genenetwork3/tests/unit/test_db_utils.py, branch migrate-to-python3.10 GeneNetwork3 REST API for data science and machine learning http://git.genenetwork.org/genenetwork3/atom?h=migrate-to-python3.10 2023-04-06T09:43:56+00:00 Fix linting issues 2023-04-06T09:43:56+00:00 Frederick Muriuki Muriithi 2023-04-06T09:43:56+00:00 urn:sha1:db6457bfbcccce35162d9d2ece988c7c8c8f9308 Remove deprecated `gn3.db_utils.database_connector` function 2023-04-06T09:31:05+00:00 Frederick Muriuki Muriithi 2023-04-06T09:31:05+00:00 urn:sha1:17abad9300e4a96a14f94da486ef8307f7d27e06 Remove the deprecated function and fix a myriad of bugs that arise from removing the function. Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils tests: Set up fixture and mock out config variable 2023-03-23T15:41:38+00:00 Frederick Muriuki Muriithi 2023-03-23T15:41:38+00:00 urn:sha1:98e9726405df3cce81356534335259a446b0c458 Update test: include port in parsed data from mysql uri 2022-08-30T10:54:23+00:00 Frederick Muriuki Muriithi 2022-08-30T10:54:23+00:00 urn:sha1:45b9bcb015d2b563a82ac334be68a84ec28d0f8c Fix some linting issues 2022-03-11T08:51:02+00:00 Frederick Muriuki Muriithi 2022-03-11T08:51:02+00:00 urn:sha1:9691e225724e041997c74f8665dcbfa12bb1c579 Fix tests, and issues caught by tests 2022-03-08T05:07:38+00:00 Frederick Muriuki Muriithi 2022-03-08T05:07:38+00:00 urn:sha1:e30f9a9b746f7dcdc8707e66cc65e580e6f83f47 Fix some issues caught by tests due to changes introducing the hand-off of the partial correlations computations to an external process Fix some issues due to the changes that introduce context managers for database connections Update some tests to take the above two changes into consideration Fix a myriad of linter issues 2022-02-21T13:23:06+00:00 Frederick Muriuki Muriithi 2022-02-21T13:23:06+00:00 urn:sha1:a35fce27875d9db80dce1976b6f8ee8c00ecfe0a * 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 Use pytest's "mark" feature to categorise tests 2022-02-17T03:37:30+00:00 Frederick Muriuki Muriithi 2022-02-14T03:56:32+00:00 urn:sha1:74044f3c7985308b4996da3a52f91c5c20a19194 Use pytest's `mark` feature to explicitly categorise the tests and run them per category Integrate correlation API 2021-04-12T06:54:12+00:00 Alexander Kabui 2021-04-12T06:54:12+00:00 urn:sha1:31ac939f58bf7b6d353ced995ca395376203b25f - add new api for gn2-gn3 sample r integration - delete map for sample list to values - add db util file - add python msql-client dependency - add db for fetching lit correlation results - add unittests for db utils - add tests for db_utils - modify api for fetching lit correlation results - refactor Mock Database Connector and unittests - add sql url parser - add SQL URI env variable - refactor code for db utils - modify return data for lit correlation - refactor tissue correlation endpoint - replace db_instance with conn