| Age | Commit message (Expand) | Author |
|---|
| 2023-01-24 | search: Rename the mb prefix to position....* gn3/api/search.py (parse_query): Rename the mb prefix to position.
| Arun Isaac |
| 2023-01-24 | search: Assume triplets mean synteny is requested....* gn3/api/search.py (query_subqueries, query_terms, parse_synteny_field,
is_synteny_on, remove_synteny_field): Delete functions.
(parse_query): Assume triplets mean synteny is requested.
| Arun Isaac |
| 2023-01-24 | search: Use comprehension when splitting location....* gn3/api/search.py (parse_location_field): Use comprehension.
| Arun Isaac |
| 2023-01-24 | docs: Add information on running the OAuth2 server without HTTPS | Frederick Muriuki Muriithi |
| 2023-01-23 | auth: Add missing module | Frederick Muriuki Muriithi |
| 2023-01-23 | auth: create group: Fix group creation....* gn3/auth/authorisation/checks.py: Enable passing user to authorisation
checking function. Raise error on authorisation failure for consistent error
handling.
* gn3/auth/authorisation/groups.py: Add user to group, updating the privileges
as appropriate.
* gn3/auth/authorisation/resources.py: Fix resources querying
* gn3/auth/authorisation/roles.py: Assign/revoke roles by name
* gn3/auth/authorisation/views.py: Create group
* migrations/auth/20221108_01_CoxYh-create-the-groups-table.py: Add
group_metadata field
* tests/unit/auth/fixtures/group_fixtures.py: fix tests
* tests/unit/auth/test_groups.py: fix tests
* tests/unit/auth/test_resources.py: fix tests
* tests/unit/auth/test_roles.py: fix tests
| Frederick Muriuki Muriithi |
| 2023-01-21 | tests: roles - Extract values from Maybe object | Frederick Muriuki Muriithi |
| 2023-01-21 | tests: Fix linting errors | Frederick Muriuki Muriithi |
| 2023-01-21 | auth: Groups - Fetch all existing groups | Frederick Muriuki Muriithi |
| 2023-01-21 | auth: Roles - Fix bug with role retrieval. | Frederick Muriuki Muriithi |
| 2023-01-21 | auth: Fix saving of scope values. Add scope items. | Frederick Muriuki Muriithi |
| 2023-01-20 | mypy: minor fixes to typing errors | Frederick Muriuki Muriithi |
| 2023-01-20 | auth: rename revocation endpoint | Frederick Muriuki Muriithi |
| 2023-01-20 | auth: Save token with update...If the token already exists, then update the details rather than trying to
insert.
| Frederick Muriuki Muriithi |
| 2023-01-20 | auth: Setup the user correctly...* gn3/auth/authentication/oauth2/grants/password_grant.py: Return user rather
than boolean
* gn3/auth/authentication/oauth2/models/oauth2client.py: provide optional
`user` argument to allow flexibility in setting up the client's user
* gn3/auth/authentication/oauth2/models/oauth2token.py: Set token and client
user correctly
* gn3/auth/authentication/oauth2/server.py: Set token user from the request
| Frederick Muriuki Muriithi |
| 2023-01-20 | auth: Add development utils/tools...To avoid having to manually rebuild some default data for exploration of
concepts while developing the system, add a way to build up the test users and
oauth2 clients to use for testing.
| Frederick Muriuki Muriithi |
| 2023-01-19 | tests: Add unit tests for search....* tests/unit/test_search.py: New file.
| Arun Isaac |
| 2023-01-19 | search: Downcase before applying SI suffix....* gn3/api/search.py (apply_si_suffix): Downcase before applying SI suffix.
| Arun Isaac |
| 2023-01-19 | search: Use decimals, not floats, to manipulate range limits....Decimals are exact and do not introduce tiny errors in the range limits like
floats are wont to do.
* gn3/api/search.py: Import Decimal from decimal.
(apply_si_suffix): Use decimals, not floats, to manipulate range limits.
| Arun Isaac |
| 2023-01-19 | search: Only look for SI suffix in the last character....Suffixes are the last character, not everything but the last character.
* gn3/api/search.py (apply_si_suffix): Only look for SI suffix in the last
character.
| Arun Isaac |
| 2023-01-19 | search: Apply SI suffix only if last character is an actual suffix....Prior to this commit, when there was no SI suffix (such as in a plain
suffix-less number), the last digit would be dropped!
* gn3/api/search.py (apply_si_suffix): Apply SI suffix only if last character
is an actual suffix.
| Arun Isaac |
| 2023-01-19 | auth: Fix user registration...The code checking for errors was buggy and would let empty values through.
The sqlite3.IntegrityError exception was not being handled correctly, and
would cause a failure in the application.
This commit fixes the issues noted above.
