| Age | Commit message (Expand) | Author |
|---|
| 2024-03-13 | Rename "the_client" to "_client"....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-13 | Remove unused imports....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-13 | Auto-pep8 this file....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-13 | Define Privilege/Role using frozen dataclass....* gn_auth/auth/authorisation/privileges.py: Import dataclass. Remove
NamedTuple import.
(Privilege): Use frozen dataclass.
(Privelege.dictify): Delete.
* gn_auth/auth/authorisation/resources/groups/views.py: Import
dataclasses.asdict.
(group_privileges): Replace dictify with asdict.
(add_priv_to_role): Ditto.
(delete_priv_from_role): Ditto.
* gn_auth/auth/authorisation/resources/models.py:
(assign_resource_user): Replace dictify with asdict.
(unassign_resource_user): Ditto.
* gn_auth/auth/authorisation/resources/system/views.py: Import
dataclasses.asdict. Remove dictify import.
(system_roles): Replace dictify with asdict.
* gn_auth/auth/authorisation/resources/views.py:
(resource_users): Replace dictify with asdict.
(resources_authorisation): Ditto.
* gn_auth/auth/authorisation/roles/models.py: Remove dictify and
NameTuple import.
(Role): Use frozen dataclass.
(Role.dictify): Replace dictify(priv) with asdict(priv).
* gn_auth/auth/authorisation/roles/views.py: Import
dataclasses.asdict. Remove dictify import.
(view_role): Replace dictify with asdict.
* gn_auth/auth/authorisation/users/views.py:
(user_roles): Replace dictify with asdict.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-13 | Define OAuth2Client using frozen dataclass....* gn_auth/auth/authentication/oauth2/models/oauth2client.py: Import
dataclass, cached_property and ClientMixin. Remove NamedTuple import.
(OAuth2Client): Use frozen dataclass and explicitly inherit from
ClientMixin.
(OAuth2Client.token_endpoint_auth_method): Make this a cached
property.
(OAuth2Client.client_type): Ditto.
(OAuth2Client.id): Ditto.
(OAuth2Client.grant_types): Ditto.
(OAuth2Client.redirect_uris): Ditto.
(OAuth2Client.response_types): Ditto.
(OAuth2Client.scope): Ditto.
(OAuth2Client.get_allowed_scope): Autopep-8 it.
(client): Autopep-8 it and use kw args for OAuthClient.
(client_by_id_and_secret): Ditto.
(oauth2_clients): Ditto.
(save_client): Ditto.
(delete_client): Ditto.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-13 | Define GroupRole using frozen dataclass....* gn_auth/auth/authorisation/resources/groups/models.py: Import
dataclasses.asdict. Remove dictify import.
(GroupRole): Use frozen dataclass.
(GroupRole.dictify): Replace dictify(...) with self.role.dictify().
* gn_auth/auth/authorisation/resources/groups/views.py:
(group_roles): Replace dictify with asdict.
(view_group_role): Ditto.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-13 | Define Group using a frozen dataclass....* gn_auth/auth/authorisation/data/genotypes.py: Import
dataclasses.asdict.
(link_genotype_data): Replace dictify with asdict.
* gn_auth/auth/authorisation/data/mrna.py: Import dataclasses.asdict.
(link_mrna_data): Replace dictify with asdict.
* gn_auth/auth/authorisation/data/phenotypes.py: Import
dataclasses.asdict.
(link_phenotype_data): Replace dictify with asdict.
* gn_auth/auth/authorisation/resources/groups/models.py: Import
dataclass.
(Group): Use frozen dataclass.
(Group.dictify): Delete.
(GroupRole.dictify): Replace dictify with asdict.
* gn_auth/auth/authorisation/resources/groups/views.py: Import
dataclasses.asdict. Remove dictify import.
(list_groups): Replace dictify with asdict.
(create_group): Ditto.
* gn_auth/auth/authorisation/resources/views.py:
(resource_users): Replace dictify with asdict.
* gn_auth/auth/authorisation/users/views.py: Import
dataclasses.asdict. Remove dictify import.
(user_details): Replace dictify with asdict.
(user_group): Ditto.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-13 | Define OAuth2Token using a frozen dataclass....* gn_auth/auth/authentication/oauth2/endpoints/introspection.py
(IntrospectionEndpoint.introspect_token): Replace token.get_scope()
with token.scope.
