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2021-05-06Because each permutations value is returned as an array, need to just take ↵zsloan
the first item to convert to numbers
2021-04-27Convert to array and transpose R/qtl scanone results when not using ↵zsloan
cofactors. For some reason the rows/columns are inverted when converted to a python object when doing scanone with cofactors vs without cofactors
2021-04-27Randomized cross object filename, since I think it throws an error if the ↵zsloan
same file is being written to simultaneously (or being written to while it's being read)
2021-04-27Stopped using the scanone function pointer when doing R/qtl mapping, since ↵zsloan
the results are not converted into a Python object in a way that preserves marker names (which is important because pseudomarkers can be added) Instead the marker names are extracted from the scanone results using R immediately after they're generated, and then passed to process_rqtl_results
2021-04-22Account for situations where the trait symbol is null for ProbeSet traits; ↵zsloan
previously it could throw an error
2021-04-22Added JS that sets the 'add to collection' dropdown to default to the ↵zsloan
collection the use set as their default collection
2021-04-19Specify only getting the first two items after splitting the trait/dataset ↵zsloan
input string
2021-04-19Removedu nused function from network_graph.pyzsloan
2021-04-19Removed commented out js filezsloan
2021-04-19Fixed NIAAA link because apparently it was changedzsloan
2021-04-19Removed unused codezsloan
2021-04-14Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2021-04-14Added JS that automatically selects the default collection if it's setzsloan
2021-04-14Added option to set default collection to collections/view.htmlzsloan
2021-04-09Merge branch 'testing' of github.com:genenetwork/genenetwork2 into acentenoArthur Centeno
2021-04-09link to webinarsArthur Centeno
2021-04-09Changed connditional in show_trait.js to check categorical_attr_exists ↵zsloan
instead of just checking if there are case attributes
2021-04-09Replaced the conditional for whether to show 'Block samples by group' to ↵zsloan
instead check categorical_attr_exists
2021-04-09Store categorical_attr_exists as a string instead of boolean since ↵zsloan
apparently the boolean doesn't get passed to the template properly
2021-04-09Added varaiable 'categorical_attr_exists' tracking whether there are any ↵zsloan
case attributes with fewer than 10 distinct values, since it currently throws a JS error if case attributes exist but none have fewer than 10 distinct values (specifically when we have RRID as a case attribute)
2021-03-30Shifted some code out of the try/except that shouldn't have been inside itzsloan
2021-03-30Shifted the 'try' in a try/except up some to account for a possible error ↵zsloan
with calculating PCA that I don't know the cause of yet
2021-03-29Changed minimum num_overlap to 2, since there apparently need to be that ↵zsloan
many shared samples torun scipy.stats.pearsonr/spearmanr
2021-03-29Check if a trait in a collection is a properly structured string to avoid an ↵zsloan
error caused by an empty string be stored in a collection's trait list
2021-03-26Split rat RRID by _ in order to pull out just the ID number, since the ↵zsloan
number is needed for the links
2021-03-26Added try/except to deal with the possibility of user_id being stored in ↵zsloan
Redis as both string and bytes
2021-03-19Added other BXD individual groups to the list of BXD groups used when ↵zsloan
drawing the Gene Band
2021-03-17Added the RRID urls for mouse and rat to webqtlConfigzsloan
2021-03-17Fixed the logic for creating the RRID links to account for the fact that the ↵zsloan
rat IDs don't have any prefix with a colon
2021-03-17Added a check for if there's a second value for case attributes, for ↵zsloan
situations where a case attribute also has a link
2021-03-17Added URL as second value for RRID case attributes, so it can be displayed ↵zsloan
in the trait page sample table
2021-03-16Fixed test_check_resource_availability_of_super_user to account for user_id ↵zsloan
being returned as bytes instead of a str
2021-03-16Added try/except to convert owner_id to bytes if necessaryzsloan
2021-03-16Fixed encoding in load_json_from_redis to account for the first that column ↵zsloan
values are sometimes stored as bytes and sometimes as strings
2021-03-16Fixed encoding to make get_user_groups work properly, since the user IDs for ↵zsloan
groups in Redis are stored as strings
2021-03-16Removed unnecessary encoding of user_id from authentication_tools.pyzsloan
2021-03-16Removed unnecessary decoding when getting user_id from UserSessionzsloan
2021-03-12Fixed imports in send_forgot_password_email since they apparently needed to ↵zsloan
be changed for Python 3.8
2021-03-07Right-aligned the Mean column for phenotype global searchzsloan
2021-03-07Limited Mean for phenotype global search to 3 decimal placeszsloan
2021-03-04Fixed issue that caused JS to break when trait description contains a ↵zsloan
newline character
2021-03-03Checked if pre_publication_description is NULL, because there was an error ↵zsloan
resulting from a trait missing both pre_publication_description and pubmed ID
2021-02-23Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2021-02-23This should fix the issue with Haplotype Analyst sample names/values not ↵zsloan
being displayed correctly
2021-02-19Fixed test_gen_menu to reflect updated queryzsloan
2021-02-19Fixed TestCheckResourceAvailability to make it work after realizing that ↵zsloan
Redis.smembers apparently returns values as bytes
2021-02-19Fixed test_run_mapping.py to make export_mapping_results test work correctlyzsloan
2021-02-19Patched utility.authentication_tools.g as TestUserSession because otherwise ↵zsloan
the str.encode failed on the mock.Mock() object, and this also seems consistent with the way it's done in a later method
2021-02-18Increased sample table width added for each case attribute. At some point ↵zsloan
this needs to be made 'smarter,' since this might look funny if all case attribute column are narrow
2021-02-18Committing changes that added some fields to mapping export - one of the ↵zsloan
tests I changed assumed these changes were already made, so including them should fix that
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 04:03:38 +0000