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2021-05-08api: router: Inject MySQL object when fetching menu itemsBonfaceKilz
2021-05-08tests: test_gen_menu: Update failing testsBonfaceKilz
Update tests to use (and mock) the injected MySQL connection object.
2021-05-07Check if num_bootstrap is in start_vars, since it won't exist for ↵zsloan
non-qtlreaper methods
2021-05-07Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2021-05-07Fixed issue that caused /submit_trait page to not load properlyzsloan
2021-05-07Add typing + autopep8 formattingAlexander Kabui
2021-05-07remove comments prettify htmlAlexander Kabui
2021-05-07minor fixAlexander Kabui
2021-05-07fix tweets widthAlexander Kabui
2021-05-07modify blog list uiAlexander Kabui
2021-05-07add function for fetching blogsAlexander Kabui
2021-05-07add template for blogsAlexander Kabui
2021-05-07add blogs blueprintAlexander Kabui
2021-05-06Forgot to add brackets around list comprehension, so added themzsloan
2021-05-06Merge pull request #565 from zsloan/bug/fix_rqtl_covariateszsloan
Stopped using the scanone function pointer when doing R/qtl mapping, …
2021-05-06Used a list comprehension for perm_vals as mentioned in Bonface's commentzsloan
2021-05-06Merge branch 'testing' into bug/fix_rqtl_covariateszsloan
2021-05-06Because each permutations value is returned as an array, need to just take ↵zsloan
the first item to convert to numbers
2021-05-06Fixed vertical position of loading text so that it should be positioned in ↵zsloan
the center vertically
2021-05-06Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2021-05-06Include group and species in form parameters for mapping results page, so ↵zsloan
they can be included in the loading page if the map is reloaded
2021-05-06Include group/species in form parameters on trait page so they can be ↵zsloan
displayed on mapping loading page
2021-05-06Changed the way metadata is displayed on the mapping loading pagezsloan
2021-05-06Delete model.py and it's referencesBonfaceKilz
* wqflask/wqflask/database.py (init_db): Remove references to "wqflask.model" * wqflask/wqflask/model.py: Delete it.
2021-05-06wqflask: user_manager: Delete usermanager.py and it's referencesBonfaceKilz
This module is not used anywhere.
2021-05-06wqflask: database: Remove loggingBonfaceKilz
2021-05-05Added whether GEMMA is using LOCO to mapping loading pagezsloan
2021-05-05Added genotype file to mapping loading pagezsloan
2021-05-05Removed an unused item from mapping_input_listzsloan
2021-05-05Added a number of new metadata items to the mapping loading page, such as ↵zsloan
covariates and permutation/bootstrap numbers
2021-05-05Added mapping download button above the results tablezsloan
2021-05-05Made change that should cause clicking the R/qtl tab to make it compute; ↵zsloan
also removed a console.log
2021-05-05Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2021-05-05Removed broken Genome Browser link from index pagezsloan
2021-05-05base: species: Remove redundant assignmentBonfaceKilz
2021-05-05api: gen_menu: Remove "+" when concatenating strings inside bracketsBonfaceKilz
2021-05-05tests: test_species: Update failing testsBonfaceKilz
2021-05-05base: chromosomes: Fetch the chromosomes lazilyBonfaceKilz
2021-05-05base: species: Rewrite Chromosomes using a dataclassBonfaceKilz
2021-05-05base: species: Rewrite IndChromosome using a dataclassBonfaceKilz
2021-05-05base: trait: Remove logging informationBonfaceKilz
The log adds unnecessary noise in addition to creating unwanted side-effects.
2021-05-05base: species: Rewrite TheSpecies class using a dataclassBonfaceKilz
2021-05-05base: species: Remove unused importBonfaceKilz
2021-05-05base: species: Format SQL queriesBonfaceKilz
2021-05-05templates: test_species: Add tests for instantiating ChromosomesBonfaceKilz
2021-05-05tests: test_species: Test that IndChromosome instantiates correctlyBonfaceKilz
2021-05-05tests: test_species: Add test cases for TestTheSpecies classBonfaceKilz
2021-05-04Removed unused rpy import in run_mapping.pyzsloan
2021-05-03Account for the possibility of the R being returned as 0.999... by scipy ↵zsloan
when a trait is correlated against itself - before the 0.999... was preventing it from switching to calculating Spearman for the values above the diagonal in the correlation matrix
2021-04-30Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
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