genenetwork3/scripts, branch auth/implement-authorization-code-flowGeneNetwork3 REST API for data science and machine learning
http://git.genenetwork.org/genenetwork3/atom?h=auth%2Fimplement-authorization-code-flow2023-04-19T15:07:19+00:00oauth2: Link the phenotype traits to user groups.2023-04-19T15:07:19+00:00Frederick Muriuki Muriithi2023-04-19T14:49:58+00:00urn:sha1:735adc012cc5d974eb8eabb26eda6c483af0da1aFix minor linting and typing issues2023-04-19T12:59:26+00:00Frederick Muriuki Muriithi2023-04-19T12:59:26+00:00urn:sha1:2a7e8b7ffdf260a643c7fcd615c8982d3268347fauth: Setup selected traits correctly2023-04-19T12:13:04+00:00Frederick Muriuki Muriithi2023-04-19T11:42:31+00:00urn:sha1:9a0c6fd1759e13fa7a934852f87e9aa4c62d7dfd
Fix bugs with setting up of the selected traits for use while filtering the
search results.
auth: Consistently JSON encode values.2023-04-18T11:10:47+00:00Frederick Muriuki Muriithi2023-04-18T10:57:49+00:00urn:sha1:0958648c62452a53d0f66d7401261015e39d2fb8
Consistently encode all values for the top-level keys stored in redis to avoid
issues with json encode/decode
Hook up code to use external search script for phenotypes2023-04-17T11:42:05+00:00Frederick Muriuki Muriithi2023-04-17T11:42:05+00:00urn:sha1:8af8105444522c2c71b5ddd36a550e964cddffbfauth: Add external script to search for phenotypes2023-04-14T11:14:20+00:00Frederick Muriuki Muriithi2023-04-14T10:19:31+00:00urn:sha1:2b7ecb52fa5f568d7d48fc324bae8231343543bd
We need a search through the available phenotype traits in the database when
linking the traits to user groups. Unfortunately, the Xapian Search indexes do
not (and should not) include the internal identifiers we use to disambiguate
the traits.
On the other hand, we do not want to present the user with traits that have
already been linked to any user group within the search results.
The script in this commit, together with the modified queries for fetching the
phenotype data form a "hack" of sorts to wrap around the way the search works
while ensuring we do not present the user with "non-actionable" (linked)
traits in the search results.
Remove deprecated `gn3.db_utils.database_connector` function2023-04-06T09:31:05+00:00Frederick Muriuki Muriithi2023-04-06T09:31:05+00:00urn: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
Enable use of `database_connection` in scripts without current_app2023-04-05T11:51:04+00:00Frederick Muriuki Muriithi2023-04-04T07:07:03+00:00urn:sha1:3d873435f0d464864d4d691d6be4db40931fac05
There is need to run external scripts using the same configurations as the
application but without the need to couple the script to the application.
In this case, we provide the needed configuration directly in the CLI, and
modify the existing `gn3.db_utils.database_connection` function to allow it to
work coupled to the app or otherwise.
scripts: Fallback to 1 worker when indexing.2023-02-13T17:36:09+00:00Arun Isaac2023-02-13T17:35:13+00:00urn:sha1:283e7f08701ed80cdfeb8773df38c0c30227a10c
* scripts/index-genenetwork (worker_queue): Set default number of workers to 1
if the number of CPUs cannot be determined.
scripts: Type hint xapian indexing script.2023-02-13T17:36:09+00:00Arun Isaac2023-02-13T17:33:27+00:00urn:sha1:152d0fb36b76b7c68d8202ba3665617bad3e684b
* scripts/index-genenetwork: Import Callable, Generator, Iterable and List
from typing. Type hint all functions.