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2023-09-27guix-bioinformatics: Update guix channel URLFrederick Muriuki Muriithi
2023-09-27typing: fix and ignore typing issues.Frederick Muriuki Muriithi
2023-09-27linting: Remove unused import, handle unused variableFrederick Muriuki Muriithi
2023-09-27Bug: Fix issue with viewing resources of type "group".Frederick Muriuki Muriithi
2023-09-26Update queryFrederick Muriuki Muriithi
Replace `group_user_roles_on_resources` table with `user_roles` for the query that checks whether the user has appropriate permissions to act on a specific resource.
2023-09-26Handle AuthorisationError at the top-levelFrederick Muriuki Muriithi
Add an error handler to gracefully handle the custom AuthorisationError at the application's top-level to avoid having to manually handle it everywhere that the error (and its sub-classes) might be raised.
2023-09-26Handle temporary edge casesFrederick Muriuki Muriithi
Fetching resource data: system and group categories of resources do not have associated genetic data. This commit adds some code to temporarily handle that case as an edge case before I can devote more time to fixing the issue in a much better way.
2023-09-26Add `public-view` role. Assign it to users.Frederick Muriuki Muriithi
Add a new `public-view` role to be assigned to all users on all resources that are defined as publicly viewable. Update code to make assign `public-view` role to a newly registered user for all publicly viewable roles. Update the code to assign/revoke the `public-view` role to/from users whenever the resource is toggled to and from being publicly viewable. Ensure that `public-view` is not revoked from system-administrators. Ensure that `public-view` is not revoked from the group administrators of the group that owns the resource.
2023-09-26Update fetching a single roleFrederick Muriuki Muriithi
2023-09-26Initialise package to handle resources of type "system".Frederick Muriuki Muriithi
2023-09-26Update /roles endpoint: rework code for new `user_roles` functionFrederick Muriuki Muriithi
The way the `gn_auth.auth.authorisation.roles.models.user_roles` function works has changed: this commit updates the code to take that into consideration and fix any errors.
2023-09-26Add default `REDIS_URI` configuration.Frederick Muriuki Muriithi
2023-09-26Add System resource, and group resource(s) to list of user resourcesFrederick Muriuki Muriithi
* The system resource is public, and should be present for all users. * Each user that is a member of a group, should have their group show up in their list of resources. * Fix the SQL join: add an `ON ...` clause.
2023-09-26Update `user_roles`: Return roles for user by resource.Frederick Muriuki Muriithi
2023-09-26Move `groups` package under `resources` packageFrederick Muriuki Muriithi
With user groups being resources that users can act on (with the recent changes), this commit moves the `groups` module to under the `resources` module. It also renames the `*_resources.py` modules by dropping the `_resources` part since the code is under the `resources` module anyway.
2023-09-26Update tests & fixtures to conform to schema changesFrederick Muriuki Muriithi
2023-09-26Remove group from resource objectsFrederick Muriuki Muriithi
With the new schema, not all Resource objects are "owned" by a group. Those that are, are linked together through a different db table (`resource_ownership`). This commit removes the `Group` object from `Resource` objects and updates the `resource_ownership` where relevant.
2023-09-26Raise exception if no group for `resource_group`Frederick Muriuki Muriithi
Rather than using pymonad's Maybe monad and dealing with the complexity it introduces, raise an exception if there is no group found for the given resource.
2023-09-26Add `resource_group` function to retrieve the owning groupFrederick Muriuki Muriithi
Some resources are "owned" by specific user groups. This commit adds a way to retrieve those "owners" where relevant.
2023-09-26Extract resource-type-specific code into separate modulesFrederick Muriuki Muriithi
For easier maintenance, extract the code that relates to specific resource types/categories into separate modules, each dealing with a single resource type/category.
2023-09-26Extract basic resource types to a separate module.Frederick Muriuki Muriithi
2023-09-26Fix foreign-key refs. Merge tables.Frederick Muriuki Muriithi
* Link the `role_id` field to the `roles` table rather than the `group_roles` table. * Merge the data in the `group_user_roles_on_resources` table in the `user_roles` table to have a single point-of-truth for all user roles on resources.
2023-09-26Add a 'system' resourceFrederick Muriuki Muriithi
Add a 'system' resource to allow users to have roles they can use to act on the system itself.
2023-09-26migrations: Create `group_resources` table.Frederick Muriuki Muriithi
2023-09-26Drop `group_id` from resources tableFrederick Muriuki Muriithi
Drop the `group_id` from the `resources` table and update all dependent tables to fix FOREIGN KEY constraints to ensure integrity of the data.
2023-09-26Add `system` and `group` resource categories.Frederick Muriuki Muriithi
2023-09-26Resources refactor: Add `resource_ownership` tableFrederick Muriuki Muriithi
New table to link resources to groups, where relevant.
2023-09-19Remove pinned commitFrederick Muriuki Muriithi
2023-09-06Update yoyo-migration and mypyFrederick Muriuki Muriithi
Update the dependencies to enable the use of Python-3.10
2023-08-31Add documentation on troubleshooting tokensFrederick Muriuki Muriithi
2023-08-31Indent the code with `guix-devel-mode`Frederick Muriuki Muriithi
2023-08-30Replace `(...) with (list ...): Fixes "undefined gexp" failure.Frederick Muriuki Muriithi
Replace the backquoted expression in the (arguments ...) section of the package definition to fix the error where the build could not find the variable gexp
2023-08-30Include missing module.Frederick Muriuki Muriithi
2023-08-25Fix linting issues with package definition.Frederick Muriuki Muriithi
2023-08-24Add LICENSE fileFrederick Muriuki Muriithi
2023-08-23Add gunicorn as a dependency.Frederick Muriuki Muriithi
2023-08-23pylint: Load extra checkers.Frederick Muriuki Muriithi
2023-08-23pylint: Remove statement calling non-existent memberFrederick Muriuki Muriithi
2023-08-23pylint: replace ellipsis with statement raising exception.Frederick Muriuki Muriithi
2023-08-23pylint: Replace `lambda ...` statements with `def ...`Frederick Muriuki Muriithi
2023-08-16Do not use current-filename.Frederick Muriuki Muriithi
For some reason, current-filename does not work with Guix channels. This change was provided by Arun Isaac<arunisaac@systemreboot.net> but I could not seem to figure out how to download the patches from protonmail therefore I give the credit here.
2023-08-16Fix typo in package name.Frederick Muriuki Muriithi
2023-08-16Do not find the exact version for Guix package.Frederick Muriuki Muriithi
Finding the exact version number is a lot of work for a minor cosmetic effect. This change was suggested by Arun. I could not figure out how to download the patch from protonmail directly, so I have to give credit here.
2023-08-16Remove definition (use on in `guix-bioinformatics`)Frederick Muriuki Muriithi
2023-08-16Add `guix-bioinformatics` and `guix-past` as channel dependencies.Frederick Muriuki Muriithi
2023-08-16Avoid extreme nesting for single-package channel.Frederick Muriuki Muriithi
2023-08-14Set version to hard-coded value in checkoutFrederick Muriuki Muriithi
2023-08-14Fix bugsFrederick Muriuki Muriithi
2023-08-14Wrap package definition in `(define-public ...)`Frederick Muriuki Muriithi
2023-08-14Add missing dependencyFrederick Muriuki Muriithi
Define `python-authlib` package.
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