genenetwork2/scripts/maintenance, branch lmdb-code/refactoring GeneNetwork (2nd generation) http://git.genenetwork.org/genenetwork2/atom?h=lmdb-code%2Frefactoring 2023-03-08T20:35:53+00:00 Add DataAnalyzer.py script to maintenance scripts 2023-03-08T20:35:53+00:00 zsloan 2023-03-08T20:35:53+00:00 urn:sha1:638ee60bc2930ebe3b73814dab6aa3b124211345 Give speciesid single quotes like the other config_dic keys, just for consistency 2022-06-03T19:32:14+00:00 zsloan 2022-06-03T19:32:14+00:00 urn:sha1:13450230b635194ffb6682e41d77cbaef2ca4b8b Allow GenoFreezeId to be passed in configurations to load_genotypes.py 2022-06-03T19:31:42+00:00 zsloan 2022-06-03T19:31:42+00:00 urn:sha1:f8ea5626edffbe358215f8c31bc257c9c8b7be34 Use context manager with database connection 2022-03-10T05:55:26+00:00 Frederick Muriuki Muriithi 2022-03-10T05:55:26+00:00 urn:sha1:4a7e2c1602ed82aabd7d04953067ba49cb1cebff Use the `with` context manager with database connections and cursors to ensure that they are closed once they are no longer needed. Where it was not feasible to use the `with` context manager without a huge refactor/rewrite, the cursors and connections are closed manually. Fix load_phenotypes to run with GN2 latest 2021-05-13T08:05:30+00:00 Arthur Centeno 2021-05-13T08:05:30+00:00 urn:sha1:0dd04c5ca0521f59f93b45663bdfd67c916a9f3c Replace map on strip with a list comprehension that calls strip() 2020-10-28T22:23:22+00:00 BonfaceKilz 2020-10-28T22:23:22+00:00 urn:sha1:a56e5e9d5d0c3f157599677e937deb0bbb71debb * scripts/maintenance/readProbeSetSE_v7.py: In Python3 you can't map string.strip on a list of strings. Instead use a list comprehension and apply strip() on each element of the list. * wqflask/wqflask/marker_regression/plink_mapping.py: Ditto. * wqflask/wqflask/snp_browser/snp_browser.py: Ditto. Replace "string.split" & "string.join" with python's inbuilt methods 2020-08-26T22:42:41+00:00 BonfaceKilz 2020-08-26T22:18:11+00:00 urn:sha1:357ca458695fbc60c97de3d1cdf89034a8722bc5 Replace tabs with spaces 2020-08-26T19:23:40+00:00 BonfaceKilz 2020-08-26T19:23:40+00:00 urn:sha1:768de71f09b116cad0f42c792c22a7dc410ea2f4 * scripts/maintenance/readProbeSetMean_v7.py: Run python-autopep8 on this file. Remove extra whitespace(or add it) from comma separated items 2020-08-19T00:57:05+00:00 BonfaceKilz 2020-08-19T00:57:05+00:00 urn:sha1:db41cd49b6d8ccd2c3318209118ffe098bc9293e See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib> Make Python more idiomatic 2020-08-19T00:45:49+00:00 BonfaceKilz 2020-08-19T00:45:49+00:00 urn:sha1:3aaa28ea762c496eeb84e09e45194e3fd2a51673 Run `2to3-3.8 -f idioms -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-idioms>