* gn3/auth/authorisation/roles.py: fix bug in generating query params
* gn3/auth/authorisation/views.py: fix error checking code. Raise exception if
email is already registered.
| Frederick Muriuki Muriithi |
| 2023-01-18 | search: Ensure limits of chromosomal interval is non-negative....* gn3/api/search.py (parse_location_field): Ensure limits of chromosomal
interval is non-negative.
| Arun Isaac |
| 2023-01-18 | search: Convert point locations to a +/- 50 kbase range....* gn3/api/search.py (parse_location_field): Convert point locations to a +/-
50 kbase range.
| Arun Isaac |
| 2023-01-18 | Pass species and species prefix as a single query argument....* gn3/api/search.py (parse_location_field): Accept a single species query
argument instead of separate species and species prefix arguments.
(parse_query): Pass parse_location_field a single species query argument.
| Arun Isaac |
| 2023-01-18 | auth: Fix tests after enforcing FOREIGN KEY constraint...Fix a number of tests and fixtures that were not conforming to the FOREIGN KEY
constraints:
* Each test that creates a new "object" needs to clean up after itself
* Each fixture that sets up test data needs to clean up after itself
| Frederick Muriuki Muriithi |
| 2023-01-18 | auth: Allow non-member users to access group resources...Allow users that are not members of a particular group to be granted access to
that group's resources via an explicit role assignment. This is accomplished
by removing the `FOREIGN KEY(group_id, user_id)` constraint.
| Frederick Muriuki Muriithi |
| 2023-01-18 | auth: Enable FOREIGN KEY constraint for the connections...Enable the FOREIGN KEY constraints for the connections to the database to help
with queries that would otherwise lead to data corruption.
| Frederick Muriuki Muriithi |
| 2023-01-18 | pylintrc: Disable no-else-return check....else-return statements are closer to the cond ladders in lisp. They feel
better composed, more symmetric and less like non-local exits. They should not
be discouraged.
* .pylintrc (disable): Add no-else-return.
| Arun Isaac |
| 2023-01-18 | Tolerate WEIGHT operator in parsed search queries....* gn3/api/search.py (remove_synteny_field): Tolerate WEIGHT operator in parsed
search queries.
| Arun Isaac |
| 2023-01-18 | Implement synteny search....* gn3/api/search.py: Import gzip, Path from pathlib and curry from
pymonad.tools.
(IntervalLiftoverFunction): New variable.
(query_subqueries, query_terms, field_processor_or, liftover,
liftover_interval, parse_synteny_field, is_synteny_on, remove_synteny_field):
New functions.
(parse_location_field): Generalize to support synteny searches.
(parse_query): Support synteny search queries.
(search_results): Pass synteny files directory to parse_query.
| Arun Isaac |
| 2023-01-18 | Support location shorthands in search queries....* gn3/api/search.py: Import partial and reduce from functools. Import Callable
from typing.
(ChromosomalPosition, ChromosomalInterval, FieldProcessor): New classes.
(apply_si_suffix, combine_queries, parse_location_field, interval_start,
interval_end): New functions.
(parse_query): Add field processors for location shorthands.
| Arun Isaac |
| 2023-01-18 | Split off search query parsing into separate function....* gn3/api/search.py (parse_query): New function.
(search_results): Use parse_query.
| Arun Isaac |
| 2023-01-16 | auth: update privileges format...Save privileges with ids of the form <top-level>:<sub-level>:<privilege-name>
rather than using a UUID, to reduce indirection levels.
* migrations/auth/20230116_01_KwuJ3-rework-privileges-schema.py: new migration
to change the schema and IDs for the privileges.
* Update code to use new privileges format
* gn3/auth/authorisation/checks.py
* gn3/auth/authorisation/groups.py
* gn3/auth/authorisation/privileges.py
* gn3/auth/authorisation/resources.py
* gn3/auth/authorisation/roles.py
* migrations/auth/20230116_01_KwuJ3-rework-privileges-schema.py
* tests/unit/auth/fixtures/role_fixtures.py
* tests/unit/auth/test_groups.py
* tests/unit/auth/test_privileges.py
* tests/unit/auth/test_roles.py
| Frederick Muriuki Muriithi |
| 2023-01-11 | auth: assign default role. separate group creation from group admin...A newly registered user will have the ability to create a group.
Once a user is a member of a group, either by creating a new group, or being
added to a group, they should not be able to create any more groups, i.e. they
lose the 'create-group' (and/or equivalent) privileges.
This means that the group-administration privileges should be separated from
the group-creation privilege.
* gn3/auth/authorisation/roles.py: assign default roles to user on
registration
* gn3/auth/authorisation/views.py: assign default roles to user on
registration
* migrations/auth/20230111_01_Wd6IZ-remove-create-group-privilege-from-group-leader.py:
separate group-creation role from group-administration role.
