genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2022-02-08	db: traits: Allow insertions of "0" in resp. sample values tables	BonfaceKilz
	When editing values from "x" to "0"(or any other value) when editing data, an "update" statement was being run; thereby no new value was being inserted. To the end user, modifying an "x" value to something else meant that no value was being inserted. This commit fixes that by doing an insert whenever a change from "x" to "0" is performed. * gn3/db/traits.py (update_sample_data): Add insert statements whenever an "update" statement returns a 0 row-count.
2022-02-08	db: traits: Insert "count" instead of "error" in "NStrain" table	BonfaceKilz

2022-02-03	db: Fetch correct sample data	BonfaceKilz

2022-02-02	Fix R/qtl covar bug	zsloan
	The rqtl_wrapper script was throwing an error when only a single categorical covariate was used. This is apparently because "covars[,name]" throws an error in such a situation. Using just "covars" in such a situation prevents the error. So I just added an if statement checking the number of covariates. There might be some better way to deal with this in R, but this is the best I could come up with.
2022-02-02	Remove PublishFreeze from retrieve_publish_trait_info query	zsloan
	The PublishFreeze table isn't necessary in phenotype queries, since PublishFreeze.Id = InbredSet.Id (for the purposes of identifying traits, at least)
2022-02-02	Fix bug where sample values of 0 were being treated as False	zsloan
	In line 91 of gn3/db/traits.py, there was an if statement "if record[key] else 'x'" that was treating values of 0 as False, so I changed it to explicitly check that values aren't None
2022-02-02	Fix retrieve_publish_trait_data query	zsloan
	The PublishFreeeze table is actually unnecessary for this query, since the group ID (inbred_set_id) should be passed in and that ID is in the PublishXRef table (so no neeed to join with PublishFreeze)
2022-02-02	response object error fix	Alexander Kabui

2022-02-02	pep8 formatting	Alexander Kabui

2022-02-02	remove comments	Alexander Kabui

2022-02-02	return 401 on request fail	Alexander Kabui

2022-02-02	refactor code for invoking ctl script	Alexander Kabui

2022-02-02	pep8 formatting	Alexander Kabui

2022-02-02	match case string input to boolean	Alexander Kabui

2022-02-02	fix for parametric input	Alexander Kabui

2022-02-02	use user input significance	Alexander Kabui

2022-02-02	new line fix	Alexander Kabui

2022-02-02	add new json output	Alexander Kabui

2022-02-02	fix comprehension list	Alexander Kabui

2022-02-02	Revert "Use guix shell shortcut with guix.scm file"	BonfaceKilz
	This reverts commit f676c291967f8a81836b73c5a5dcd3c65e02552c.
2022-01-27	Use guix shell shortcut with guix.scm file	jgart

2022-01-24	README: Add pylint and mypy CI badges.	Arun Isaac
	We now have separate CI jobs for the pylint and mypy tests. * README.md: Add pylint and mypy CI badges.
2022-01-22	minor refactoring	Alexander Kabui

2022-01-22	function override:fix target specific output file for network	Alexander Kabui

2022-01-22	generate network	Alexander Kabui

2022-01-22	process ctl plot data img	Alexander Kabui

2022-01-22	generate ctl plots for each trait	Alexander Kabui

2022-01-22	read stdout data;handle exceptions	Alexander Kabui

2022-01-22	generate required json data for ctl api	Alexander Kabui

2022-01-22	fixes for ctl script:generate ctl ctl_significant json	Alexander Kabui

2022-01-22	bugfixes for script;create pheno and geno objects	Alexander Kabui

2022-01-22	add endpoint for ctl	Alexander Kabui

2022-01-22	init file to call ctl script	Alexander Kabui

2022-01-22	generate lineplot	Alexander Kabui

2022-01-22	minor fix:read input data from json file	Alexander Kabui

2022-01-22	export json data	Alexander Kabui

2022-01-22	get significant interactions	Alexander Kabui

2022-01-22	perform the ctl scan	Alexander Kabui

2022-01-22	fetch genotypes and phenotype files	Alexander Kabui

2022-01-22	init script ctl analysis	Alexander Kabui

2022-01-21	README: Update link to CI badge.	Arun Isaac
	The CI has been moved to penguin2, and this is accompanied by a URI change. * README.md: Update link to CI badge.
2022-01-12	Update return type. Remove duplicate import.	Frederick Muriuki Muriithi
	The function is a generator function, since it uses a `yield` statement, and thus returns a generator object, that contains a tuple object. This fixes that. We also remove a duplicate import.
2022-01-12	Indent code correctly	Frederick Muriuki Muriithi
	Indent the code correctly.
2022-01-12	Deduplicate query to fetch data for 'Publish' traits	Frederick Muriuki Muriithi
	The queries run in the `get_trait_csv_sample_data` and `retrieve_publish_trait_data` functions in the `gn3.db.traits` module were mostly similar. This commit changes that, by making the `get_trait_csv_sample_data` function make use of the results from calling the `retrieve_publish_trait_data` function.
2022-01-10	Check for path existence	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2022-01-10	Fix dataset retrieval query for `Geno` traits	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2022-01-10	Use the correct letter case for the keys	Frederick Muriuki Muriithi
	* Use the correct case for the keys inorder to retrieve the correct values.
2022-01-10	Surround statement with parens for readability	Frederick Muriuki Muriithi

2022-01-10	Indicate that string is an f-string	Frederick Muriuki Muriithi
	* The string had the f-string syntax to format the values to be inserted into the string, but was missing the 'f' before the opening quotes to signify to python that this was an f-string. This commit fixes that.
2022-01-10	Convert keys to string	Frederick Muriuki Muriithi
	* Some traits have a name composed of all numerals, which leads to the names being interpreted as numbers. This commit forces them to string to avoid subtle bugs where the code fails.