| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-09-21 | Fix query in update_cross_reference | zsloan | |
| 2023-09-05 | Delete un-used import | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Fix C3001: Lambda expression assigned to a variable | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Remove un-necessary string concatenation | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Replace "escape_string" with safe-query parameters | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Remove type annotations for "none_case_attrs" variables | Munyoki 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> | |||
| 2023-08-24 | 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 | zsloan | |
| Currently there's a lot of duplicated code, so I need to ask how best to simplify it later | |||
| 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 ↵ | zsloan | |
| assay resources, and change their naming accordingly | |||
| 2023-08-04 | Remove the ORM-dependent `update` function. | Frederick Muriuki Muriithi | |
| 2023-08-02 | Add deprecation notice to ORM-dependent `update` function | Frederick Muriuki Muriithi | |
| Add a deprecation notice to discourage other devs from using the deprecated `update` function. | |||
| 2023-08-02 | Remove ORM-dependent `insert` function | Frederick Muriuki Muriithi | |
| Remove the object-relation-mapping dependent `insert` function to prevent it being used in the code down the line. | |||
| 2023-08-02 | Remove ORM-dependent `fetchall` and `fetchone` functions | Frederick Muriuki Muriithi | |
| Remove Object-Relational Mapping dependent function, `fetchall` and `fetchone` so as to prevent theirs use in the code moving forward. | |||
| 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 | Frederick Muriuki Muriithi | |
| Extract the reusable function into a separate `query_tools` module for use in other modules. | |||
| 2023-07-18 | Bug: Change from `_id` to `id_` to avoid downstream breakage. | Frederick Muriuki Muriithi | |
| The downstream code expects `id_` not `_id`. | |||
| 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 | Frederick 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) | |||
| 2023-07-17 | Fix dict key name | Frederick Muriuki Muriithi | |
| Remove extra colon (:) at the end of the name that was leading to the number of cases not being presented as expected. | |||
| 2023-07-12 | Bug: Set the `data_exists` variable within the context manager | Frederick 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. | |||
| 2023-07-12 | Bug: Retrieve configs from app, not environment | Frederick 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. | |||
| 2023-06-15 | Fetch genotypes from virtuoso | Munyoki 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> | |||
| 2023-06-12 | Delete unused import | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-12 | Fetch phenotypes from virtuoso | Munyoki 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> | |||
| 2023-06-12 | Delete unused get_trait_metadata function | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-07 | Add publication end-point | Munyoki 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> | |||
| 2023-06-07 | Nest duplicate entries into a list from a sparql result | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-06 | Pass geoSeries as a URL | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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