genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2022-04-12	Strip any newline, tab or carriage-return chars from sample data	BonfaceKilz
	* 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>
2022-04-07	Fix pylint errors	BonfaceKilz

2022-04-07	Use case attribute id inside brackets if present during insertions	BonfaceKilz
	* 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.
2022-04-07	Use case attribute id inside brackets if present during insertions	BonfaceKilz
	* 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.
2022-04-07	Use case attribute id inside brackets if present during updates	BonfaceKilz
	* 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.
2022-04-07	Add method for fetching the case_attributes	BonfaceKilz
	* 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.
2022-04-07	Run python black on file	BonfaceKilz
	* gn3/db/sample_data.py: Run "python black -l 79 ..."
2022-03-14	Dummy White Space commit to fix laminar	BonfaceKilz

2022-03-12	Fix mypy issues	BonfaceKilz

2022-03-12	Fix pylint issues	BonfaceKilz

2022-03-12	Store the first element as strain_id	BonfaceKilz

2022-03-12	Append the strain name when extracting "actions"	BonfaceKilz
	* 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.
2022-03-12	Apply auto-pep8 to sample_data.py and it's test file	BonfaceKilz

2022-03-12	Add missing return type-annotations	BonfaceKilz
	* tests/unit/db/test_sample_data.py (delete_sample_data): Add missing return type for type annotations. (insert_sample_data): Ditto.
2022-03-12	Update how data is updated by re-using existing functions	BonfaceKilz
	* 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.
2022-03-12	Create action dict that's created when updating data	BonfaceKilz
	* 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.
2022-03-12	Remove check for inserted data when inserting individual data	BonfaceKilz
	* 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.
2022-03-12	Make `_map` a constant	BonfaceKilz
	* gn3/db/sample_data.py: Now constant, `_MAP`. (delete_sample_data)[__delete_data]: Replace `_map` with `_MAP`. (insert_sample_data)[__insert_data]: Ditto.
2022-03-12	Fix faulty SQL query string when deleting case-attributes	BonfaceKilz

2022-03-12	Explicitly get CaseAttributeId and fix broken sql query	BonfaceKilz
	* 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.
2022-03-12	Remove duplicate params	BonfaceKilz
	* gn3/db/sample_data.py (insert_sample_data)[__insert_case_attribute]: Remove extra parameters.
2022-03-12	Remove dead code	BonfaceKilz

2022-03-12	Check whether publish data already exists before inserting	BonfaceKilz
	* 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.
2022-03-12	Fetch id's separately for the insertion edge-case	BonfaceKilz
	* 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.
2022-03-12	Extract a strain name given a csv string and it's header	BonfaceKilz
	* 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.
2022-03-12	Allow deleting case-attribute data during deletion	BonfaceKilz
	* gn3/db/sample_data.py (delete_sample_data): Modify this function to allow deleting case-attribute values.
2022-03-12	Allow inserting case-attribute data during inserts	BonfaceKilz
	* gn3/db/sample_data.py (insert_sample_data): Modify this function to allow inserting case-attribute values.
2022-03-12	Fetch InbredSetId	BonfaceKilz
	* 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.
2022-03-12	Create a new function for retrieving strain_id and publishdata_id	BonfaceKilz
	* 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.
2022-03-12	Move operations on sample_data to it's own module	BonfaceKilz