genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2022-07-22	mypy fixes	Alexander_Kabui

2022-07-22	pep8 fixes	Alexander_Kabui

2022-07-22	linting and tests fixes	Alexander_Kabui

2022-07-22	import rust_correlation when running gn3 as lib	Alexander_Kabui

2022-07-22	compute num overlap	Alexander_Kabui

2022-07-22	fix for bug splitting list data	Alexander_Kabui

2022-07-22	minor fixes for parsing data	Alexander_Kabui

2022-07-22	code to parse tissue correlation input	Alexander_Kabui

2022-07-22	mypy pylint fixes	Alexander_Kabui

2022-07-22	code to fetch correct sample corr data	Alexander_Kabui

2022-07-22	delete dead_code;rename variables	Alexander_Kabui

2022-07-22	add unittests	Alexander_Kabui

2022-07-22	minor fixes	Alexander_Kabui

2022-07-11	Allow CORS everywhere by default	Frederick Muriuki Muriithi
	Allow the resources (endpoints) to be accessible from anywhere on the internet by default, while still allowing for restriction via CLI environment variable on a case by case basis.
2022-06-29	use explicit parameters	Alexander_Kabui

2022-06-29	fix issues	Alexander_Kabui

2022-06-29	lint test file	Alexander

2022-06-29	pylint fixes	Alexander

2022-06-29	add tests	Alexander

2022-06-29	add test data	Alexander

2022-06-29	minor fixes	Alexander

2022-06-29	handle tmp files generation	Alexander

2022-06-29	parse output data	Alexander

2022-06-29	pep8 formatting	Alexander

2022-06-29	new variable: CORRELATION_COMMAND	Alexander

2022-06-29	init test correlation rust module	Alexander

2022-06-29	init rust correlation module	Alexander

2022-06-28	Parse the method from UI before passing it to external process	Frederick Muriuki Muriithi
	To reduce the chances of the system failing due to the external process being launched with the wrong parameters, add a parsing stage that converts the method from the UI into a form acceptable by the CLI script. * gn3/commands.py: parse the method from UI * scripts/partial_correlations.py: simplify the acceptable methods
2022-06-21	tests: test_file_utils: Replace pytest.mark.skip with unittest.skip	BonfaceKilz
	"python setup.py test" won't skip "pytest.mark.skip" thereby leading to build failure when you try to package gn3.
2022-06-21	setup.py: Remove commented out "ipfshttpclient" line	BonfaceKilz

2022-06-21	gn3: fs_helpers: Fix pylint errors	BonfaceKilz
	* gn3/fs_helpers.py: Remove unused "pathlib" import. (cache_ipfs_file): Disable "unused-argument" warting.
2022-06-21	test_file_utils: Disable test cases for "cache_ipfs_file"	BonfaceKilz
	* tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit): Skip it. (test_cache_ipfs_file_cache_miss): Ditto.
2022-06-21	gn3: fs_helpers: Remove ipfshttpclient	BonfaceKilz
	This library pollutes the Genenetwork2 profile with an old version "dataclasses" thereby causing it to fail.
2022-06-21	setup.py: Remove ipfshttpclient	BonfaceKilz

2022-06-21	integration: test_gemma: Skip "GemmaAPITest"	BonfaceKilz

2022-06-21	Replace lint code with human-readable text	BonfaceKilz
	* gn3/db/correlations.py (__fetch_data__): Use a more readable code as opposed to an error code.
2022-06-21	db: correlations: Ignore pylint error	BonfaceKilz
	* gn3/db/correlations.py (__fetch_data__): Ignore "Too many args" [R0913] error.
2022-06-21	db: correlations: Ignore types	BonfaceKilz
	* gn3/db/correlations.py (__build_query__): Ignore the "sample_ids" and "joins" types when calling build_query_sgo_lit_corr (fetch_all_database_data): Ignore the return type. TODO: Ping Alex/Arun to fix this.
2022-06-21	db: datasets.py: Ignore results from sparql.queryAndConvert	BonfaceKilz
	ATM, it's very difficult to work the correct type that is returned. Ignore this for now and fix this later.
2022-06-21	mypy.ini: Ignore missing lmdb mypy stubs	BonfaceKilz

2022-06-20	Update README: export env variables explicitly	Frederick Muriuki Muriithi

2022-06-20	gn3: genodb: Retire get function.	Arun Isaac
	* gn3/genodb.py (get): Delete function. (matrix): Use db.txn.get instead of get.
2022-06-20	gn3: genodb: Match class and function names of GenotypeMatrix.	Arun Isaac
	* gn3/genodb.py (GenotypeMatrix): Match class and function names.
2022-06-20	gn3: genodb: Remove db, nrows and ncols fields from GenotypeMatrix.	Arun Isaac
	db is unused. nrows and ncols are available in the array and transpose numpy arrays. * gn3/genodb.py (GenotypeMatrix)[db, nrows, ncols]: Delete fields. * gn3/genodb.py (matrix): Do not initialize db, nrows and ncols fields.
2022-06-20	gn3: genodb: Mention reading entire matrix in module docstring.	Arun Isaac
	* gn3/genodb.py: Mention reading entire matrix in module docstring.
2022-06-20	Restrict partial correlation method choices	Frederick Muriuki Muriithi
	- Have "Pearson's r" and "Spearman's rho" as the only valid choices for the partial correlations
2022-06-17	gn3: genodb: Rename Matrix named tuple to GenotypeMatrix.	Arun Isaac
	* gn3/genodb.py (Matrix): Rename to GenotypeMatrix. (matrix): Update invocation of Matrix.
2022-06-17	gn3: genodb: Allow retrieval of the entire genotype matrix.	Arun Isaac
	* gn3/genodb.py: Document nparray in the module docstring. (nparray): New function.
2022-06-17	gn3: genodb: Read optimized storage for the current matrix.	Arun Isaac
	The genotype database now stores the current version of the matrix alone in a read-optimized form, while storing the older versions of the matrix in a more compressed form. We are only interested in the current version of the matrix. So, always use the read optimized storage. * gn3/genodb.py (Matrix)[row_pointers, column_pointers]: Delete fields. [array, transpose]: New fields. * gn3/genodb.py (matrix, row, column): Read from read-optimized storage. (vector_ref): Delete function.
2022-06-09	gn3: genodb: Remove blank line in module docstring.	Arun Isaac
	* gn3/genodb.py: Remove blank line in module docstring.