Age | Commit message (Expand) | Author |
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 |
2023-08-04 | 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 |
2023-07-31 | 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 |
2023-07-21 | 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 | 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 |
2023-07-06 | Provide the client_id as part of the post request. | 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 |
2023-07-03 | Enable deletion of OAuth2 clients. | Frederick Muriuki Muriithi |
2023-06-30 | Edit some of the details of OAuth2 clients | Frederick Muriuki Muriithi |
2023-06-30 | List all OAuth2 clients. | Frederick Muriuki Muriithi |
2023-06-23 | Fetch 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 |
2023-06-20 | Fix conflicts | zsloan |
2023-06-20 | Bug: Don't overwrite/delete old collections | Frederick Muriuki Muriithi |
2023-06-15 | Fetch genotypes from virtuoso...* 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>
| Munyoki Kilyungi |
2023-06-13 | Namespace session variable...Extract the functions acting on the session into a separate module and
namespace the session variable to prevent conflicts.
| Frederick Muriuki Muriithi |
2023-06-12 | Delete unused import...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-12 | Fetch phenotypes from virtuoso...* gn3/api/metadata.py: Import get_phenotype_metadata.
(phenotype): New end-point.
* gn3/db/rdf.py (get_phenotype_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-06-12 | Correct publication function docstring...* gn3/api/metadata.py (publication): Update docstring.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |