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2023-09-05Fix C3001: Lambda expression assigned to a variableMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Remove un-necessary string concatenationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Replace "escape_string" with safe-query parametersMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Remove type annotations for "none_case_attrs" variablesMunyoki Kilyungi
* 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>
2023-08-24Change get_pheno_csv_sample_data to use group ID instead of phenotype IDzsloan
2023-08-17Fix query for fetching DataId when inserting ProbeSet datazsloan
2023-08-17Fix a couple remaining issues with function parameterszsloan
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 editingzsloan
Currently there's a lot of duplicated code, so I need to ask how best to simplify it later
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 ↵zsloan
assay resources, and change their naming accordingly
2023-08-04Remove the ORM-dependent `update` function.Frederick Muriuki Muriithi
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.
2023-07-26Fix 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
2023-07-21Update 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 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.
2023-06-15Fetch 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>
2023-06-12Delete unused importMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Fetch phenotypes from virtuosoMunyoki Kilyungi
* 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>
2023-06-12Delete unused get_trait_metadata functionMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-07Add publication end-pointMunyoki Kilyungi
* 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>
2023-06-07Nest duplicate entries into a list from a sparql resultMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Pass geoSeries as a URLMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Rename gn:geoPlatform -> gn:geoPlatformUrlMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Match how dataset metadata is fetched with GN1Munyoki Kilyungi
* gn3/db/rdf.py (sparql_query): Parse CONSTRUCTS and SELECTS differently. (strip_url): Rename to ... (get_url_local_name): ... this. (get_dataset_metadata): Fetch extra fields in RDF. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-25 19:47:13 +0000