| Age | Commit message (Expand) | Author |
|---|
| 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...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.
| Frederick Muriuki Muriithi |
| 2023-03-20 | Disable fetching case-attributes when getting sample data...* 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>
| Munyoki Kilyungi |
| 2023-03-20 | auth: data: Enable offset in queries...Enable the 'OFFSET' clause in the queries to allow for progressive fetching of
data from the database using the 'Previous' and 'Next' buttons.
| Frederick Muriuki Muriithi |
| 2023-03-20 | auth: data: List Phenotypes at the trait level...For Phenotypes, list the Phenotype traits rather than the dataset(s).
| Frederick Muriuki Muriithi |
| 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...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.
| Frederick Muriuki Muriithi |
| 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...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.
| Frederick Muriuki Muriithi |
| 2023-03-13 | auth: separate user detail migration from data migration...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.
| Frederick Muriuki Muriithi |
| 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...Implement the code to migrate the data from redis to SQLite.
| Frederick Muriuki Muriithi |
| 2023-03-09 | auth: data migration: Data migration outline...Provide an outline of the data migration steps to be taken from some results
of the experiments with the data in redis.
| Frederick Muriuki Muriithi |
| 2023-03-09 | auth: introspection: Protect introspection endpoint...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.
| Frederick Muriuki Muriithi |
| 2023-03-08 | auth: users: Use the same basic functions for password hashing...To avoid repeating the same thing in multiple places, leading to errors and
breakages, reuse the same basic functions for password hashing.
| Frederick Muriuki Muriithi |
| 2023-03-08 | Replace Bcrypt with Argon2 for better security....Bcrypt is now somewhat vulnerable to offline cracking, so we move our password
hashing over to Argon2.
| Frederick Muriuki Muriithi |
| 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...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.
| Frederick Muriuki Muriithi |
| 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...* 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>
| Munyoki Kilyungi |
| 2023-03-01 | Open lmdb path in readonly mode...* 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>
| Munyoki Kilyungi |
| 2023-03-01 | Create API endpoint for fetching trait metadata...* 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>
| Munyoki Kilyungi |
| 2023-03-01 | Fetch trait metadata from RDF...* gn3/db/rdf.py (get_dataset_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-02-28 | auth: Unlink data from resources...Enable the data editor to unlink data from a particular resource.
data-access-levels-endpoint | Frederick Muriuki Muriithi |
| 2023-02-28 | auth: Unlink data from resources...Enable the data editor to unlink data from a particular resource.
| Frederick Muriuki Muriithi |
| 2023-02-27 | auth: Endpoint to get access levels for data...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.
| Frederick Muriuki Muriithi |
| 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)...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.
| Frederick Muriuki Muriithi |
| 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....Load the data that is attached to a particular resource together with the
resource.
List any unlinked data: useful when linking data to resources.
| Frederick Muriuki Muriithi |
| 2023-02-21 | auth: migrations: Link to data in main db...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.
| Frederick Muriuki Muriithi |
| 2023-02-13 | scripts: Fallback to 1 worker when indexing....* scripts/index-genenetwork (worker_queue): Set default number of workers to 1
if the number of CPUs cannot be determined.
| Arun Isaac |
| 2023-02-13 | scripts: Type hint xapian indexing script....* scripts/index-genenetwork: Import Callable, Generator, Iterable and List
from typing. Type hint all functions.
| Arun Isaac |
