genenetwork3/gn3/api, branch auth/implement-authorization-code-flow GeneNetwork3 REST API for data science and machine learning http://git.genenetwork.org/genenetwork3/atom?h=auth%2Fimplement-authorization-code-flow 2023-04-17T12:24:36+00:00 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> Create API endpoint for fetching trait metadata 2023-03-01T19:03:39+00:00 Munyoki Kilyungi 2023-02-14T21:25:20+00:00 urn:sha1:104723d9954359cbc10140c36d4ae4f8d2f4f7f4 * gn3/api/metadata.py (dataset_metadata): New function and endpoint. (jsonify_dataset_metadata): Rename to dataset_metadata. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> search: Use decimals, not floats, when converting to megabases. 2023-01-24T19:03:19+00:00 Arun Isaac 2023-01-24T18:59:24+00:00 urn:sha1:a9c011099b9e5fcf66dde8f4ceb87ac90838aa7b * gn3/api/search.py (parse_location_field): Use decimals, not floats, when converting to megabases. search: Support SI suffixes and point locations. 2023-01-24T19:03:19+00:00 Arun Isaac 2023-01-24T18:48:20+00:00 urn:sha1:bf376b14593a29b48fd2558baff946d0495ae329 * gn3/api/search.py (parse_position_field): New function. (parse_query): Associate the position prefix with the parse_position_field field processor. search: Abstract out parsing of position spec into separate function. 2023-01-24T18:30:05+00:00 Arun Isaac 2023-01-24T18:17:57+00:00 urn:sha1:e5bcdbc83031c10092f1405b847695ecefbada44 * gn3/api/search.py (parse_position): New function. (parse_location_field): Use parse_position. * tests/unit/test_search.py: Import parse_position from gn3.api.search. (test_parse_position_close_to_zero_location): New test. search: Alias the position prefix with pos. 2023-01-24T13:45:53+00:00 Arun Isaac 2023-01-24T13:44:47+00:00 urn:sha1:d33454f3e7fb7810fd4b7a987e6a68b3c48ec98e * gn3/api/search.py (parse_query): Alias the position prefix with pos. search: Rename the mb prefix to position. 2023-01-24T13:44:00+00:00 Arun Isaac 2023-01-24T13:44:00+00:00 urn:sha1:ecb8929c4a749ff24e8d3086331ce149dc66b574 * gn3/api/search.py (parse_query): Rename the mb prefix to position. search: Assume triplets mean synteny is requested. 2023-01-24T13:22:20+00:00 Arun Isaac 2023-01-24T13:14:04+00:00 urn:sha1:be2034b4e6666861c42702d663e1638c06e4793a * gn3/api/search.py (query_subqueries, query_terms, parse_synteny_field, is_synteny_on, remove_synteny_field): Delete functions. (parse_query): Assume triplets mean synteny is requested.