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2022-08-25revert for commit 6db3b2af8fc09999996d3acc09890a06f179c669;BugAlexander_Kabui
2022-08-23Remove conn.commit() and conn.rollback()...* gn3/db/__init__.py (update): Delete conn.commit() and conn.rollback() (insert): Ditto. * gn3/db/case_attributes.py (insert_case_attribute_audit): Ditto. (reject_case_attribute): Ditto. (approve_case_attribute): Ditto. * gn3/db/sample_data.py (update_sample_data): Ditto. (delete_sample_data): Ditto. (insert_sample_data): Ditto. Munyoki Kilyungi
2022-08-22Use non-default MySQL port if present...By default, MySQL/Mariadb connects at port 3306, however, the configuration variable `SQL_URI` could contain a different port. In that case, this commit allows the system to connect to the non-default port. Frederick Muriuki Muriithi
2022-08-12Add mandatory/expected fields to parsed data.Frederick Muriuki Muriithi
2022-08-10Fix returned value for 'parse_correlation_output'...* Always return dict * Fix internal '__parse_line__' to always have a valid return Frederick Muriuki Muriithi
2022-08-10code refactoringFrederick Muriuki Muriithi
2022-08-10remove unnecessary parsing of floatsAlexander_Kabui
2022-08-10code refactoringFrederick Muriuki Muriithi
2022-08-10remove unnecessary parsing of floatsAlexander_Kabui
2022-08-10enhancements for rust tissueFrederick Muriuki Muriithi
2022-08-10pylint fixesAlexander_Kabui
2022-08-10update test;parse outputAlexander_Kabui
2022-08-10code refactoringAlexander_Kabui
2022-08-10remove unnessary codeAlexander_Kabui
2022-08-10remove unnecessary parsing of floatsAlexander_Kabui
2022-08-10merge for resultsAlexander_Kabui
2022-08-10enhancements for rust tissueAlexander_Kabui
2022-08-03Refactor: Remove unnecessary whitespace and nameFrederick Muriuki Muriithi
2022-08-03Refactor: Remove unnecessary iterations and name...* remove extra iteration that is unnecessary * remove unnecessary variables Frederick Muriuki Muriithi
2022-07-29New script to run sample correlations...* README.md: update mypy's invocation * scripts/argparse_actions.py: new file - implement custom FileCheck action for argparse * scripts/sample_correlations.py: new file - implement new script to run sample correlations in an external process Frederick Muriuki Muriithi
2022-07-29Fix failing tests...* gn3/computations/correlations.py: rename function * mypy.ini: deactivate mypy error about missing imports * tests/integration/test_correlation.py: mock correct function * tests/unit/computations/test_correlation.py: test correct function Frederick Muriuki Muriithi
2022-07-28Add command to run the sample correlations in an external processFrederick Muriuki Muriithi
2022-07-28Update sample correlations code to use multiprocessing...* To help speed up the processing of the correlations, convert the `compute_all_sample_correlation` function to use the multiprocessing module. Frederick Muriuki Muriithi
2022-07-22mypy fixesAlexander_Kabui
2022-07-22pep8 fixesAlexander_Kabui
2022-07-22linting and tests fixesAlexander_Kabui
2022-07-22import rust_correlation when running gn3 as libAlexander_Kabui
2022-07-22compute num overlapAlexander_Kabui
2022-07-22fix for bug splitting list dataAlexander_Kabui
2022-07-22minor fixes for parsing dataAlexander_Kabui
2022-07-22code to parse tissue correlation inputAlexander_Kabui
2022-07-22mypy pylint fixesAlexander_Kabui
2022-07-22code to fetch correct sample corr dataAlexander_Kabui
2022-07-22delete dead_code;rename variablesAlexander_Kabui
2022-07-22add unittestsAlexander_Kabui
2022-07-22minor fixesAlexander_Kabui
2022-07-11Allow CORS everywhere by default...Allow the resources (endpoints) to be accessible from anywhere on the internet by default, while still allowing for restriction via CLI environment variable on a case by case basis. Frederick Muriuki Muriithi
2022-06-29use explicit parametersAlexander_Kabui
2022-06-29fix issuesAlexander_Kabui
2022-06-29lint test fileAlexander
2022-06-29pylint fixesAlexander
2022-06-29add testsAlexander
2022-06-29add test dataAlexander
2022-06-29minor fixesAlexander
2022-06-29handle tmp files generationAlexander
2022-06-29parse output dataAlexander
2022-06-29pep8 formattingAlexander
2022-06-29new variable: CORRELATION_COMMANDAlexander
2022-06-29init test correlation rust moduleAlexander
2022-06-29init rust correlation moduleAlexander