| Age | Commit message (Expand) | Author |
|---|
| 2024-03-21 | Delete commented out import....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-21 | Rename "the_code" to "_code"....* 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>
| Munyoki Kilyungi |
| 2024-03-13 | Delete a debug print query....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>
| Munyoki Kilyungi |
| 2024-03-13 | Rename users -> fetch_users....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>
| Munyoki Kilyungi |
| 2024-03-13 | Delete dictify....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>
| Munyoki Kilyungi |
| 2024-03-13 | Remove unused imports....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-13 | Define AuthorisationCode using frozen dataclass....* 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>
| Munyoki Kilyungi |
| 2024-03-13 | Define Resource/ResourceCategory using frozen dataclass....* 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>
| Munyoki Kilyungi |
| 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 | setup.py: Fix pylint errors....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| 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 |
| 2024-03-02 | Use `find_packages()` and include static files and templates. | Frederick Muriuki Muriithi |
| 2024-03-01 | Put `GN_AUTH_SECRETS` config in the main configuration file. | Frederick Muriuki Muriithi |
| 2024-03-01 | Configs: Check that all mandatory settings exist and are non-empty. | Frederick Muriuki Muriithi |
| 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 |
| 2024-02-27 | Remove use of instance path in configurations. | Frederick Muriuki Muriithi |
| 2024-02-27 | Update base template. | Frederick Muriuki Muriithi |
| 2024-01-30 | Add exception traces to error outputs. | Frederick Muriuki Muriithi |
| 2024-01-29 | Error handling: Handle 404 error. | Frederick Muriuki Muriithi |
| 2023-12-19 | README: Replace pylint and mypy CI badges with all-tests CI badge. | Arun Isaac |
| 2023-12-19 | guix: Add gn-auth-all-tests....* .guix/modules/gn-auth.scm: Import python-pylint from (gnu packages
check) and python-mypy from (gnu packages python-check).
(gn-auth-all-tests): New variable.
| Arun Isaac |
| 2023-12-19 | guix: Inherit gn-auth package from guix-bioinformatics....* .guix/modules/gn-auth.scm (gn-auth): Inherit from gn-auth in
guix-bioinformatics.
| Arun Isaac |
| 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 |
| 2023-12-05 | mypy: Deactivate search for flask_cors stubs | Frederick Muriuki Muriithi |
| 2023-12-05 | Add missing scripts and update code to invoke them...Copy the missing scripts over from GN3 and update them for
gn-auth. Update the code to invoke the scripts correctly. Set up
correct redis keys for use with the scripts.
| Frederick Muriuki Muriithi |
| 2023-12-05 | Enable CORS to allow access from GN2 javascript | 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 | Make existing user admin using core system functions...Use the core system functions to both fetch the user and make them
into a system admin, rather than fetching with raw queries. This way,
if the way the users are fetched, or made into an admin, changes, we
do not need to update the scripts for most part.
| 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 |
| 2023-11-17 | Bug: Update query in script...Update query in script to provide resource_id for the user_roles tabel.
| Frederick Muriuki Muriithi |
| 2023-11-17 | Add styles. | Frederick Muriuki Muriithi |
| 2023-11-17 | Setup path to static paths correctly. | Frederick Muriuki Muriithi |
