| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2023-07-19 | Extract reusable code to separate module...Extract the reusable function into a separate `query_tools` module for use in
other modules.
| Frederick Muriuki Muriithi |
| 2023-07-18 | Bug: Change from `_id` to `id_` to avoid downstream breakage....The downstream code expects `id_` not `_id`.
| Frederick Muriuki Muriithi |
| 2023-07-18 | Fix wrong import, and typing issues. | Frederick Muriuki Muriithi |
| 2023-07-18 | Fetch a single publication by `PublicationId` | Frederick Muriuki Muriithi |
| 2023-07-18 | Fetch metadata for a single phenotype. | Frederick Muriuki Muriithi |
| 2023-07-18 | Fetch single phenotype trait by `dataset_id` and `trait_name`. | Frederick Muriuki Muriithi |
| 2023-07-18 | Bug: Fetch group name by dataset_id...Change the code to fetch the group name by the dataset ID, since according to
usage[1] of the `retrieve_group_name` function, the value passed in is the
`dataset_id` and not the `group_id`.
Change the name from `retrieve_group_name` to `retrieve_phenotype_group_name`
to more clearly indicate that this function concerns itself with the groups
that relate to phenotypes.
[1](https://github.com/genenetwork/genenetwork2/blob/1bbb0430732b7fa5102d7dcbda80ebda252f5424/wqflask/wqflask/metadata_edits.py)
| Frederick Muriuki Muriithi |
| 2023-07-17 | Fix dict key name...Remove extra colon (:) at the end of the name that was leading to the number
of cases not being presented as expected.
| Frederick Muriuki Muriithi |
| 2023-07-12 | Bug: Set the `data_exists` variable within the context manager...The `cursor.fetchone()` call that was used as the condition to the `if` was
called outside of the context manager, and therefore would always give a
non-truthy value at best and an inconsistent result at worst.
This commit gets the value before the context manager has exited and stores it
for later use.
| Frederick Muriuki Muriithi |
| 2023-07-12 | Bug: Retrieve configs from app, not environment...Retrieve the configuration values from the application object, not from the
environment. We are assured of having the configuration values set in the
application - we do not have that assurance for the environment.
| Frederick Muriuki Muriithi |
| 2023-07-12 | Move documentation comment to beginning of function | Frederick Muriuki Muriithi |
| 2023-07-11 | Revert "Skip tests broken by Python-3.10 temporarily"...This reverts commit f52247c15f3694f3dd5fd0fd79c3e15376137e07.
| Frederick Muriuki Muriithi |
| 2023-07-11 | Trigger CI | Munyoki Kilyungi |
| 2023-07-06 | Provide the client_id as part of the post request. | Frederick Muriuki Muriithi |
| 2023-07-05 | Skip tests broken by Python-3.10 temporarily...Skip the tests that have been broken by the migrations to Python-3.10
temporarily, until we can fix them.
| Frederick Muriuki Muriithi |
| 2023-07-05 | Update test: create throw-away variable...* Commit `b529c700` changes the return value to a tuple of values rather than
a single string value. Handle that in the test.
| Frederick Muriuki Muriithi |
| 2023-07-04 | Fix minor UI bug | Frederick Muriuki Muriithi |
| 2023-07-03 | Spruce up UI...Make UI somewhat consistent with the GN2 UI.
| Frederick Muriuki Muriithi |
