genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
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
2020-04-24	Replaced hard-coded instances of GN2 urls with ones pulled from settings file	zsloan

2020-04-06	Added Mean column for phenotype traits in search and global search result tables	zsloan

2020-03-09	I think this should complete consolidating all the collections code.	zsloan

2020-03-03	Forgot to replace code referring to hmac function user_manager	zsloan

2020-02-06	Fixed encoding issue	zsloan

2020-01-22	Fixed issue that caused submitting temp traits to not work	zsloan

2020-01-08	Made change that I think should fix the unicode stuff once and for all	zsloan

2019-12-04	Fixed error that sometimes occurs if there's no mean expression and changed ↵	zsloan
	index page header style a little
2019-11-21	Use updated phenotype display IDs for all phenotypes with codes now, not ↵	zsloan
	just unpublished ones
2019-11-21	Added 3-letter codes to unpublished phenotype traits and fixed issue with ↵	zsloan
	ordering phenotype results from searches
2019-10-04	Fixed issue where there was an error if the REST API used for aliases was down	zsloan
	Added option to download as JPEG in addition to SVG for basic stats figures
2019-08-01	Updated aliases to get all species aliases and remove duplicates	zsloan

2019-08-01	Added wikidata aliases	zsloan
	Fixed year to not be a hyperlink when no pubmed id Fixed first column width so it doesn't go onto two lines for trait details
2019-08-01	Made some more aesthetic changes to various pages and charts/figures	zsloan
	Added some information to the mapping loading page
2019-07-18	Made change that should fix encoding issue, fingers crossed	zsloan

2019-05-06	Removed some unused imports of htmlgen	zsloan
	Fixed a bug that sometimes occurred in search results Changed order of items on index page
2019-03-18	- Added PCA traits to correlation matrix. You can't change their names yet ↵	zsloan
	or add them to a collection from the corr matrix page, but you can click them and access them from the trait page. I'll add the option to access them from the corr matrix page as well, but adding the option to change their names might be trickier since they're currently used as their Redis keys. I need some better way of passing the Redis key around so it can be stored in collections, but this is tricky without changing the structure in ElasticSearch - Fixed the way temp traits work so you can use them with various functions, like mapping, correlations, network graph, etc - Fixed some appearance issue where the network graph options were too wide if a trait name was too long