genenetwork3/gn3/auth/authorisation/data, branch auth/implement-authorization-code-flow GeneNetwork3 REST API for data science and machine learning http://git.genenetwork.org/genenetwork3/atom?h=auth%2Fimplement-authorization-code-flow 2023-04-24T08:45:45+00:00 auth: Return the actual privileges for the user 2023-04-24T08:45:45+00:00 Frederick Muriuki Muriithi 2023-04-24T08:45:45+00:00 urn:sha1:3e2198e39bc229553d118f367fbd2f9932a9a76b Previously, the `oauth2/data/authorisation` endpoint was returning hard-coded values for the privileges assigned to the user for each resource. In this change, we rework to return the actual privileges for the user. oauth2: Link the phenotype traits to user groups. 2023-04-19T15:07:19+00:00 Frederick Muriuki Muriithi 2023-04-19T14:49:58+00:00 urn:sha1:735adc012cc5d974eb8eabb26eda6c483af0da1a Fix minor linting and typing issues 2023-04-19T12:59:26+00:00 Frederick Muriuki Muriithi 2023-04-19T12:59:26+00:00 urn:sha1:2a7e8b7ffdf260a643c7fcd615c8982d3268347f auth: Setup selected traits correctly 2023-04-19T12:13:04+00:00 Frederick Muriuki Muriithi 2023-04-19T11:42:31+00:00 urn:sha1:9a0c6fd1759e13fa7a934852f87e9aa4c62d7dfd Fix bugs with setting up of the selected traits for use while filtering the search results. auth: phenotypes - provide default empty list for selected traits. 2023-04-19T08:31:14+00:00 Frederick Muriuki Muriithi 2023-04-19T08:31:14+00:00 urn:sha1:85610fc9670c0496bff045be0e148e3d2b3357d3 auth: Pass `--per-page` and `--selected` options. 2023-04-18T11:10:47+00:00 Frederick Muriuki Muriithi 2023-04-18T11:10:02+00:00 urn:sha1:280f7970f3a63c2afa06f55ad59233260da2e2b9 Hook up code to use external search script for phenotypes 2023-04-17T11:42:05+00:00 Frederick Muriuki Muriithi 2023-04-17T11:42:05+00:00 urn:sha1:8af8105444522c2c71b5ddd36a550e964cddffbf auth: Delete code that is no longer used 2023-04-17T06:24:54+00:00 Frederick Muriuki Muriithi 2023-04-17T06:24:54+00:00 urn:sha1:85abf12d364c626af9177deb0398849845bcc6c3 Decouple `gn3.db_utils` from `flask.current_app`. 2023-04-15T16:35:53+00:00 Frederick Muriuki Muriithi 2023-04-15T16:35:53+00:00 urn:sha1:dbf0f9f0d34c9969aa6ae76f556745a9eb122106 Decouple the `gn3.db_utils` module from the global `flask.current_app` object, ensuring that the database uri value is passed in as a required argument to the `gn3.db_utils.database_connection` function. auth: Add external script to search for phenotypes 2023-04-14T11:14:20+00:00 Frederick Muriuki Muriithi 2023-04-14T10:19:31+00:00 urn: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.