genenetwork3/gn3/api, branch technical-specification GeneNetwork3 REST API for data science and machine learning http://git.genenetwork.org/genenetwork3/atom?h=technical-specification 2022-03-30T08:41:52+00:00 Revert "Run json.loads on request.get_json, since request.get_json was just returning a string" 2022-03-30T08:41:52+00:00 Frederick Muriuki Muriithi 2022-03-30T08:28:00+00:00 urn:sha1:0c6654ec8bd71297ca7d97899933f98d526b6725 This reverts commit b93b22386056347d8002dd2e403425beeb4657cd. The appropriate fix should have been in GN2. The original statement args = request.get_json() was correct, since `request.get_json()` should return a python object parsed from the JSON string in the request. Unfortunately, GN2 was encoding the request data two times, which led to the call returning a JSON-encoded string instead of the expected object. The issue has been fixed in GN2 and therefore, the "fix" here can be reverted. Run json.loads on request.get_json, since request.get_json was just returning a string 2022-03-28T17:31:32+00:00 zsloan 2022-03-28T17:31:32+00:00 urn:sha1:b93b22386056347d8002dd2e403425beeb4657cd Fixes pylint errors 2022-03-22T19:18:26+00:00 zsloan 2021-10-12T20:54:47+00:00 urn:sha1:47c38fe08f27a7de58430c2f7f5635a9ba5836c8 Fix issue that causes R/qtl to always run pair-scan even if pair-scan isn't selected 2022-03-22T19:08:01+00:00 zsloan 2021-08-28T00:46:10+00:00 urn:sha1:64aedf4202efc4e50648d496d2a8eed3fc828b2f Added genofile name to inputs for processing R/qtl pair-scan results, since it's needed to store the proximal/distal markers for each position 2022-03-22T19:08:01+00:00 zsloan 2021-08-26T20:17:14+00:00 urn:sha1:40e85090b60ef002723b614fd712b6affbd68176 Fix imports to import both process_rqtl_mapping and process_rqtl_pairscan in api/rqtl.py 2022-03-22T19:08:01+00:00 zsloan 2021-07-29T19:46:34+00:00 urn:sha1:444095309a8841a0998e74f2f4eba2c3fea6890f Added pairscan boolean kwarg and process_rqtl_pairscan function for reading in pairscan results + renamed process_rqtl_output to process_rqtl_mapping to distinguish between that and pairscan 2022-03-22T19:07:59+00:00 zsloan 2021-07-26T20:47:37+00:00 urn:sha1:9a8ab0ea1bbfc82c79cb8183c37200a09ab27d9c 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 Create database connections within context managers 2022-03-08T05:00:16+00:00 Frederick Muriuki Muriithi 2022-03-08T05:00:16+00:00 urn:sha1:eae345ed252c01e541d64c7e5b60b488d84268c6 Use the `with` context manager to open database connections, so as to ensure that those connections are closed once the call is completed. This hopefully avoids the 'too many connections' error