genenetwork3/gn3/api, 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>
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>
Correct publication function docstring
2023-06-12T12:35:40+00:00
Munyoki Kilyungi
2023-06-08T11:43:08+00:00
urn:sha1:e4489c48bf5d1c9cb72b8cc1eccc603f1178ecbf
* gn3/api/metadata.py (publication): Update docstring.
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>
Remove trait_metadata endpoint
2023-06-07T06:42:25+00:00
Munyoki Kilyungi
2023-06-07T06:37:01+00:00
urn:sha1:8801f6d57a9347a724cc7ed6e1b5ce9600782034
* gn3/api/metadata.py: Remove get_trait_metadata import.
(trait_metadata): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Rename dataset_metadata -> dataset
2023-06-05T21:47:58+00:00
Munyoki Kilyungi
2023-06-05T21:34:37+00:00
urn:sha1:86de51055cde3d29a7c088467d281d3b32b6b6be
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Create new endpoint for fetching GeneRIF entries
2023-04-17T12:24:36+00:00
Munyoki Kilyungi
2023-04-14T12:37:31+00:00
urn:sha1:d04779286b49346946120a5801509ba80ee987ba
* 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>
Remove deprecated `gn3.db_utils.database_connector` function
2023-04-06T09:31:05+00:00
Frederick Muriuki Muriithi
2023-04-06T09:31:05+00:00
urn:sha1:17abad9300e4a96a14f94da486ef8307f7d27e06
Remove the deprecated function and fix a myriad of bugs that arise from
removing the function.
Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
Fetch sampledata
2023-03-01T19:03:39+00:00
Munyoki Kilyungi
2023-03-01T12:48:15+00:00
urn:sha1:32c144cdf41d2f109901d34930296f34fa51323e
* gn3/api/sampledata.py (get_sampledata): New end-point.
* gn3/app.py: Register above end-point.
* gn3/settings.py: Add new conf variable for LMDB.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>