* tests/unit/auth/fixtures/user_fixtures.py: Add group-creation role to test
user
* tests/unit/auth/test_roles.py: Add the group-creation role explicitly in the
expected results for the test
| Frederick Muriuki Muriithi |
| 2023-01-11 | auth: Add missing import | Frederick Muriuki Muriithi |
| 2023-01-05 | auth: Persist the user's registration details...If the registration details pass the validations steps, then persist the
details in the database and respond with details about the newly created user.
* gn3/auth/authentication/users.py: new functions
* `save_user`: create and persist a new user
* `set_user_password`: hash and persist the new password for the given user
* gn3/auth/authorisation/views.py: Persist the user details and respond with
the newly persisted user details.
| Frederick Muriuki Muriithi |
| 2023-01-04 | auth: Add `/register-user` endpoint...* gn3/app.py: register top-level error handlers. reorganise oauth2 blueprint.
* gn3/auth/__init__.py: reorganise oaut2 blueprint.
* gn3/auth/authentication/oauth2/views.py: reorganise oauth2 blueprint.
* gn3/auth/authorisation/exceptions.py -> gn3/auth/authorisation/errors.py
* gn3/auth/authorisation/groups.py: rename file/module
* gn3/auth/authorisation/resources.py: rename file/module
* gn3/auth/authorisation/views.py: Add `/register-user` endpoint
* gn3/auth/blueprint.py: reorganise oauth2 blueprint.
* gn3/errors.py: register top-level error handlers.
| Frederick Muriuki Muriithi |
| 2023-01-04 | auth: return group info as part of user details...* gn3/app.py: import blueprint from authorisation views inorder to get all
endpoints
* gn3/auth/authentication/oauth2/views.py: remove the `/user` endpoint
* gn3/auth/authorisation/views.py: add the `/user` endpoint and add the group
information to the user details.
| Frederick Muriuki Muriithi |
| 2023-01-04 | auth: Return only non-resource roles on `/user-roles` endpoint...Resource roles will be returned as part of the resources request.
* gn3/auth/authorisation/roles.py: Simplify query - only get non-resource
roles
* gn3/auth/authorisation/views.py: update docstring
| Frederick Muriuki Muriithi |
| 2023-01-03 | auth: Fetch all of a user's roles....* gn3/auth/authorisation/roles.py: Fetch roles from DB
* gn3/auth/authorisation/views.py: Provide API endpoint for user roles
* tests/unit/auth/test_roles.py: Tests to check fetching roles works correctly
Fix linting and typing issues in the following files:
* gn3/auth/authentication/oauth2/resource_server.py
* gn3/auth/authentication/oauth2/views.py
* tests/unit/auth/fixtures/oauth2_client_fixtures.py
| Frederick Muriuki Muriithi |
| 2023-01-03 | auth: rename fixtures: test_* -> fxtr_*...Since test functions are defined starting with "test_", rename the fixture to
more clearly indicate it is a fixture (fxtr_*), an not a test in itself.
| Frederick Muriuki Muriithi |
| 2022-12-31 | auth: Document new ideas for privileges | Frederick Muriuki Muriithi |
| 2022-12-28 | auth: Add resource server and /user endpoint...Add a resource server with the validator for the bearer token to protect the
resources endpoints.
Add a protected `/user` endpoint that returns the user details for valid
tokens.
* gn3/auth/authentication/oauth2/resource_server.py: new file
* gn3/auth/authentication/oauth2/views.py: add /user endpoint
| Frederick Muriuki Muriithi |
| 2022-12-23 | Update how to set configurations in README | zsloan |
| 2022-12-23 | Add a couple necessary environment variables | zsloan |
| 2022-12-22 | tests: Setup environment variables and configs...* gn3/settings.py: leave `OAUTH2_ACCESS_TOKEN_GENERATOR` in its default
setting
* tests/unit/auth/fixtures/oauth2_client_fixtures.py: setup
`AUTHLIB_INSECURE_TRANSPORT` before running the OAuth2 tests
* tests/unit/conftest.py: setup the test application's configuration correctly
for the tests.
| Frederick Muriuki Muriithi |
| 2022-12-22 | auth: implement OAuth2 flow....Add code to implement the OAuth2 flow.
* Add test fixtures for setting up users and OAuth2 clients
* Add tests for token generation with the "Password Grant" flow
* Fix some issues with test due to changes in the database connection's
row_factory
oauth2_auth_flow | Frederick Muriuki Muriithi |
| 2022-12-21 | auth: oauth2: users: Add expected property...* gn3/auth/authentication/users.py: authlib expects the user object to have a
`get_user_id` method.
| Frederick Muriuki Muriithi |
| 2022-12-21 | migrations: create the authorisation_code table...* migrations/auth/20221219_03_PcTrb-create-authorisation-code-table.py: new
migration
* tests/unit/auth/test_migrations_create_tables.py: test new migration
| Frederick Muriuki Muriithi |
