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2020-11-17use better function namesAlexanderlacuna
2020-11-12refactor codeAlexanderlacuna
2020-11-12add pep8 fixes in marker_regression/gemma_mapping.pyAlexanderlacuna
2020-11-12add test for parse gemma output in marker_regression/gemma_mapping.pyAlexanderlacuna
2020-11-12modify tests for marker regressionAlexanderlacuna
2020-11-11add tests for marker_regression/rqtl_mapping.pyAlexanderlacuna
2020-11-11add tests for marker_regression/qtlreaper_mapping.pyAlexanderlacuna
2020-11-11add tests for marker_regression/run_mapping.pyAlexanderlacuna
2020-11-11add tests for marker_regression/gemma_mapping.pyAlexanderlacuna
2020-11-10add tests for write input for browser in marker_regression/run_mapping.pyAlexanderlacuna
2020-11-10add tests for export_mapping_results in marker_regression/run_mapping.pyAlexanderlacuna
2020-11-09correct typo and variable namingAlexanderlacuna
2020-11-09refactor test_run_gemma functionAlexanderlacuna
2020-11-09remove whitespace in marker_regressionAlexanderlacuna
2020-11-09remove unnecessary side_effect set to NoneAlexanderlacuna
2020-11-09add tests for geno_db_exists in marker_regression/run_mapping.pyAlexanderlacuna
2020-11-09add test for get_genofile_samplelist in marker_regression/run_mapping.pyAlexanderlacuna
2020-11-09mock logger in marker_regression/gemma_mapping.pyAlexanderlacuna
2020-11-09add test for run_gemma function in marker_regression/gemma_mapping.pyAlexanderlacuna
2020-11-09refactor marker_regression/gemma-mapping.py run-gemma function to avoid ↵Alexanderlacuna
Index Error
2020-11-08add tests for marker_regression/plink_mapping.pyAlexanderlacuna
2020-11-08add tests for marker_regression/gemma_mappingAlexanderlacuna
2020-11-08Change defaultline argument in the build_line_list from None to empty stringAlexanderlacuna
2020-11-06Removed the page selection from the top of the table because it created an ↵zsloan
awkward gap between the column show/hide buttons and the table, and this table will be changed to use Scroller instead of paging soon regardless
2020-11-06Changed the show/hide column buttons to use DataTables API + a few other ↵zsloan
changes (for some reason none of my changes could be pushed from one of my local branches to origin/testing, so they're combined in this commit) - Fixed a couple column header glossary links to point to GN1 - Added trait_list.css for styling a couple elements common to similar pages (like correlations or view collection)
2020-11-06Added min-width for the divs containing the analysis tools and table ↵zsloan
options, since they would look weird if the window shrunk below a certain width Also made some indentation more consistent
2020-11-06Added new css file for pages that have trait list tables (not sure what else ↵zsloan
to call them, but pages like search results, view collection, and correlation results)
2020-11-06Increased the min-width for the show_trait page container div for all the ↵zsloan
accordion sections, since previously it could get too narrow and cause text to extend beyong the borders of each accordion area
2020-11-06After I changed some class names in the trait page to use - instead of _ (to ↵zsloan
keep naming consistent) I forgot to change the references in show_trait_mapping_tools.js (which broke the functionality of clicking a tab doing mapping)
2020-11-04Merge pull request #480 from zsloan/bug/correlation_sort_fixzsloan
Fix sorting on the Tissue and Literature r/rho columns in correlation page
2020-11-04Changed numeric-html sorting for the Tissue/Lit r columns to ↵zsloan
natural-minus-na so it deals with the "--" values * wqflask/wqflask/templates/correlation_page.html - Replaced numeric-html sorting with natural-minus-na for the lit/tissue r columns
2020-11-04Merge pull request #475 from Alexanderlacuna/test-showtraitBonfaceKilz
Add more tests for show trait module
2020-11-04correct a typoAlexanderlacuna
2020-11-04remove extra whitespaceAlexanderlacuna
2020-11-04remove whitespace in line 119-120Alexanderlacuna
2020-11-04remove whitespaceAlexanderlacuna
2020-11-04remove whitespace and assertIsAlexanderlacuna
2020-11-03Merge pull request #479 from zsloan/bug/haplotype_analyst_error_fixzsloan
Bug/haplotype analyst error fix
2020-11-03Changed the syntax for the "sort" function in the docstring of GeneralObject ↵zsloan
to be compatible with Python 3 syntax * wqflask/base/GeneralObject.py - edited docstring to be correct for Python 3
2020-11-03Fixed a sort used when doing the haplotype analysis to be compatible with ↵zsloan
Python 3 * wqflask/wqflask/marker_regression/display_mapping_results.py - The arguments for sort are different in Python 3, so it was changed to be compatible
2020-11-03Merge pull request #478 from zsloan/loading_page_n_fixzsloan
Joined sample names in primary_samples and all_samples with commas be…
2020-11-03Joined sample names in primary_samples and all_samples with commas because ↵zsloan
this list was being split to get the N of samples; not sure why this was working before * wqflask/wqflask/show_trait/show_trait.py primary_samples and all_samples passed as hidden form inputs now have names split by commas so they can be counted correctly when displaying the N on the mapping loading screen
2020-11-03Update issue and PR templatesBonfaceKilz
* .github/ISSUE_TEMPLATE/bug_report.md: Provide explanations in commented out blocks. * .github/ISSUE_TEMPLATE/feature_request.md: Ditto. * .github/PULL_REQUEST_TEMPLATE.md: Ditto. * .github/ISSUE_TEMPLATE/user_story.md: Ditto.
2020-11-03Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵Alexanderlacuna
test-showtrait
2020-11-03remove unnecessary commentsAlexanderlacuna
2020-11-03add pep8 formattingAlexanderlacuna
2020-11-03add tests for the get_categorical_variables functionAlexanderlacuna
2020-11-03switch from assertFalse to assertIsAlexanderlacuna
2020-11-03Remove stale fileBonfaceKilz
* jquery.qtip.css: Delete it.
2020-11-03switch from assertTrue/False to assertIs to make the tests tighterAlexanderlacuna
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