| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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> | |||
| 2023-06-06 | Rename gn:geoPlatform -> gn:geoPlatformUrl | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-06 | Match how dataset metadata is fetched with GN1 | Munyoki 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> | |||
| 2023-06-06 | Replace taxon prefix with ncbiTaxon which references NCBI | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-02 | Replace SELECT with CONSTRUCT when fetching a dataset's metadata | Munyoki Kilyungi | |
| * gn3/db/rdf.py: Importh pymonad.Nothing. (get_dataset_metadata): Replace SELECT with CONSTRUCT. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-02 | Create a function for stripping the last bit from a URL | Munyoki Kilyungi | |
| * gn3/db/rdf.py: Import unquote and urlparse. (strip_url): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-22 | Use string literal concatenation to make genofile_path line shorter | zsloan | |
| 2023-05-22 | Fix quotes when setting genofile_path | zsloan | |
| 2023-05-22 | Fix return typing for get_trait_sample_data | zsloan | |
| 2023-05-22 | Change type from 'any' to 'Any' | zsloan | |
| 2023-05-22 | Use f-string for setting genofile_path | zsloan | |
| Also set default value for os.environ.get("GENENETWORK_FILES") | |||
| 2023-05-22 | Include encoding in open statement to address pylint W1514 | zsloan | |
| 2023-05-22 | Initialize 'line'; previous pylint complained because line might not be ↵ | zsloan | |
| initialized (if the genofile was empty, for example) | |||
| 2023-05-22 | Use 'with open()' syntax | zsloan | |
| Initialize samplelist variable | |||
| 2023-05-22 | Remove unused variable this_data | zsloan | |
| 2023-05-22 | Include all samples in trait sample data | zsloan | |
| This is necessary in order to allow for editing the values of samples that don't currently have values | |||
| 2023-05-22 | Fix sample data CSV query to only fetch distinct samples | zsloan | |
| There's probably a better way to fix this query (it was previously returning each sample twice), but DISTINCT was the easiest way I could come up with | |||
| 2023-05-22 | Fix get_trait_sample_data function | zsloan | |
| 2023-05-22 | Fix retrieve_sample_list function to correctly get genofile_path | zsloan | |
| 2023-05-22 | Commit update/insert queries, since they don't seem to be executed otherwise ↵ | zsloan | |
| after the recent changes to the DB | |||
| 2023-05-22 | Add function for retrieving group name (given group ID) | zsloan | |
| 2023-05-22 | Add function for retrieving phenotype sample data as dict | zsloan | |
| 2023-05-22 | Add function for retrieving samplelist from .geno file | zsloan | |
| 2023-04-17 | Create new endpoint for fetching GeneRIF entries | Munyoki Kilyungi | |
| * gn3/api/metadata.py: Import Template, sparql_query and RDF_PREFIXES. (get_genewiki_entries): New endpoint. * gn3/db/rdf.py: Add new constant for storing rdf prefixes. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-03-20 | Disable fetching case-attributes when getting sample data | Munyoki Kilyungi | |
| * gn3/db/sample_data.py: Remove 're' import. (get_trait_csv_sample_data): Remove fetching sample data. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-03-17 | Add conn.commit() to queries in sample_data.py | zsloan | |
 |
index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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