genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2022-03-10	Use context manager with database connection	Frederick Muriuki Muriithi
	Use the `with` context manager with database connections and cursors to ensure that they are closed once they are no longer needed. Where it was not feasible to use the `with` context manager without a huge refactor/rewrite, the cursors and connections are closed manually.
2021-10-28	Remove all elasticsearch references in gn2	BonfaceKilz

2021-04-30	autopep8: Run autopep8 100 times with target rules	BonfaceKilz
	Rules used are: E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,E242, E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306, E401,E501,E70,E701,W291,W292,W293,W391,W504,E101,E11,E121, E122,E123,E124,E125,E126,E127,E128,E129,E131,E133
2021-04-30	autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133	BonfaceKilz

2021-04-30	autopep8: Fix E501	BonfaceKilz

2021-04-30	autopep8: Fix E301,E302,E303,E304,E305,E306	BonfaceKilz

2021-04-30	autopep8: Fix E20-E27	BonfaceKilz
	Run: python -m autopep8 --in-place --recrusive ./ --select\ E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\ E242,E251,E252,E26,E265,E266,E27 -p 3
2020-08-26	Remove "from __future__ import new_feature" statements	BonfaceKilz
	See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
2020-08-20	Handle module renames in the standard library	BonfaceKilz
	Run: ``` 2to3-3.8 -f imports -w . && \ 2to3-3.8 -f imports2 -w . ``` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-imports> and <https://docs.python.org/2/library/2to3.html#2to3fixer-imports2>
2020-08-19	Remove extra whitespace(or add it) from comma separated items	BonfaceKilz
	See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19	Rename xrange() to range() and wrap existing range() calls with list	BonfaceKilz
	See: <https://docs.python.org/2/library/2to3.html#2to3fixer-xrange>
2020-08-19	Replace `izip` with python's built-in equivalent	BonfaceKilz
	Run `2to3-3.8 -f itertools -w . && 2to3-3.8 -f itertools_imports -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-itertools_imports> and <https://docs.python.org/2/library/2to3.html#2to3fixer-itertools>
2018-05-25	Fixed issue causing anonymous collections to not work on my branch and ↵	zsloan
	staging, though still not sure why it's working on production without that change Added script to convert the dryad format genotype files to BIMBAM removed db_uri from parameters of parse_db_uri in gen_select_dataset.py, since it can now just pull it from settings as a global variable
2018-05-17	Added script to quantile normalize a data set and enter its normalized ↵	zsloan
	sample data into ElasticSearch Added option to replace trait page sample/strain values with normalized ones Began editing Lei's scatterplot code Changed elasticsearch_tools' get_elasticsearch_connection so that it can also be used for purposes other than user authentication (by adding a "for_user" parameter)