genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2020-06-22	Fixed issue with temp traits not working for trait page functions like ↵	zsloan
	correlation or mapping
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
2020-05-21	Made search result table width variable again and fixed row highlighting, ↵	zsloan
	though later I need to go through and redo a bunch of CSS stuff
2020-05-07	Fixed blatseq issue and geno correlation issueblatseq_fix	zsloan

2020-05-07	Committing current progress on group manager + a minor fix in dataset.py	zsloan

2020-04-27	Added timeout for when/if it does the REST API query, so it doesn't hang ↵	zsloan
	indefinitely
2020-04-27	Made change that should allow dataset structure to be loaded from Redis ↵	zsloan
	instead of the JSON file without breaking things
2020-04-26	Removed the code that was still writing the database menu JSON	zsloan

2020-04-24	Replaced hard-coded instances of GN2 urls with ones pulled from settings file	zsloan

2020-04-24	Made a fix that should prevent the issue where new datasets cause an error ↵	zsloan
	when they're in search results
2020-04-06	Added Mean column for phenotype traits in search and global search result tables	zsloan

2020-03-27	Fixed issue where GEMMA wasn't showing up for certain groups	zsloan

2020-03-27	Added integration for using RData files with R/qtl, plus some other changes ↵	zsloan
	to how it decides which mapping methods to display on the trait page
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

2020-02-07	Users can now add and do mapping on genotype files that only include a ↵	zsloan
	subset of samples/strains Also filtered the results used by Christian's genome browser, so now it should have an easier time loading when dealing with larger numbers of markers
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

2019-12-17	Added RGD link to trait page and removed Genotation link since it isn't working	zsloan

2019-12-04	Added M to the possible non-number 'chromosome' names	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
2019-11-14	Changed code to rebuild dataset list each time you view the trait page to ↵	zsloan
	avoid having to restart each time a new dataset is added. Will need to keep an eye out for any issues, but doesn't seem to affect speed much Fixed logic for UniProt link to use UniProtId instead of protein ID
2019-11-05	Fixed issue with ordering items in correlation dataset select dropdown	zsloan

2019-10-24	Changed logic for generating drop-downs such that it shows the correct ↵	zsloan
	Phenotypes name when there's no accession ID
2019-10-18	Added UniProt link and fixed issue that caused sample lists to not be formed ↵	zsloan
	correctly in certain situations
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
2019-08-22	Changed header drop-down menu layout	zsloan
	Added a couple new third party links Added link to GN1 trait page in trait pages Fixed gene global search table appearance
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
2019-07-23	Added change to automatically update datasets list using rest api instead of ↵	zsloan
	json file Removed option to edit certain html pages, like news, policies, etc
2019-07-18	Made change that should fix encoding issue, fingers crossed	zsloan

2019-07-03	Fixed bug for creating one of the third party links on the trait page	zsloan
	Changed text in several pages (submit trait, mapping error) Changed header menu structure some
2019-06-24	Got non-LOCO GEMMA mapping working with gemma-wrapper (so caching should ↵	zsloan
	work for that now) Fixed position digits and row highlighting on interval analyst table Updated default MAF to 0.05 Updated footer text
2019-06-18	Fixed issue with sorting involving 0's on trait page	zsloan
	Fixed links to dataset info pages in search results and correlation results pages
2019-06-05	Fixed issue that caused interval mapping to not work because the python ↵	zsloan
	implementation of the reaper Dataset object doesn't include the addinterval method (so for those situations I still use reaper) Fixed issue where the last chromosome wasn't displayed for mapping results (though still need to fix issue where points are drawn too far to the right when a specific range is viewed)
2019-06-04	Added GeneMANIA link	zsloan
	Fixed issue that caused error when creating UCSC RefSeq link Fixed issue that sometimes caused an error for phenotype searches Changed some text on collections page
2019-05-24	Replaced qtlreaper Dataset object with python object	zsloan

2019-05-14	Added all of the third party links from GN1	zsloan
	Fixed issue with the script that generates the drop-down menus where phenotype/genotype datasets wouldn't show up for species without any mRNA assay datasets Added icon for smartphones/tablets Made error more informative for main search Added gene symbol column to collections (need to add something that removes the column if it's all empty)
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