genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
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)
2023-07-12	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.
2023-05-22	Use string literal concatenation to make genofile_path line shorter	zsloan

2023-05-22	Fix quotes when setting genofile_path	zsloan

2023-05-22	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	Fix retrieve_sample_list function to correctly get genofile_path	zsloan

2023-05-22	Add function for retrieving group name (given group ID)	zsloan

2023-05-22	Add function for retrieving samplelist from .geno file	zsloan

2022-11-02	Re-implement RDF related code to use monads in its own module	Munyoki Kilyungi
	* gn3/api/general.py: Replace gn3.db.datasets import with gn3.db.rdf. (dataset_metadata) <jsonify>: Replace datasets.dataset_metadata with rdf.get_dataset_metadata. * gn3/db/datasets.py: Remove unused imports. (sparql_query, dataset_metadata): Delete. * gn3/db/rdf.py: (sparql_query, get_dataset_metadata): New functions.
2022-06-21	db: datasets.py: Ignore results from sparql.queryAndConvert	BonfaceKilz
	ATM, it's very difficult to work the correct type that is returned. Ignore this for now and fix this later.
2022-02-21	Fix a myriad of linter issues	Frederick Muriuki Muriithi
	* Use `with` in place of plain `open` * Use f-strings in place of `str.format()` * Remove string interpolation from queries - provide data as query parameters * other minor fixes
2022-02-18	Remove code trying to query non-existent `TempFreeze` table	Frederick Muriuki Muriithi
	The code was migrated from GN1 with a faulty assumption that all trait types have a corresponding `*Freeze` table in the database. This assumption is not true for the `Temp` traits. This commit removes the buggy code.
2021-12-23	db: Assist mypy with explicit type declaration.	Arun Isaac
	* gn3/db/datasets.py (dataset_metadata): Assist mypy by explicitly declaring type of return dictionary.
2021-12-23	db: Fix sparql_query return type.	Arun Isaac
	* gn3/db/datasets.py: Import List from typing. (sparql_query): Set return type to List[Dict[str, Any]].
2021-12-23	db: Fix wrong continued indentation.	Arun Isaac
	* gn3/db/datasets.py (dataset_metadata): Fix wrong continued indentation.
2021-12-09	Prevent error on no result. Fix indexing	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * If the dataset name is not found, don't cause an exception, instead, return the provided search name. * Use the correct inner object
2021-12-02	Implement dataset metadata API endpoint.	Arun Isaac
	* guix.scm: Import (gnu packages rdf). (genenetwork3)[propagated-inputs]: Add python-sparqlwrapper. * gn3/settings.py (SPARQL_ENDPOINT): New variable. * gn3/api/general.py: Import datasets from gn3.db. (dataset_metadata): New API endpoint. * gn3/db/datasets.py: Import re, Template from string, Dict and Optional from typing, JSON and SPARQLWrapper from SPARQLWrapper, SPARQL_ENDPOINT from gn3.settings. (sparql_query, dataset_metadata): New functions.
2021-09-27	Update terminology: `riset` to `group`	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Update terminology to use the appropriate domain terminology according to Zachary's direction at https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926041744
2021-08-17	Fix errors: add in missing parenthesis	Muriithi Frederick Muriuki
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Call the `cursor.fetchone()` function to get results. Without the parenthesis, the code was trying to use the function itself as the results, which was a bug, and would lead to failure.
2021-08-09	Fix linting errors	Muriithi Frederick Muriuki
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add module, class and function docstrings * Deactivate some irrelevant pylint errors * Fix indentations and line-lengths
2021-08-05	Reorganise the database code	Muriithi Frederick Muriuki
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Reorganise the code to separate the datasets from the traits, and to more closely conform to the same flow as that in GN1