| Age | Commit message (Expand) | Author |
|---|
| 2023-02-02 | auth: Reorganise modules/packages for easier dev and maintenance...Split the views/routes into separate modules each dealing with a narrower
scope of the application to aid in maintenance, and help with making the
development easier.
| Frederick Muriuki Muriithi |
| 2023-01-31 | auth: Retrieve group members. | Frederick Muriuki Muriithi |
| 2023-01-31 | auth: Remove the @authenticated_p decorator...The @authenticated_p decorator (and function), is an artifact of the original
development ideas and should be removed from use.
| Frederick Muriuki Muriithi |
| 2023-01-31 | auth: Set the token scope as a string, not a list...Setting the scope as a list of strings was leading to errors when attempting
to logout. This commit leaves the scope as a string to avoid the errors.
| Frederick Muriuki Muriithi |
| 2023-01-30 | auth: Do not treat not finding a group as an error...Stop treating not finding a group for a user as an error, since that is an
actual expected state in the system at some point. Rather, restore the use of
Maybe rather than using Either.
We can raise the NotFoundError at the API level rather than at database
retrival level.
| Frederick Muriuki Muriithi |
| 2023-01-30 | auth: API: retrieve resources | Frederick Muriuki Muriithi |
| 2023-01-30 | auth: groups: cleanup code...Refactor to use the `.either` method call in a cleaner way.
Rework the imports.
| Frederick Muriuki Muriithi |
| 2023-01-30 | auth: API: Retrieve a user's group...Add endpoint to retrieve the group in which the user is a member.
| Frederick Muriuki Muriithi |
| 2023-01-28 | auth: Enable retrieval of a role by id. | Frederick Muriuki Muriithi |
| 2023-01-28 | auth: rework dictify...Define a Protocol type to use with the `dictify` function and implement the
`dictify` methods for the various classes.
| Frederick Muriuki Muriithi |
| 2023-01-28 | auth: Store error_code in Exception for flexibility...To allow for different error codes for the various exceptions, store the
error_code in the exception objects and retrieve it from there when generating
the response.
| Frederick Muriuki Muriithi |
| 2023-01-25 | Some comments | Pjotr Prins |
| 2023-01-24 | search: Use decimals, not floats, when converting to megabases....* gn3/api/search.py (parse_location_field): Use decimals, not floats, when
converting to megabases.
| Arun Isaac |
| 2023-01-24 | search: Support SI suffixes and point locations....* gn3/api/search.py (parse_position_field): New function.
(parse_query): Associate the position prefix with the parse_position_field
field processor.
| Arun Isaac |
| 2023-01-24 | search: Abstract out parsing of position spec into separate function....* gn3/api/search.py (parse_position): New function.
(parse_location_field): Use parse_position.
* tests/unit/test_search.py: Import parse_position from gn3.api.search.
(test_parse_position_close_to_zero_location): New test.
| Arun Isaac |
| 2023-01-24 | search: Alias the position prefix with pos....* gn3/api/search.py (parse_query): Alias the position prefix with pos.
| Arun Isaac |
| 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 |
| 2023-01-23 | 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 | 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 | 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: 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 | 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 |
