| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2023-02-10 | Return empty tuple rather than Nothing...When user has no roles assigned, return an empty tuple rather than
pymonad.maybe.Nothing to ease maintenance.
| Frederick Muriuki Muriithi |
| 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...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.
| Frederick Muriuki Muriithi |
| 2023-02-10 | auth: migrations: new privilege and role...Add a new data distribution privilege
Add a new system-administrator role
| Frederick Muriuki Muriithi |
| 2023-02-09 | auth: Reject request to join a group....* 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.
| Frederick Muriuki Muriithi |
| 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...* gn3/db/matrix.py (get_nth_matrix): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-02-06 | Get total number of versions that a database has...* gn3/db/matrix.py (get_total_versions): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-02-06 | Add method to fetch the current matrix...* gn3/db/matrix.py: New file.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-02-06 | auth: resource: Enable viewing the details of a resource. | Frederick Muriuki Muriithi |
| 2023-02-03 | auth: commit missing module. | Frederick Muriuki Muriithi |
| 2023-02-03 | oauth: enable resource creation | Frederick Muriuki Muriithi |
| 2023-02-03 | auth: tests: mock token acquisition. Fix minor bugs. | Frederick Muriuki Muriithi |
| 2023-02-02 | auth: Improve authorisation...Retrieve the token, and user in the authorisation decorator to enable checking
of privileges.
| Frederick Muriuki Muriithi |
| 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 | tests: Expect exact integer value when applying SI suffix....* tests/unit/test_search.py (test_apply_si_suffix_kilo,
test_apply_si_suffix_mega, test_apply_si_suffix_giga): Update docstring
indicating that we expect the exact integer value.
| Arun Isaac |
| 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 |
