genenetwork3/gn3/db, 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>
Disable fetching case-attributes when getting sample data
2023-03-20T19:00:38+00:00
Munyoki Kilyungi
2023-03-20T12:14:53+00:00
urn:sha1:48d045e54b44b5e3fdadb7e8bf4d878c052655d9
* gn3/db/sample_data.py: Remove 're' import.
(get_trait_csv_sample_data): Remove fetching sample data.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Add conn.commit() to queries in sample_data.py
2023-03-17T18:27:42+00:00
zsloan
2023-03-17T18:27:42+00:00
urn:sha1:a1a376db4848a3ccd74c9c384efacea4579ce165
Change get_all_species query to order by Family
2023-03-17T18:27:03+00:00
zsloan
2023-03-17T18:27:03+00:00
urn:sha1:047e11c611977814e29f5b636c8583171bf579e3
Open lmdb path in readonly mode
2023-03-01T19:03:39+00:00
Munyoki Kilyungi
2023-03-01T12:46:13+00:00
urn:sha1:e32dacc9648908a73855d99e7681cb4d7aa4f98e
* gn3/db/matrix.py (get_total_versions, get_nth_matrix,
get_current_matrix): Open lmdb in readonly mode.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Fetch trait metadata from RDF
2023-03-01T19:03:39+00:00
Munyoki Kilyungi
2023-02-14T21:24:57+00:00
urn:sha1:01e12ddb0c7f71c8c1700a4fac0b9447d83f3f9f
* gn3/db/rdf.py (get_dataset_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Get the N-th matrix given N, an index value
2023-02-06T15:14:19+00:00
Munyoki Kilyungi
2023-02-06T12:05:56+00:00
urn:sha1:3cc5e7b57b0ca9bd5143d746022cb69349023a68
* gn3/db/matrix.py (get_nth_matrix): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Get total number of versions that a database has
2023-02-06T15:14:19+00:00
Munyoki Kilyungi
2023-02-06T11:40:04+00:00
urn:sha1:faf223207015077d0afc36c7cc7cf1fc29976c7f
* gn3/db/matrix.py (get_total_versions): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Add method to fetch the current matrix
2023-02-06T15:14:19+00:00
Munyoki Kilyungi
2023-02-06T11:32:27+00:00
urn:sha1:8bfb1f9e9f74f41eb251eb025838244cc5c256eb
* gn3/db/matrix.py: New file.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
gn3: (gn3.random -> gn3.chancy): Rename module to avoid conflicts.
2022-12-21T00:39:52+00:00
Frederick Muriuki Muriithi
2022-12-21T00:39:52+00:00
urn:sha1:daa3a9cade431b21bbc48b690c16dcb8746f3dce
Rename the `gn3.random` module to gn3.chancy to avoid conflicts with Python's
`random` module.
* gn3/random.py -> gn3/chancy.py: rename module
* gn3/commands.py: update import
* gn3/computations/partial_correlations.py: update import
* gn3/computations/qtlreaper.py: update import
* gn3/computations/rust_correlation.py: update import
* gn3/db/correlations.py: update import
* gn3/db/traits.py: update import
* gn3/heatmaps.py: update import
* tests/integration/conftest.py: update import