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2023-03-01Open lmdb path in readonly modeMunyoki Kilyungi
* gn3/db/matrix.py (get_total_versions, get_nth_matrix, get_current_matrix): Open lmdb in readonly mode. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-03-01Create API endpoint for fetching trait metadataMunyoki Kilyungi
* gn3/api/metadata.py (dataset_metadata): New function and endpoint. (jsonify_dataset_metadata): Rename to dataset_metadata. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-03-01Fetch trait metadata from RDFMunyoki Kilyungi
* gn3/db/rdf.py (get_dataset_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-02-28auth: Unlink data from resourcesdata-access-levels-endpointFrederick Muriuki Muriithi
Enable the data editor to unlink data from a particular resource.
2023-02-28auth: Unlink data from resourcesFrederick Muriuki Muriithi
Enable the data editor to unlink data from a particular resource.
2023-02-27auth: Endpoint to get access levels for dataFrederick Muriuki Muriithi
When the endpoint is accessed with a list of traits, it should/will respond with the access privileges for each of the traits attached for the active user.
2023-02-24auth: resources: Fix query for data not linked to resourcesFrederick Muriuki Muriithi
2023-02-24auth: resources: Fix queries loading resources data.Frederick Muriuki Muriithi
2023-02-24auth: resources: Link data to resources.Frederick Muriuki Muriithi
2023-02-23auth: Link data in MySQL to the groups (in SQLite)Frederick Muriuki Muriithi
In order for the group leaders (and other resource creators) to be able to link data to the resources, the data needs to be first linked to the relevant group. This commit enables the system admin to link the data in MySQL to the groups.
2023-02-22auth: List data not linked to any group.Frederick Muriuki Muriithi
2023-02-21auth: db: DEBUG: Output quer(y|ies) that were run.Frederick Muriuki Muriithi
2023-02-21auth: resources: Attach resource data and list unlinked data.Frederick Muriuki Muriithi
Load the data that is attached to a particular resource together with the resource. List any unlinked data: useful when linking data to resources.
2023-02-10Return empty tuple rather than NothingFrederick Muriuki Muriithi
When user has no roles assigned, return an empty tuple rather than pymonad.maybe.Nothing to ease maintenance.
2023-02-09auth: Reject request to join a group.Frederick Muriuki Muriithi
* gn3/auth/authorisation/groups/models.py: Modify function to either accept or reject join requests. * gn3/auth/authorisation/groups/views.py: Provide endpoint to reject join requests. * migrations/auth/20230207_01_r0bkZ-create-group-join-requests-table.py: Prevent user from applying to join the same group more than once.
2023-02-09auth: users: Check whether a user has an active join request.Frederick Muriuki Muriithi
2023-02-08auth: groups: handle join requests.Frederick Muriuki Muriithi
2023-02-07auth: groups: Enable users to request to join group.Frederick Muriuki Muriithi
2023-02-06Get the N-th matrix given N, an index valueMunyoki Kilyungi
* gn3/db/matrix.py (get_nth_matrix): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-02-06Get total number of versions that a database hasMunyoki Kilyungi
* gn3/db/matrix.py (get_total_versions): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-02-06Add method to fetch the current matrixMunyoki Kilyungi
* gn3/db/matrix.py: New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-02-06auth: resource: Enable viewing the details of a resource.Frederick Muriuki Muriithi
2023-02-03auth: commit missing module.Frederick Muriuki Muriithi
2023-02-03oauth: enable resource creationFrederick Muriuki Muriithi
2023-02-03auth: tests: mock token acquisition. Fix minor bugs.Frederick Muriuki Muriithi
2023-02-02auth: Improve authorisationFrederick Muriuki Muriithi
Retrieve the token, and user in the authorisation decorator to enable checking of privileges.
2023-02-02auth: Reorganise modules/packages for easier dev and maintenanceFrederick Muriuki Muriithi
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.
2023-01-31auth: Retrieve group members.Frederick Muriuki Muriithi
2023-01-31auth: Remove the @authenticated_p decoratorFrederick Muriuki Muriithi
The @authenticated_p decorator (and function), is an artifact of the original development ideas and should be removed from use.
2023-01-31auth: Set the token scope as a string, not a listFrederick Muriuki Muriithi
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.
2023-01-30auth: Do not treat not finding a group as an errorFrederick Muriuki Muriithi
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.
2023-01-30auth: API: retrieve resourcesFrederick Muriuki Muriithi
2023-01-30auth: groups: cleanup codeFrederick Muriuki Muriithi
Refactor to use the `.either` method call in a cleaner way. Rework the imports.
2023-01-30auth: API: Retrieve a user's groupFrederick Muriuki Muriithi
Add endpoint to retrieve the group in which the user is a member.
2023-01-28auth: Enable retrieval of a role by id.Frederick Muriuki Muriithi
2023-01-28auth: rework dictifyFrederick Muriuki Muriithi
Define a Protocol type to use with the `dictify` function and implement the `dictify` methods for the various classes.
2023-01-28auth: Store error_code in Exception for flexibilityFrederick Muriuki Muriithi
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.
2023-01-25Some commentsPjotr Prins
2023-01-24search: Use decimals, not floats, when converting to megabases.Arun Isaac
* gn3/api/search.py (parse_location_field): Use decimals, not floats, when converting to megabases.
2023-01-24search: Support SI suffixes and point locations.Arun Isaac
* gn3/api/search.py (parse_position_field): New function. (parse_query): Associate the position prefix with the parse_position_field field processor.
2023-01-24search: Abstract out parsing of position spec into separate function.Arun Isaac
* 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.
2023-01-24search: Alias the position prefix with pos.Arun Isaac
* gn3/api/search.py (parse_query): Alias the position prefix with pos.
2023-01-24search: Rename the mb prefix to position.Arun Isaac
* gn3/api/search.py (parse_query): Rename the mb prefix to position.
2023-01-24search: Assume triplets mean synteny is requested.Arun Isaac
* 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.
2023-01-24search: Use comprehension when splitting location.Arun Isaac
* gn3/api/search.py (parse_location_field): Use comprehension.
2023-01-23auth: Add missing moduleFrederick Muriuki Muriithi
2023-01-23auth: create group: Fix group creation.Frederick Muriuki Muriithi
* 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
2023-01-21auth: Groups - Fetch all existing groupsFrederick Muriuki Muriithi
2023-01-21auth: Roles - Fix bug with role retrieval.Frederick Muriuki Muriithi
2023-01-21auth: Fix saving of scope values. Add scope items.Frederick Muriuki Muriithi
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