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2024-03-21Add extra endpoint to get user authorisation given a resource name.Munyoki Kilyungi
* gn_auth/auth/authorisation/resources/models.py (user_roles_on_resources): New function. * gn_auth/auth/authorisation/resources/views.py (resources_authorisation): New endpoint. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-21Revert "Add an extra endpoint for metadata authorisation."Munyoki Kilyungi
This reverts commit f5e833c0d72eaec80425203b15210ed304cc4811. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-21Fix typo.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-21Replace "the" prefix with an underscore.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-21Delete dead comment.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-21Rename the_user -> _user.Munyoki Kilyungi
* gn_auth/auth/authentication/oauth2/models/oauth2client.py (client): Rename the_user -> _user. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-21Delete commented out import.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-21Rename "the_code" to "_code".Munyoki Kilyungi
* gn_auth/auth/authentication/oauth2/grants/authorisation_code_grant.py (__query_authorization_code__): Rename the_code -> _code. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-13Delete a debug print query.Munyoki Kilyungi
Debugging this if necessary should be handled by pdb. * gn_auth/auth/authentication/users.py (fetch_users): Delete print statement. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-13Rename users -> fetch_users.Munyoki Kilyungi
Use verbs for methods. * gn_auth/auth/authentication/oauth2/models/oauth2client.py (OAuth2Client): (oauth2_clients): Rename users -> fetch_users. * gn_auth/auth/authentication/users.py (users): Ditto. (fetch_users): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-13Delete dictify.Munyoki Kilyungi
This module is redundant since dataclasses already provides the asdict method. * gn_auth/auth/dictify.py: Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-13Remove unused imports.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-13Define AuthorisationCode using frozen dataclass.Munyoki Kilyungi
* gn_auth/auth/authentication/oauth2/models/authorization_code.py: Import dataclass, asdict, cached_property and AuthorizationCodeMixin. Remove NamedTuple import. (AuthorisationCode): Use frozen dataclass and explicitly inherit from AuthorizationCodeMixin. Delete unnecessary comment. (AuthorisationCode.response_type): Make this a cached_property. (AuthorisationCode.get_nonce): Delete. This is not defined in the RFC6749 spec. (save_authorisation_code): Replace _asdict() with asdict(...). Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-13Define Resource/ResourceCategory using frozen dataclass.Munyoki Kilyungi
* gn_auth/auth/authorisation/resources/base.py: Import dataclass and asdict. Remove NamedTuple and dictify. (ResourceCategory): Use frozen dataclass. (ResourceCategory.dictify): Delete. (Resource): Use frozen dataclass. (Resource.dictify): Delete. * gn_auth/auth/authorisation/resources/models.py: Delete dictify import. (assign_resource_user): Replace dictify with asdict. (unassign_resource_user): Ditto. * gn_auth/auth/authorisation/resources/views.py: Import asdict. Remove dictify import. (list_resource_categories): Replace dictify with asdict. (create_resource): Ditto. (view_resource): Ditto. (__safe_get_requests_page__): Ditto. * gn_auth/auth/authorisation/users/views.py: (user_resources): Replace dictify with asdict. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-13Rename "the_client" to "_client".Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-13Remove unused imports.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-13Auto-pep8 this file.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-13Define Privilege/Role using frozen dataclass.Munyoki Kilyungi
* 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>
2024-03-13Define OAuth2Client using frozen dataclass.Munyoki Kilyungi
* 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>
2024-03-13Define GroupRole using frozen dataclass.Munyoki Kilyungi
* 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>
2024-03-13Define Group using a frozen dataclass.Munyoki Kilyungi
* 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>
2024-03-13Define OAuth2Token using a frozen dataclass.Munyoki Kilyungi
* 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>
2024-03-13Define User using a frozen dataclass.Munyoki Kilyungi
* 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>
2024-03-08Correctly check for the refresh_token.Munyoki Kilyungi
* 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>
2024-03-08Replace "if" branching with "monad_from_none_or_value".Munyoki Kilyungi
* 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>
2024-03-08Rename "__5_MINUTES__" to "EXPIRY_IN_SECONDS".Munyoki Kilyungi
* 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>
2024-03-08Explicitly add keyword arguments to AuthorisationCode.Munyoki Kilyungi
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>
2024-03-08Remove "raise" in auth.db Protocol classes.Munyoki Kilyungi
* gn_auth/auth/db/protocols.py (DbCursor): Remove "raise" in DBCursor Protocol. See: <https://typing.readthedocs.io/en/latest/spec/protocol.html>
2024-03-04Add an extra endpoint for metadata authorisation.Munyoki Kilyungi
* 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>
2024-03-04Fix minor typo.Munyoki Kilyungi
* gn_auth/auth/authorisation/data/views.py (authorisation): Fix typo. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-04Remove redundant error code for InvalidData.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-29Allow POST for JSON requests.Frederick Muriuki Muriithi
2024-02-28Handle the "NotFoundError" exception at the route levelFrederick Muriuki Muriithi
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.
2023-12-18Provide the correct Redis keyFrederick Muriuki Muriithi
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.
2023-11-28Remove bcrypt as a dependencyFrederick Muriuki Muriithi
BCrypt has been superceded by argon, and this commit removes it and all code depending on it from the repository.
2023-11-23Scripts: Update script for newer db schemaFrederick Muriuki Muriithi
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.
2023-11-22Move system admin creationFrederick Muriuki Muriithi
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.
2023-11-22Only commit on successful queryFrederick Muriuki Muriithi
Only commit changes if the queries are successful.
2023-11-13Bug: Fix typo in queryFrederick Muriuki Muriithi
2023-11-13Update check for adminsFrederick Muriuki Muriithi
2023-11-02mypy: Fix typing errors.Frederick Muriuki Muriithi
2023-11-02pylint: Fix linting errors.Frederick Muriuki Muriithi
2023-10-12Bugs: Fix query and provide default function for inbredset-groupFrederick Muriuki Muriithi
2023-10-10Get authorisation by resource_idsFrederick Muriuki Muriithi
Add an endpoint to help users get the resources authorisation by the resource ids.
2023-10-10Temporarily return no data for resources of types system and group.Frederick Muriuki Muriithi
2023-10-09Fetch InbredSet group resource ID by SpeciesId and InbredSetIdFrederick Muriuki Muriithi
Get the resource used to control access to the InbredSet group by that group's SpeciesId and InbredSetId.
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.