| Age | Commit message (Expand) | Author |
|---|
| 2023-10-06 | Make argument mandatory...Make the `base_dir` argument mandatory to force it to be passed in from the
point the function is called.
| Frederick Muriuki Muriithi |
| 2023-09-21 | Fix query in update_cross_reference | zsloan |
| 2023-09-05 | Delete un-used import...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Fix C3001: Lambda expression assigned to a variable...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Remove un-necessary string concatenation...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 | 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 |
| 2023-08-17 | 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 | 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 |
| 2023-08-04 | 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 |
| 2023-07-26 | 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 | 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 |
| 2023-06-15 | 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 |
| 2023-06-12 | 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 | Delete unused get_trait_metadata function...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-07 | Add publication end-point...* gn3/api/metadata.py: Import get_publication_metadata
(publication): New endpoint.
* gn3/db/rdf.py (get_dataset_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-07 | Nest duplicate entries into a list from a sparql result...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
