genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
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>
2023-04-17	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>
2023-03-01	Fetch trait metadata from RDF	Munyoki Kilyungi
	* gn3/db/rdf.py (get_dataset_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2022-12-08	Remove unused import	Frederick Muriuki Muriithi

2022-12-06	Use a dataset's name to fetch it's metadata from RDF	Munyoki Kilyungi
	* gn3/api/metadata.py (jsonify_dataset_metadata): Rewrite metadata end-point to use a dataset's name instead of it's accession_id. * gn3/db/rdf.py (get_dataset_metadata): Replace accession_id with name. Use one single RDF query instead of multiple queries.
2022-11-16	Inject SPARQLWrapper as a parameter	Munyoki Kilyungi
	* gn3/db/rdf.py: Delete gn3.setting.SPARQL_ENDPOINT import. (sparql_query): Inject SPARQLWrapper. (get_dataset_metadata): Ditto.
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.