| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-03-13 | Move doc to issue tracker | Pjotr Prins | |
| 2023-03-13 | oauth2: data: Temporarily escalate privileges to enable migration | Frederick Muriuki Muriithi | |
| The functions that fetch the unlinked data have checks to ensure they are called by users with the appropriate privileges. This commit enables a temporary escalation of privileges to enable fetching the data, so as to allow successful data migration. | |||
| 2023-03-13 | auth: separate user detail migration from data migration | Frederick Muriuki Muriithi | |
| Due to the fact that the data migration requires higher privileges than the user details, separate the user details migration endpoint from the data migrations endpoint. | |||
| 2023-03-13 | Add 'ON UPDATE/DELETE' clauses to foreign keys. | Frederick Muriuki Muriithi | |
| 2023-03-13 | auth: cURL: Add some docs on using cURL | Frederick Muriuki Muriithi | |
| 2023-03-10 | auth: data-migration: Fix minor bugs | Frederick Muriuki Muriithi | |
| 2023-03-09 | auth: redis data: migrate data in redis | Frederick Muriuki Muriithi | |
| Implement the code to migrate the data from redis to SQLite. | |||
| 2023-03-09 | auth: data migration: Data migration outline | Frederick Muriuki Muriithi | |
| Provide an outline of the data migration steps to be taken from some results of the experiments with the data in redis. | |||
| 2023-03-09 | auth: introspection: Protect introspection endpoint | Frederick Muriuki Muriithi | |
| The introspection endpoint could contain privileged information, thus requires that the endpoint be protected. This commit ensures that a user has authenticated to the system and that the client they are using be one of the allowed clients. | |||
| 2023-03-08 | auth: users: Use the same basic functions for password hashing | Frederick Muriuki Muriithi | |
| To avoid repeating the same thing in multiple places, leading to errors and breakages, reuse the same basic functions for password hashing. | |||
| 2023-03-08 | Replace Bcrypt with Argon2 for better security. | Frederick Muriuki Muriithi | |
| Bcrypt is now somewhat vulnerable to offline cracking, so we move our password hashing over to Argon2. | |||
| 2023-03-07 | auth: group_roles: Enable addition/deletion of privileges | Frederick Muriuki Muriithi | |
| 2023-03-07 | auth: resources: unassign roles on resource from a user. | Frederick Muriuki Muriithi | |
| 2023-03-07 | auth: user_by_id: Return a user or raise an exception | Frederick Muriuki Muriithi | |
| Fetching the user by id should return the user, or raise an exception. We get rid of the Maybe monad here since it is leading to some weird code flows - probably the wrong monad to use here. | |||
| 2023-03-06 | auth: privileges/roles: fix issues caught by tests. | Frederick Muriuki Muriithi | |
| 2023-03-06 | auth: resources: Enable assigning a user roles on resources | Frederick Muriuki Muriithi | |
| 2023-03-06 | auth: resources: Link role's group to the resource's group | Frederick Muriuki Muriithi | |
| 2023-03-06 | auth: resources: Get all users with access to a particular resource. | Frederick Muriuki Muriithi | |
| 2023-03-03 | auth: Enable viewing group role details. | Frederick Muriuki Muriithi | |
| 2023-03-03 | auth: group roles: enable creation and listing of group roles. | Frederick Muriuki Muriithi | |
| 2023-03-02 | auth: user registration: Rework error checking. Add email validation | Frederick Muriuki Muriithi | |
| 2023-03-01 | Fetch sampledata | Munyoki Kilyungi | |
| * gn3/api/sampledata.py (get_sampledata): New end-point. * gn3/app.py: Register above end-point. * gn3/settings.py: Add new conf variable for LMDB. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-03-01 | Open lmdb path in readonly mode | Munyoki 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> | |||
| 2023-03-01 | Create API endpoint for fetching trait metadata | Munyoki 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> | |||
| 2023-03-01 | Fetch trait metadata from RDF | Munyoki Kilyungi | |
| * gn3/db/rdf.py (get_dataset_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-02-28 | auth: Unlink data from resourcesdata-access-levels-endpoint | Frederick Muriuki Muriithi | |
| Enable the data editor to unlink data from a particular resource. | |||
| 2023-02-28 | auth: Unlink data from resources | Frederick Muriuki Muriithi | |
| Enable the data editor to unlink data from a particular resource. | |||
| 2023-02-27 | auth: Endpoint to get access levels for data | Frederick 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. | |||
| 2023-02-24 | auth: resources: Fix query for data not linked to resources | Frederick Muriuki Muriithi | |
| 2023-02-24 | auth: resources: Fix queries loading resources data. | Frederick Muriuki Muriithi | |
| 2023-02-24 | auth: resources: Link data to resources. | Frederick Muriuki Muriithi | |
| 2023-02-23 | auth: 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. | |||
| 2023-02-22 | auth: List data not linked to any group. | Frederick Muriuki Muriithi | |
| 2023-02-21 | auth: db: DEBUG: Output quer(y|ies) that were run. | Frederick Muriuki Muriithi | |
| 2023-02-21 | auth: 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. | |||
| 2023-02-21 | auth: migrations: Link to data in main db | Frederick Muriuki Muriithi | |
| Provide the `linked_group_data` table to be used to link to data in the main database. Update the `mrna_resources`, `genotype_resources` and `phenotype_resources` tables to rely on the `linked_group_data` table. | |||
| 2023-02-13 | scripts: Fallback to 1 worker when indexing. | Arun Isaac | |
| * scripts/index-genenetwork (worker_queue): Set default number of workers to 1 if the number of CPUs cannot be determined. | |||
| 2023-02-13 | scripts: Type hint xapian indexing script. | Arun Isaac | |
| * scripts/index-genenetwork: Import Callable, Generator, Iterable and List from typing. Type hint all functions. | |||
| 2023-02-10 | Return empty tuple rather than Nothing | Frederick Muriuki Muriithi | |
| When user has no roles assigned, return an empty tuple rather than pymonad.maybe.Nothing to ease maintenance. | |||
| 2023-02-10 | Fix linting errors. | Frederick Muriuki Muriithi | |
| 2023-02-10 | Add example utility script to run development server | Frederick Muriuki Muriithi | |
| 2023-02-10 | auth: CLI: Provide a way to set an existing user as a system admin | Frederick Muriuki Muriithi | |
| Provide a way to set a user as a system administrator via CLI. This method was chosen rather that using the WebUI since most users will not have access to the CLI. It also means that assigning system administration privileges will not be an accident, since one has to actually run the command manually on the CLI. | |||
| 2023-02-10 | auth: migrations: new privilege and role | Frederick Muriuki Muriithi | |
| Add a new data distribution privilege Add a new system-administrator role | |||
| 2023-02-09 | auth: 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. | |||
| 2023-02-09 | auth: users: Check whether a user has an active join request. | Frederick Muriuki Muriithi | |
| 2023-02-08 | auth: groups: handle join requests. | Frederick Muriuki Muriithi | |
| 2023-02-07 | auth: groups: Enable users to request to join group. | Frederick Muriuki Muriithi | |
| 2023-02-06 | Get the N-th matrix given N, an index value | Munyoki Kilyungi | |
| * gn3/db/matrix.py (get_nth_matrix): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-02-06 | Get total number of versions that a database has | Munyoki Kilyungi | |
| * gn3/db/matrix.py (get_total_versions): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-02-06 | Add method to fetch the current matrix | Munyoki Kilyungi | |
| * gn3/db/matrix.py: New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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