* gn_auth/auth/authentication/oauth2/models/oauth2token.py: Import
dataclass, TokenMixin and cached_property. Delete NamedTuple import.
(OAuth2Token): Use a frozen dataclass and explicitly inherit from
TokenMixin.
(OAuth2Token.expires_at): Make this a cached_property.
(OAuth2Token.check_client): Add the "# pylint ..." in it's own line.
Tested-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-13 | Define User using a frozen dataclass....* gn_auth/auth/authentication/users.py: Import dataclass. Remove
NamedTuple and Tuple import.
(User): Use a frozen dataclass.
(User.get_user_id): Delete.
(User.dictify): Ditto.
* gn_auth/auth/authorisation/data/views.py: Import dataclasses.dict.
(authorisation): Replace user._asdict() with asdict(user).
(metadata_resources): Ditto.
* gn_auth/auth/authorisation/resources/groups/views.py:
(group_members): Replace dictify with asdict.
* gn_auth/auth/authorisation/resources/models.py: Import
dataclasses.asdict.
(assign_resource_user): Replace dictify(user) with asdict(user).
(unassign_resource_user): Ditto.
* gn_auth/auth/authorisation/resources/views.py:
(resource_users): Replace dictify with asdict.
* gn_auth/auth/authorisation/users/masquerade/views.py: Import
dataclasses.asdict.
(masquerade): Replace masq_user._asdict() with asdict(masq_user).
* gn_auth/auth/authorisation/users/views.py:
(list_all_users): Replace dictify with asdict.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-08 | Correctly check for the refresh_token....* gn_auth/auth/authentication/oauth2/endpoints/utilities.py
(query_token): Replace "if" with "match" syntax. Also, correctly
check for the "refresh_token".
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-08 | Replace "if" branching with "monad_from_none_or_value"....* gn_auth/auth/authentication/oauth2/models/authorization_code.py:
Import "monad_from_none_or_value".
(authorisation_code): Replace if branching for Nothing/Just check with "monad_from_none_or_value".
* gn_auth/auth/authentication/oauth2/models/oauth2token.py: Import
"monad_from_none_or_value".
(__token_from_resultset__): Replace if branching for Nothing/Just
check with "monad_from_none_or_value".
(token_by_access_token): Ditto.
(token_by_refresh_token): Ditto.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-08 | Rename "__5_MINUTES__" to "EXPIRY_IN_SECONDS"....* gn_auth/auth/authentication/oauth2/models/authorization_code.py
(AuthorisationCode.__5_MINUTES__): Rename this to EXPIRY_IN_SECONDS.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-08 | Explicitly add keyword arguments to AuthorisationCode....This improves readability.
* gn_auth/auth/authentication/oauth2/grants/authorisation_code_grant.py
(AuthorisationCodeGrant.save_authorization_code): Use keyword arguments.
* gn_auth/auth/authentication/oauth2/models/authorization_code.py
(authorisation_code): Ditto.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-08 | Remove "raise" in auth.db Protocol classes....* gn_auth/auth/db/protocols.py (DbCursor): Remove "raise" in DBCursor
Protocol. See:
<https://typing.readthedocs.io/en/latest/spec/protocol.html>
| Munyoki Kilyungi |
| 2024-03-04 | Add an extra endpoint for metadata authorisation....* gn_auth/auth/authorisation/data/views.py: (metadata_resources): New
end-point for authorising metadata data.
* gn_auth/auth/authorisation/resources/models.py: Import sqlite3.Row.
(__metadata_resource_data__): New function.
(__assign_resource_owner_role__): Add __metadata_resource_data__
to the "resource_data_function" map.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-04 | Fix minor typo....* gn_auth/auth/authorisation/data/views.py (authorisation): Fix typo.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-04 | Remove redundant error code for InvalidData....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-29 | Allow POST for JSON requests. | Frederick Muriuki Muriithi |
| 2024-02-28 | Handle the "NotFoundError" exception at the route level...Handle the "NotFoundError" exception at the route level, since if we
do not, the application level handler takes over and simply returns a
JSON response with the details of the failure.
| Frederick Muriuki Muriithi |
| 2023-12-18 | Provide the correct Redis key...Previously, when the user would request to either import or delete the
collections they had created before logging in, the system would try
deleting the collections from the wrong key, leading to the
collections still showing up.
