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2023-08-02Add deprecation notice to ORM-dependent `update` functionFrederick Muriuki Muriithi
Add a deprecation notice to discourage other devs from using the deprecated `update` function.
2023-08-02Remove ORM-dependent `insert` functionFrederick Muriuki Muriithi
Remove the object-relation-mapping dependent `insert` function to prevent it being used in the code down the line.
2023-08-02Remove ORM-dependent `fetchall` and `fetchone` functionsFrederick Muriuki Muriithi
Remove Object-Relational Mapping dependent function, `fetchall` and `fetchone` so as to prevent theirs use in the code moving forward.
2023-08-02Integrate Temp traits to AuthFrederick Muriuki Muriithi
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.
2023-08-02Use correct variableFrederick Muriuki Muriithi
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.
2023-08-02Fix module name.Frederick Muriuki Muriithi
2023-08-02Assign `group-leader` role to the admin for automatic group.Frederick Muriuki Muriithi
2023-07-31Fix typing issueFrederick Muriuki Muriithi
2023-07-31Fix linting and typing issues.Frederick Muriuki Muriithi
2023-07-31Fix bugs. Return resource without data items.Frederick Muriuki Muriithi
* Fix bugs introduced while attempting pagination. * Return resource object without attached data items.
2023-07-31Paginate the resource data items.Frederick Muriuki Muriithi
2023-07-26Fix variable name.Frederick Muriuki Muriithi
2023-07-26Remove debug statement.Frederick Muriuki Muriithi
2023-07-26Fetch `metadata_audit` trail with direct query functions.Frederick Muriuki Muriithi
2023-07-26Function to create a metadata audit trail.Frederick Muriuki Muriithi
2023-07-26Merge pull request #126 from BonfaceKilz/fix/pin-python-3.9BonfaceKilz
Roll back to python 3.9 in .guix-channel
2023-07-26Roll back to python 3.9 in .guix-channelMunyoki Kilyungi
2023-07-21Add some debug utilities.Frederick Muriuki Muriithi
2023-07-21Update a Publication in the database.Frederick Muriuki Muriithi
2023-07-21Fetch a publication by its PubMed IDFrederick Muriuki Muriithi
2023-07-21Rename function: fetch_publication ==> fetch_publication_by_idFrederick Muriuki Muriithi
2023-07-19Make repository a guix channel.Arun Isaac
* .guix-channel: New file. * guix.scm: Move to ... * .guix/genenetwork3-package.scm: ... here. Convert into a module with public package variables.
2023-07-19Extract code dealing with ProbeSets to their own module.Frederick Muriuki Muriithi
2023-07-19Extract reusable code to separate moduleFrederick Muriuki Muriithi
Extract the reusable function into a separate `query_tools` module for use in other modules.
2023-07-18Bug: Change from `_id` to `id_` to avoid downstream breakage.Frederick Muriuki Muriithi
The downstream code expects `id_` not `_id`.
2023-07-18Fix wrong import, and typing issues.Frederick Muriuki Muriithi
2023-07-18Fetch a single publication by `PublicationId`Frederick Muriuki Muriithi
2023-07-18Fetch metadata for a single phenotype.Frederick Muriuki Muriithi
2023-07-18Fetch single phenotype trait by `dataset_id` and `trait_name`.Frederick Muriuki Muriithi
2023-07-18Bug: Fetch group name by dataset_idFrederick Muriuki Muriithi
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)
2023-07-17Fix dict key nameFrederick Muriuki Muriithi
Remove extra colon (:) at the end of the name that was leading to the number of cases not being presented as expected.
2023-07-12Bug: Set the `data_exists` variable within the context managerFrederick Muriuki Muriithi
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.
2023-07-12Bug: Retrieve configs from app, not environmentFrederick Muriuki Muriithi
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.
2023-07-12Move documentation comment to beginning of functionFrederick Muriuki Muriithi
2023-07-11Revert "Skip tests broken by Python-3.10 temporarily"Frederick Muriuki Muriithi
This reverts commit f52247c15f3694f3dd5fd0fd79c3e15376137e07.
2023-07-11Trigger CIMunyoki Kilyungi
2023-07-06Provide the client_id as part of the post request.Frederick Muriuki Muriithi
2023-07-05Skip tests broken by Python-3.10 temporarilyFrederick Muriuki Muriithi
Skip the tests that have been broken by the migrations to Python-3.10 temporarily, until we can fix them.
2023-07-05Update test: create throw-away variableFrederick Muriuki Muriithi
* Commit `b529c700` changes the return value to a tuple of values rather than a single string value. Handle that in the test.
2023-07-04Fix minor UI bugFrederick Muriuki Muriithi
2023-07-03Spruce up UIFrederick Muriuki Muriithi
Make UI somewhat consistent with the GN2 UI.
2023-07-03Enable deletion of OAuth2 clients.Frederick Muriuki Muriithi
2023-06-30Edit some of the details of OAuth2 clientsFrederick Muriuki Muriithi
2023-06-30List all OAuth2 clients.Frederick Muriuki Muriithi
2023-06-23Fetch all collections, rename variablesFrederick Muriuki Muriithi
Fetch from `__REDIS_COLLECTION_KEY__` not `"collections"` to ensure all collections are retrieved correctly. Rename from `__*_DOC__` to `__REDIS_*_KEY__` to more clearly express what the variables are about.
2023-06-20Fix conflictszsloan
2023-06-20Bug: Don't overwrite/delete old collectionsFrederick Muriuki Muriithi
2023-06-15Fetch genotypes from virtuosoMunyoki Kilyungi
* gn3/api/metadata.py: Import get_genotype_metadata. (genotype): New end-point. * gn3/db/rdf.py (get_phenotype_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-13Namespace session variableFrederick Muriuki Muriithi
Extract the functions acting on the session into a separate module and namespace the session variable to prevent conflicts.
2023-06-12Delete unused importMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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