for above.
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* gn3/db/sample_data.py (delete_sample_data): Modify this function to allow
deleting case-attribute values.
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* gn3/db/sample_data.py (insert_sample_data): Modify this function to allow
inserting case-attribute values.
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* gn3/db/sample_data.py (get_sample_data_ids): Extend to also fetch
InbredSetId.
(update_sample_data): Discard the returned value of InbredSetId.
(delete_sample_data): Ditto.
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* gn3/db/sample_data.py: Import Any, Tuple.
(get_sample_data_ids): New function that fetches the strain_id and
publishdata_id of a given data point.
(update_sample_data): Use `get_sample_data_ids`.
(delete_sample_data): Ditto.
(insert_sample_data): Ditto.
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* gn3/db/traits.py (get_trait_csv_sample_data): Update SQL to fix runtime
errors.
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* gn3/db/traits.py (get_trait_csv_sample_data): Fetch case attribute data if
it exists.
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This reverts commit 710769e84b3bc6a2bdd66effdbac0659272ed511.
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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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