| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-04-08 | auth: Link genotype datasets to groups. | Frederick Muriuki Muriithi | |
| 2023-04-06 | Fix linting issues | Frederick Muriuki Muriithi | |
| 2023-04-06 | Remove deprecated `gn3.db_utils.database_connector` function | Frederick Muriuki Muriithi | |
| Remove the deprecated function and fix a myriad of bugs that arise from removing the function. Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils | |||
| 2023-04-05 | Enable use of `database_connection` in scripts without current_app | Frederick Muriuki Muriithi | |
| There is need to run external scripts using the same configurations as the application but without the need to couple the script to the application. In this case, we provide the needed configuration directly in the CLI, and modify the existing `gn3.db_utils.database_connection` function to allow it to work coupled to the app or otherwise. | |||
| 2023-04-04 | auth: Search for linking genotype datasets. | Frederick Muriuki Muriithi | |
| 2023-04-04 | Add tables to link genotype data | Frederick Muriuki Muriithi | |
| 2023-03-23 | tests: Set up fixture and mock out config variable | Frederick Muriuki Muriithi | |
| 2023-03-23 | auth: list the species in the database. | Frederick Muriuki Muriithi | |
| 2023-03-23 | Docs: Add a note on how the configuration system works. | Frederick Muriuki Muriithi | |
| 2023-03-23 | auth: Don't try loading the user if no client is found | Frederick Muriuki Muriithi | |
| Fix the bug where the system was trying to load a user from a non-existing OAuth2 client, leading to an exception. | |||
| 2023-03-23 | conf: use flask.current_app.config not in gn3.settings | Frederick Muriuki Muriithi | |
| The configuration in gn3.settings can (and does) get overwritten by values in the environment variable `GN3_CONF` and any configurations passed in the call to the `gn3.app.create_app` function; as such, this commit changes the configuration used in the code to user the final configuration values that are in the running application's `flask.current_app.config` object. | |||
| 2023-03-22 | auth: data linking: build functions to fetch unlinked phenotypes | Frederick Muriuki Muriithi | |
| This is an initial attempt: it does not allow a search to be carried out across the data available in the database. I will need to rework this, probably start from the UI and work backward. | |||
| 2023-03-22 | auth: migrations for linking phenotype data | Frederick Muriuki Muriithi | |
| 2023-03-22 | auth: Enable linking multiple datasets to the group at once. | Frederick Muriuki Muriithi | |
| 2023-03-22 | auth: Remove the tables used for linking data to resources | Frederick Muriuki Muriithi | |
| The way data is linked to the resources needs to be reworked. This commit removes all the existing migration scripts that created the tables formerly used for linking data in preparation for reworking the system. | |||
| 2023-03-20 | Disable fetching case-attributes when getting sample data | Munyoki Kilyungi | |
| * gn3/db/sample_data.py: Remove 're' import. (get_trait_csv_sample_data): Remove fetching sample data. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-03-20 | auth: data: Enable offset in queries | Frederick Muriuki Muriithi | |
| Enable the 'OFFSET' clause in the queries to allow for progressive fetching of data from the database using the 'Previous' and 'Next' buttons. | |||
| 2023-03-20 | auth: data: List Phenotypes at the trait level | Frederick Muriuki Muriithi | |
| For Phenotypes, list the Phenotype traits rather than the dataset(s). | |||
| 2023-03-20 | Fix get_all_species test | zsloan | |
| 2023-03-18 | oauth2: resources: toggle whether a resource is public or not | Frederick Muriuki Muriithi | |
| 2023-03-18 | auth: resources: Disallow duplicate resource names. | Frederick Muriuki Muriithi | |
| 2023-03-17 | Add conn.commit() to queries in sample_data.py | zsloan | |
| 2023-03-17 | Change get_all_species query to order by Family | zsloan | |
| 2023-03-15 | auth: Data Migrations: Rework migration trigger | Frederick Muriuki Muriithi | |
| Rework the migration trigger endpoint such that it does a bulk import of all the resources in the redis store. It also expects that the user that triggers the migration have the appropriate privileges. | |||
| 2023-03-14 | auth: Fix some linting and typing issues. | Frederick Muriuki Muriithi | |
| 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> | |||
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| GeneNetwork3 REST API for data science and machine learning |
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