GeneNetwork (2nd generation) http://git.genenetwork.org/genenetwork2/atom?h=lmdb-code%2Frefactoring 2022-09-12T02:37:46+00:00 2022-09-12T02:37:46+00:00 Frederick Muriuki Muriithi 2022-09-12T02:36:51+00:00 urn:sha1:a693630f8330a04be0942a3acc27f0028ff7d8d1 Only add a value to the path if it is actually set 2022-02-17T17:23:09+00:00 Arun Isaac 2022-02-17T17:20:20+00:00 urn:sha1:84a1f972cab8d7976919a65c7bc4e14a76d78d02 redis needs to be started and managed as a separate service. We create a flag NO_REDIS so that it can be so. If NO_REDIS is not defined, the present behavior of starting redis remains. Thus current use cases are not broken. * bin/genenetwork2: Allow for not starting redis with the NO_REDIS flag. 2022-02-08T04:57:50+00:00 Frederick Muriuki Muriithi 2022-01-31T03:46:50+00:00 urn:sha1:04203f785e5a8c86509089bc68340e1e01162ffd 2022-01-29T06:42:44+00:00 Frederick Muriuki Muriithi 2021-12-10T06:52:38+00:00 urn:sha1:c0d4de52e28135b002ab18ff59ac0fb6fd827a4f * When developing the GN2 code, there are times we need to use the latest code in GN3, and rather than manually editing the `bin/genenetwork` file every time we need that, this commit enables the use of an environment variable. In this case, launching the application with something like: $ env GN3_DEV_REPO_PATH="$HOME/genenetwork3" ...\ ./bin/genenetwork2 ./the_settings.py -gunicorn-dev will add the path to the development version to the PYTHONPATH. If the GN3_DEV_REPO_PATH variable is not set, then the PYTHONPATH is not altered, and would be as if there is no development version of GN3 in use. 2022-01-29T06:42:44+00:00 Frederick Muriuki Muriithi 2021-12-06T14:58:28+00:00 urn:sha1:a01033438a85e3097e4ade30e9a208fd5109d4e1 Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add UI elements to trigger the partial correlations feature * Connect partial correlation view to the application * Point to correct application element for gunicorn 2022-01-28T20:53:53+00:00 zsloan 2022-01-28T20:53:53+00:00 urn:sha1:b9f16a3b28c4d996ac91befa5a919a9e0a7ac981 The PYTHONPATH apparently needs to be updated to 3.9, because 3.8 throws an error (at least on production). 2022-01-28T19:40:10+00:00 zsloan 2022-01-28T19:40:10+00:00 urn:sha1:631504680ce31b1a181cf6617e87ef0cc2cefa26 It seems that this also needed to be reverted, because I was getting the error below (which was prevented by reverting to #! /bin/bash): ./bin/genenetwork2: 135: ./bin/genenetwork2: Syntax error: redirection unexpected 2022-01-28T08:08:24+00:00 Arun Isaac 2022-01-28T08:08:24+00:00 urn:sha1:fadf0b836d512c9839f91df77f5f957e7aca6a1c This reverts commit f4e336eb1ea526156e112cff97a3ec8137a2bc90. 2022-01-28T08:08:20+00:00 Arun Isaac 2022-01-28T08:08:20+00:00 urn:sha1:2b629077ba1ec52233c118707d44dca2fb5e6afb This reverts commit 344e428126b60932bff4c62c5ded8c36519155e8. 2022-01-27T12:25:20+00:00 Frederick Muriuki Muriithi 2022-01-27T07:37:03+00:00 urn:sha1:627f86392f082b9a42bd9efeb59e7ee9374932b3 In posix shell, string indexing is undefined. This commit replaces the string indexing with a more portable implementation.