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* gn_auth/auth/authentication/oauth2/models/oauth2client.py
(client): Rename the_user -> _user.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* 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>
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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>
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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>
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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>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* 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>
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* 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>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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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>
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* gn_auth/auth/db/protocols.py (DbCursor): Remove "raise" in DBCursor
Protocol. See:
<https://typing.readthedocs.io/en/latest/spec/protocol.html>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* 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>
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* gn_auth/auth/authorisation/data/views.py (authorisation): Fix typo.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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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.
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* .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.
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* .guix/modules/gn-auth.scm (gn-auth): Inherit from gn-auth in
guix-bioinformatics.
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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.
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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.
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BCrypt has been superceded by argon, and this commit removes it and
all code depending on it from the repository.
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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.
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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.
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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.
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Only commit changes if the queries are successful.
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Update query in script to provide resource_id for the user_roles tabel.
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