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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
2021-04-30Fixed issue where Network Graph wouldn't show edges if multiple nodes had ↵zsloan
the same trait name; instead use combo of trait name and dataset name as the edge IDs
2021-04-30webtests: Delete itBonfaceKilz
These are no longer used
2021-04-30autopep8: Run autopep8 100 times with target rulesBonfaceKilz
Rules used are: E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,E242, E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306, E401,E501,E70,E701,W291,W292,W293,W391,W504,E101,E11,E121, E122,E123,E124,E125,E126,E127,E128,E129,E131,E133
2021-04-30autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133BonfaceKilz
2021-04-30autopep8: Fix E101, E11BonfaceKilz
2021-04-30autopep8: Fix W504BonfaceKilz
2021-04-30autopep8: Fix W291, W292, W293, W391BonfaceKilz
2021-04-30autopep8: Fix E70 and E701BonfaceKilz
2021-04-30autopep8: Fix E501BonfaceKilz
2021-04-30autopep8: Fix E401BonfaceKilz
2021-04-30autopep8: Fix E301,E302,E303,E304,E305,E306BonfaceKilz
2021-04-30autopep8: Fix E20-E27BonfaceKilz
Run: python -m autopep8 --in-place --recrusive ./ --select\ E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\ E242,E251,E252,E26,E265,E266,E27 -p 3
2021-04-29I think the import of collect.py got removed with recent changes, so I'm ↵zsloan
adding it back
2021-04-29Merge pull request #569 from zsloan/bug/network_graph_fixeszsloan
Bug/network graph fixes
2021-04-29Merge branch 'testing' into bug/network_graph_fixeszsloan
2021-04-29Fix corr_scatter_plot url to include method - without method it was throwing ↵zsloan
an error
2021-04-29Don't draw edges between a trait and itselfzsloan
2021-04-29Changed the way sample data is fetched for network graph to include parents/f1szsloan
2021-04-29Merge pull request #566 from BonfaceKilz/Feature/Add-upload-data-formsBonfaceKilz
Chore/Cosmetic-changes
2021-04-29Merge branch 'testing' into Feature/Add-upload-data-formsBonfaceKilz
2021-04-29Run `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'
2021-04-29base: trait: Remove unused functionBonfaceKilz
* wqflask/base/trait.py (jsonable_table_row): Delete it.
2021-04-29base: data_set: Remove unused methodBonfaceKilz
* wqflask/base/data_set.py (Dataset.get_accession_id): Delete it.
2021-04-29base: data_set: Apply pep-8BonfaceKilz
2021-04-29base: data_set: Remove unused methodBonfaceKilz
* wqflask/base/data_set.py (riset): Delete class method.
2021-04-29base: data_set: Rewrite data_set using @dataclassBonfaceKilz
@dataclasses should be used to hold only data. Since dataset only encapsulates data, re-writing it using a dataclass makes it more readable and easier to follow.
2021-04-29tests: test_data_set: Update testBonfaceKilz
2021-04-29tests: unit: test_data_set: Remove unused mockBonfaceKilz
2021-04-29wqflask: show_trait: Autopep-8 bufferBonfaceKilz
2021-04-29wqflask: show_trait: Remove unused imports.BonfaceKilz
* wqflask/wqflask/show_trait/show_trait.py: Delete unused imports.
2021-04-29wqflask: Add new js file for processing menu entriesBonfaceKilz
* wqflask/wqflask/static/new/javascript/dataset_select_menu_edit_trait.js: New file. Copy of dataset_select_menu_orig.js that will later modified... * wqflask/wqflask/templates/edit_trait.html: Use :point_up:.
2021-04-29templates: edit_trait.html: Trim form to only contain selection menuBonfaceKilz
2021-04-29templates: edit_trait.html: Add extra fields for the formBonfaceKilz
Add form elements for selecting group, type, and dataset. This mimics the home page.
2021-04-29templates: edit_trait.html: Add comment headersBonfaceKilz
The comment headers mark different sections.
2021-04-29wqflask: views: Add new function for selecting a datasetBonfaceKilz
* wqflask/wqflask/views.py(edit_trait_page): New function.
2021-04-29templates: edit_trait.html: New fileBonfaceKilz
Copy of submit_trait.html. This is a copy; that'll form the basis of the new edit page.
2021-04-29wqflask: views: Replace dict de-structuring with kw argumentsBonfaceKilz
* wqflask/wqflask/views.py (submit_trait_form): Use kw arguments when passing variables to the template. This is more readable.
2021-04-28Merge pull request #568 from zsloan/bug/fix_gemma_temptrait_covariateszsloan
Fix the way temp traits are displayed when selecting covariates from a collection
2021-04-28Added 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)
2021-04-28Merge pull request #567 from zsloan/bug/fix_gemma_temptrait_covariateszsloan
Account for temp traits when adding covariates with GEMMA mapping
2021-04-28Account for temp traits when adding covariates with GEMMA mappingzsloan
2021-04-28wqflask: views: Delete stale commentsBonfaceKilz
2021-04-28wqflask: views: Apply pep-8BonfaceKilz
2021-04-28Use right block level commentsBonfaceKilz
2021-04-28Remove stale commentsBonfaceKilz
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