genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
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.
2022-01-10	Remove all pairs with 'None' as the value	Frederick Muriuki Muriithi
	* Remove all key-value pairs whose value is None.
2022-01-10	Fix error in query: Replace '=' with 'IN'	Frederick Muriuki Muriithi

2022-01-10	Replace unoptimised function with optimised one	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Replace unoptimised function with one optimised to give better performance. The optimisation done here is to fetch multiple items/traits from the database per query, rather than the original form, which fetched a single item/trait from the database per query.