genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2021-04-30	autopep8: Fix W504	BonfaceKilz

2021-04-29	Merge branch 'testing' into Feature/Add-upload-data-forms	BonfaceKilz

2021-04-29	Run `sed -i 's/(object)//g'`	BonfaceKilz
	See: https://is.gd/pL7IJF Ran: find . \( -type d -name .git -prune \) -o -type f -print0 \| xargs -0 sed -i 's/(object)//g'
2021-04-29	base: trait: Remove unused function	BonfaceKilz
	* wqflask/base/trait.py (jsonable_table_row): Delete it.
2021-04-28	Added something to jsonable in trait.py to account for temp traits (this is ↵	zsloan
	necessary for them to show up correctly when selecting traits from collections in pop-up windows, like when selecting cofactors for mapping)
2021-03-03	Checked if pre_publication_description is NULL, because there was an error ↵	zsloan
	resulting from a trait missing both pre_publication_description and pubmed ID
2021-02-18	Fixed missing colon	zsloan

2021-02-18	Fixed checking permissions in trait.py	zsloan

2021-02-11	Ensure trait description_display is set	zsloan

2020-12-07	Changed the logic in create_trait so that permissions should always be set, ↵	zsloan
	and added an assert that 'name' is passed instead of using if/else, since it should always be passed
2020-12-01	Merge pull request #482 from zsloan/feature/corr_table_changes	zsloan
	Feature/corr table changes
2020-11-18	Fixed issue where the cofactor trait descriptions didn't work correctly	zsloan
	for genotype/snp cofactors (the code previously only accounted for probeset/phenotype cofactors, so it was treating genotypes/snps like phenotype traits)
2020-11-18	Fixed issue that was causing scatterplot cofactors to not work if the	zsloan
	cofactors were genotypes (because it tried to get the "description_display" which doesn't exist for genotype traits)
2020-11-11	Switched checking if a trait is confidential to checking if it has a pubmed ↵	zsloan
	ID for the purposes of showing pre-publication abbreviation/description
2020-10-12	Merge branch 'testing' into build/python3-migration	BonfaceKilz

2020-10-09	Apply PEP 8 to buffer	BonfaceKilz
	* wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8 * wqflask/wqflask/collect.py: Ditto * wqflask/base/trait.py: Ditto
2020-10-02	Ignore utf-8 encoding errors	BonfaceKilz
	* wqflask/base/trait.py (retrieve_trait_info): Add extra param to ignore errors such as: "utf-8 codec can't decode byte 0xb5 in position 0: invalid start byte" thrown in Python3.
2020-10-01	Convert trait attributes to utf-8 strings if they were bytes	BonfaceKilz

2020-09-28	Merge branch 'build/python3-migration' of ↵	BonfaceKilz
	github.com:BonfaceKilz/genenetwork2 into build/python3-migration
2020-09-28	Fix casting error	BonfaceKilz
	* wqflask/base/trait.py (retrieve_trait_info): If the description_string or discription_display value return a None object, evaluate to an empty string. Fixes errors related to len(None).
2020-09-28	Merge branch 'testing' into build/python3-migration	BonfaceKilz

2020-09-28	Fix casting error	BonfaceKilz
	* wqflask/base/trait.py (retrieve_trait_info): If the description_string or discription_display value return a None object, evaluate to an empty string. Fixes errors related to len(None).
2020-09-28	Convert None to "" in if statement	BonfaceKilz
	* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork error: float argument required, not NoneType)"
2020-09-17	Convert "target_string" to a str type	BonfaceKilz
	* wqflask/base/trait.py (retrieve_trait_info): Convert "target_string" to a str, otherwise an exception will be thrown if it's None.
2020-09-17	Apply pep8	BonfaceKilz
	* wqflask/base/trait.py: Apply pep8. * wqflask/utility/authentication_tools.py: Ditto.
2020-08-27	Remove python2 string processing to utf-8	BonfaceKilz
	* wqflask/base/trait.py: Remove python2 codecs.BOM_UTF8 methods. * wqflask/wqflask/search_results.py: Remove utf-8 decode method on string.
2020-08-27	Replace mysqldb's "escape" with the one from utils.db_tools	BonfaceKilz
	Mysqldb's escape returns a binary string. Use utils.db_tools which adds an extra step of converting the binary string to a string.
2020-08-27	Replace "string.split" & "string.join" with python's inbuilt methods	BonfaceKilz

2020-08-26	Remove "from __future__ import new_feature" statements	BonfaceKilz
	See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
2020-08-26	Rename "unicode" to "str"	BonfaceKilz
	See: <https://docs.python.org/2/library/2to3.html#2to3fixer-unicode>
2020-08-20	Add backward support for urllib	BonfaceKilz
	* wqflask/base/trait.py: Remove unused imports * wqflask/db/call.py (Bench): Add urllib2 fallback for python2
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	Handle the rename of urllib and urllib2 to the urllib package	BonfaceKilz
	See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19	Replace backtick repr with the repr() function	BonfaceKilz
	* wqflask/base/trait.py: See <https://docs.python.org/2/library/2to3.html#2to3fixer-repr>
2020-08-19	Wrap `raise` statements in parenthesis	BonfaceKilz
	Run `2to3-3.8 -f raise -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raise>
2020-08-19	Fix dictionary iteration methods	BonfaceKilz
	Run `2to3-3.8 -f dict -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-dict> and <https://stackoverflow.com/questions/17695456/why-does-python-3-need-dict-items-to-be-wrapped-with-list>
2020-07-21	Fixed issue that caused group codes to be wrong sometimes	zsloan

2020-07-14	Added binary casting to phenotype trait info query to fix unicode issue	zsloan

2020-07-08	Removed remaining unused references to the old qtlreaper	zsloan

2020-07-06	Temporarily commented out the line in trait.py doing the encoding until we ↵	zsloan
	figure out the real solution to that issue
2020-07-06	Fixed some of the logic with how traits are authenticated to avoid situation ↵	zsloan
	where a trait is authenticated twice
2020-06-29	Change that hopefully fixes some encoding stuff	zsloan

2020-06-24	Temporary partial fix to issue of resources without info; need to add ↵	zsloan
	something that automatically inserts resources with default privileges
2020-06-20	Fixed ports for proxy (though I need to add the port to global variables) ↵	zsloan
	and also simplified the check_owner_or_admin function a little
2020-06-20	Added some admin functionality and fixed issue with temp traits	zsloan

2020-06-17	Adding all the authentication stuff	zsloan

2020-06-05	Commiting other current group/resource management code, plus the new files	zsloan

2020-06-04	Added back in trait info queries for situations where the proxy isn't running	zsloan

2020-06-04	Really should have split this into many more commits:	zsloan
	- Now use proxy to pull trait data and hide traits/results that the user doesn't have view permission for - Created a factory method for creating trait ob so it can return None when user doesn't have view permissions (this is why such a large number of files are changed) - Added metadata to permutation export - Added current group management code - Added fixed password verification e-mail code
2020-05-28	Added lines calling proxy for publish datasets + added some resource redis ↵	zsloan
	queries and a missing import for the hmac functions