This commit fixes that by providing the code with the correct Redis
key to act upon.
| Frederick Muriuki Muriithi |
| 2023-11-28 | Remove bcrypt as a dependency...BCrypt has been superceded by argon, and this commit removes it and
all code depending on it from the repository.
| Frederick Muriuki Muriithi |
| 2023-11-23 | Scripts: Update script for newer db schema...The schema changed a while back, and the script that is used to make
all existing data public needs to be updated for the new schema. This
commit does exactly that.
| Frederick Muriuki Muriithi |
| 2023-11-22 | Move system admin creation...Make the system admin creation code part of the core system, and
simply call it from the script(s). This will help with maintenance,
since the changes are done in a single place only.
| Frederick Muriuki Muriithi |
| 2023-11-22 | Only commit on successful query...Only commit changes if the queries are successful.
| Frederick Muriuki Muriithi |
| 2023-11-13 | Bug: Fix typo in query | Frederick Muriuki Muriithi |
| 2023-11-13 | Update check for admins | Frederick Muriuki Muriithi |
| 2023-11-02 | mypy: Fix typing errors. | Frederick Muriuki Muriithi |
| 2023-11-02 | pylint: Fix linting errors. | Frederick Muriuki Muriithi |
| 2023-10-12 | Bugs: Fix query and provide default function for inbredset-group | Frederick Muriuki Muriithi |
| 2023-10-10 | Get authorisation by resource_ids...Add an endpoint to help users get the resources authorisation by the
resource ids.
| Frederick Muriuki Muriithi |
| 2023-10-10 | Temporarily return no data for resources of types system and group. | Frederick Muriuki Muriithi |
| 2023-10-09 | Fetch InbredSet group resource ID by SpeciesId and InbredSetId...Get the resource used to control access to the InbredSet group by that
group's SpeciesId and InbredSetId.
| Frederick Muriuki Muriithi |
| 2023-09-27 | typing: fix and ignore typing issues. | Frederick Muriuki Muriithi |
| 2023-09-27 | linting: Remove unused import, handle unused variable | Frederick Muriuki Muriithi |
| 2023-09-27 | Bug: Fix issue with viewing resources of type "group". | Frederick Muriuki Muriithi |
| 2023-09-26 | Update query...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.
| Frederick Muriuki Muriithi |
| 2023-09-26 | Handle temporary edge cases...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.
| Frederick Muriuki Muriithi |
| 2023-09-26 | Add `public-view` role. Assign it to users....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.
| Frederick Muriuki Muriithi |
| 2023-09-26 | Update fetching a single role | Frederick Muriuki Muriithi |
| 2023-09-26 | Initialise package to handle resources of type "system". | Frederick Muriuki Muriithi |
| 2023-09-26 | Update /roles endpoint: rework code for new `user_roles` function...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.
| Frederick Muriuki Muriithi |
| 2023-09-26 | Add System resource, and group resource(s) to list of user resources...* 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.
| Frederick Muriuki Muriithi |
| 2023-09-26 | Update `user_roles`: Return roles for user by resource. | Frederick Muriuki Muriithi |
| 2023-09-26 | Move `groups` package under `resources` package...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.
| Frederick Muriuki Muriithi |
| 2023-09-26 | Remove group from resource objects...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.
| Frederick Muriuki Muriithi |
| 2023-09-26 | Raise exception if no group for `resource_group`...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.
| Frederick Muriuki Muriithi |
| 2023-09-26 | Add `resource_group` function to retrieve the owning group...Some resources are "owned" by specific user groups. This commit adds a
way to retrieve those "owners" where relevant.
| Frederick Muriuki Muriithi |
| 2023-09-26 | Extract resource-type-specific code into separate modules...For easier maintenance, extract the code that relates to specific
resource types/categories into separate modules, each dealing with a
single resource type/category.
| Frederick Muriuki Muriithi |
| 2023-09-26 | Extract basic resource types to a separate module. | Frederick Muriuki Muriithi |
| 2023-08-23 | pylint: Remove statement calling non-existent member | Frederick Muriuki Muriithi |
