genenetwork3/gn3/db, branch migrate-to-python3.10
GeneNetwork3 REST API for data science and machine learning
http://git.genenetwork.org/genenetwork3/atom?h=migrate-to-python3.10
2023-07-10T08:36:47+00:00
Fix linting errors caused by bump to Python 3.10
2023-07-10T08:36:47+00:00
Frederick Muriuki Muriithi
2023-07-10T08:36:47+00:00
urn:sha1:c6ac30d4ccc26553a12e8c37cdf9078cbe9084b3
Fetch genotypes from virtuoso
2023-06-15T18:27:59+00:00
Munyoki Kilyungi
2023-06-15T12:40:58+00:00
urn:sha1:9193597f12631bcf33ce768f2842132bd22a41c3
* 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>
Delete unused import
2023-06-12T12:35:40+00:00
Munyoki Kilyungi
2023-06-12T12:33:23+00:00
urn:sha1:e0f3efca45ac471c3113c473df53288c5b98eb54
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Fetch phenotypes from virtuoso
2023-06-12T12:35:40+00:00
Munyoki Kilyungi
2023-06-08T11:44:38+00:00
urn:sha1:fa2ce410d4730b136f24555c049cef3d6dac1102
* 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>
Delete unused get_trait_metadata function
2023-06-12T12:35:40+00:00
Munyoki Kilyungi
2023-06-08T11:01:54+00:00
urn:sha1:96bb0d6f2eb76de8481e0ff1c2afd08ccf7e64fa
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Add publication end-point
2023-06-07T06:42:25+00:00
Munyoki Kilyungi
2023-06-07T06:39:58+00:00
urn:sha1:4da80ca9c17bdd28e2689895ab6acb1ec0c70d33
* 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>
Nest duplicate entries into a list from a sparql result
2023-06-07T06:42:25+00:00
Munyoki Kilyungi
2023-06-07T06:38:52+00:00
urn:sha1:c68d64a2966750283ecd1290d26eee2797fedcad
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Pass geoSeries as a URL
2023-06-06T09:37:50+00:00
Munyoki Kilyungi
2023-06-06T09:36:23+00:00
urn:sha1:095d8bbbbc2c7c02508b2796085e203a95b135b6
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Rename gn:geoPlatform -> gn:geoPlatformUrl
2023-06-05T23:04:41+00:00
Munyoki Kilyungi
2023-06-05T23:03:42+00:00
urn:sha1:a03ce5be2ab4c1413f260146d552302a2e832f1d
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Match how dataset metadata is fetched with GN1
2023-06-05T21:47:58+00:00
Munyoki Kilyungi
2023-06-05T21:45:38+00:00
urn:sha1:2a025c10fb287068c8e8e93eb95c91fef4ca55cb
* 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>