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2023-08-17Combine pheno/mrna update functions + some other fixeszsloan
2023-08-17Fix queries for fetching group nameszsloan
2023-08-17Fix fetch_trait query for phenotypeszsloan
2023-08-17Fix a few misnamed tables in mrna delete/insert functionszsloan
2023-08-17Implement ProbeSet sample data editing...Currently there's a lot of duplicated code, so I need to ask how best to simplify it later zsloan
2023-08-17Fix probeset sample data and CSV sample data functionszsloan
2023-08-17Fix query for retrieving mrna dataset group namezsloan
2023-08-17Fix get_mrna_sample_data queryzsloan
2023-08-17Fix mrna group name queryzsloan
2023-08-17Remove Id select from probeset metadata query, since it's included in colszsloan
2023-08-17Add function for retrieving mRNA Assay group namezsloan
2023-08-17Make several sample_data fetching functions specific to phenotype or mrna ass...zsloan
2023-08-04Remove the ORM-dependent `update` function.Frederick Muriuki Muriithi
2023-08-02Add deprecation notice to ORM-dependent `update` function...Add a deprecation notice to discourage other devs from using the deprecated `update` function. Frederick Muriuki Muriithi
2023-08-02Remove 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
2023-08-02Remove 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
2023-08-02Integrate 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
2023-07-31Fix typing issueFrederick Muriuki Muriithi
2023-07-31Fix linting and typing issues.Frederick Muriuki Muriithi
2023-07-31Fix bugs. Return resource without data items....* Fix bugs introduced while attempting pagination. * Return resource object without attached data items. Frederick Muriuki Muriithi
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
2023-07-21Add 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
2023-07-19Extract code dealing with ProbeSets to their own module.Frederick Muriuki Muriithi
2023-07-19Extract reusable code to separate module...Extract the reusable function into a separate `query_tools` module for use in other modules. Frederick Muriuki Muriithi
2023-07-18Bug: Change from `_id` to `id_` to avoid downstream breakage....The downstream code expects `id_` not `_id`. Frederick Muriuki Muriithi
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_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
2023-07-17Fix 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
2023-07-12Bug: 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
2023-07-12Bug: 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
2023-07-12Move documentation comment to beginning of functionFrederick Muriuki Muriithi
2023-07-06Provide the client_id as part of the post request.Frederick Muriuki Muriithi
2023-07-04Fix minor UI bugFrederick Muriuki Muriithi
2023-07-03Spruce up UI...Make UI somewhat consistent with the GN2 UI. Frederick Muriuki Muriithi
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 variables...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. Frederick Muriuki Muriithi
2023-06-20Fix conflictszsloan
2023-06-20Bug: Don't overwrite/delete old collectionsFrederick Muriuki Muriithi