| Age | Commit message (Expand) | Author |
|---|
| 2023-09-05 | Remove un-necessary string concatenation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Remove pylint skip...* gn3/auth/authentication/oauth2/models/oauth2token.py
(introspect_token, check_permission): Delete "pylint:
disable=[no-self-use]". R0022: Useless option value for 'disable',
'no-self-use' was moved to an optional extension, see
https://pylint.pycqa.org/en/latest/whatsnew/2/2.14/summary.html#removed-checkers.
* gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py
(delete_authorization_code): Ditto.
* tests/unit/test_heatmaps.py (test_cluster_traits):
Delete "pylint: disable=R0201". R0022: Useless option value for
'disable', 'no-self-use' was moved to an optional extension, see
https://pylint.pycqa.org/en/latest/whatsnew/2/2.14/summary.html#removed-checkers.
* tests/unit/computations/test_partial_correlations.py
(test_tissue_correlation): Ditto.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Remove unused import...* tests/unit/test_file_utils.py: Delete gn3.cache_ipfs_file
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Replace "escape_string" with safe-query parameters...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Delete IPFS tests...* tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit,
test_cache_ipfs_file_cache_miss): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Remove type annotations for "none_case_attrs" variables...* gn3/db/sample_data.py (update_sample_data, delete_sample_data,
insert_sample_data): Remove type hints for "none_case_attrs".
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-08-24 | Change get_pheno_csv_sample_data to use group ID instead of phenotype ID | zsloan |
| 2023-08-18 | Commit on success, rollback on error. | Frederick Muriuki Muriithi |
| 2023-08-17 | Fix query for fetching DataId when inserting ProbeSet data | zsloan |
| 2023-08-17 | Fix a couple remaining issues with function parameters | zsloan |
| 2023-08-17 | Fix tests to work with changes | zsloan |
| 2023-08-17 | Combine pheno/mrna update functions + some other fixes | zsloan |
| 2023-08-17 | Fix queries for fetching group names | zsloan |
| 2023-08-17 | Fix fetch_trait query for phenotypes | zsloan |
| 2023-08-17 | Fix a few misnamed tables in mrna delete/insert functions | zsloan |
| 2023-08-17 | Implement ProbeSet sample data editing...Currently there's a lot of duplicated code, so I need to ask how best to simplify it later
| zsloan |
| 2023-08-17 | Fix probeset sample data and CSV sample data functions | zsloan |
| 2023-08-17 | Fix query for retrieving mrna dataset group name | zsloan |
| 2023-08-17 | Fix get_mrna_sample_data query | zsloan |
| 2023-08-17 | Fix mrna group name query | zsloan |
| 2023-08-17 | Remove Id select from probeset metadata query, since it's included in cols | zsloan |
| 2023-08-17 | Add function for retrieving mRNA Assay group name | zsloan |
| 2023-08-17 | Make several sample_data fetching functions specific to phenotype or mrna ass... | zsloan |
| 2023-08-14 | auth: Remove documentation...The authentication/authorisation stuff is being moved to a separate
repository. This commit removes the documentation for how to run migrations
from this repository since it has been moved over to the new repository.
| Frederick Muriuki Muriithi |
| 2023-08-04 | Remove unused import | Frederick Muriuki Muriithi |
| 2023-08-04 | Remove tests for deleted function. | Frederick Muriuki Muriithi |
| 2023-08-04 | Remove the ORM-dependent `update` function. | Frederick Muriuki Muriithi |
| 2023-08-02 | Add deprecation notice to ORM-dependent `update` function...Add a deprecation notice to discourage other devs from using the deprecated
`update` function.
| Frederick Muriuki Muriithi |
| 2023-08-02 | Remove ORM-dependent `insert` function...Remove the object-relation-mapping dependent `insert` function to prevent it
being used in the code down the line.
| Frederick Muriuki Muriithi |
| 2023-08-02 | Remove ORM-dependent `fetchall` and `fetchone` functions...Remove Object-Relational Mapping dependent function, `fetchall` and `fetchone`
so as to prevent theirs use in the code moving forward.
| Frederick Muriuki Muriithi |
| 2023-08-02 | Integrate Temp traits to Auth...Temporary traits are not saved to the database, and have no attached
resource (at this time). As such, make them all simply public-read to enable
access for users.
This might change after more information on usage of temporary traits is
collected and considered.
| Frederick Muriuki Muriithi |
| 2023-08-02 | Use correct variable...After copying the calls to assign appropriate roles to the admin in the
script, I forgot to update the variable name. This commit fixes that.
| Frederick Muriuki Muriithi |
| 2023-08-02 | Fix module name. | Frederick Muriuki Muriithi |
| 2023-08-02 | Assign `group-leader` role to the admin for automatic group. | Frederick Muriuki Muriithi |
| 2023-07-31 | Fix typing issue | Frederick Muriuki Muriithi |
| 2023-07-31 | Fix linting and typing issues. | Frederick Muriuki Muriithi |
| 2023-07-31 | Fix bugs. Return resource without data items....* Fix bugs introduced while attempting pagination.
* Return resource object without attached data items.
| Frederick Muriuki Muriithi |
| 2023-07-31 | Paginate the resource data items. | Frederick Muriuki Muriithi |
| 2023-07-26 | Fix variable name. | Frederick Muriuki Muriithi |
| 2023-07-26 | Remove debug statement. | Frederick Muriuki Muriithi |
| 2023-07-26 | Fetch `metadata_audit` trail with direct query functions. | Frederick Muriuki Muriithi |
| 2023-07-26 | Function to create a metadata audit trail. | Frederick Muriuki Muriithi |
| 2023-07-26 | Merge pull request #126 from BonfaceKilz/fix/pin-python-3.9...Roll back to python 3.9 in .guix-channel | BonfaceKilz |
| 2023-07-26 | Roll back to python 3.9 in .guix-channel | Munyoki Kilyungi |
| 2023-07-21 | Add some debug utilities. | Frederick Muriuki Muriithi |
| 2023-07-21 | Update a Publication in the database. | Frederick Muriuki Muriithi |
| 2023-07-21 | Fetch a publication by its PubMed ID | Frederick Muriuki Muriithi |
| 2023-07-21 | Rename function: fetch_publication ==> fetch_publication_by_id | Frederick Muriuki Muriithi |
| 2023-07-19 | Make repository a guix channel....* .guix-channel: New file.
* guix.scm: Move to ...
* .guix/genenetwork3-package.scm: ... here. Convert into a module with public
package variables.
| Arun Isaac |
| 2023-07-19 | Extract code dealing with ProbeSets to their own module. | Frederick Muriuki Muriithi |
