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2020-11-11Switched checking if a trait is confidential to checking if it has a pubmed ↵zsloan
ID for the purposes of showing pre-publication abbreviation/description
2020-11-10* wqflask/wqflask/correlation/show_corr_results.py - Changed some of the ↵zsloan
parameters sent to the correlation table * wqflask/wqflask/templates_correlation_page.html - Fixed some column defs and removed unused table configuration code
2020-11-10Added CSS file for all pages that include a table of traitszsloan
2020-11-05Converted correlation table for ProbeSet target datasets to use the JSON ↵zsloan
input and removed the unused table html
2020-11-05Added some additional necessary fields to generate_corr_json in ↵zsloan
show_corr_results.py
2020-11-05Removed html from generate_corr_json since that will be done by the column ↵zsloan
definitions after passing the data to DataTables as JSON
2020-11-05Imported Scroller and used it with correlation page tablezsloan
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
2020-11-03use assertTrue and assertFalse in while testing booleanAlexanderlacuna
2020-11-02Merge pull request #476 from zsloan/correlation_errors_fixzsloan
Correlation errors fix
2020-11-02Created function for encoding the column value as bytes when fetching from ↵zsloan
the JSON-formatted string pulled from Redis (since this was needed after the Python 3 switchover) * wqflask/utility/redis_tools.py - Created function load_json_from_redis that encodes the key (column_value) when fetching a value from the JSON pulled from Redis
2020-11-02Changed correlation page logic to skip over traits that share fewer than 6 ↵zsloan
samples + traits that user doesn't have permission to access * wqflask/wqflask/correlation/show_corr_results.py - Moved the num_overlap check so that it never attempts to calculate the correlation if it's too low + checked if trait_object is None in the main loop (since it would be returned as None if the user doesn't have permissions
2020-11-02add better formattingAlexanderlacuna
2020-11-02add function docstringAlexanderlacuna
2020-11-02add tests for show trait moduleAlexanderlacuna
2020-11-01Merge pull request #472 from Alexanderlacuna/test-branchBonfaceKilz
Adding more Test for show_trait module
2020-10-31Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵Alexanderlacuna
test-branch
2020-10-31Removed a line adding the ceiling of the Max LRS to the Y axis, since it has ↵zsloan
the potential to cause an axis tick to appear above the figure * wqflask/wqflask/marker_regression/display_mapping_results.py - Removed a line adding the ceiling of the max LRS/LOD value to the Y axis
2020-10-31remove redundant classesAlexanderlacuna
2020-10-31use descriptive variable namesAlexanderlacuna
2020-10-31Use more descriptive variable and class namesAlexanderlacuna
2020-10-30Merge pull request #474 from zsloan/mapping_y_axis_fixzsloan
Mapping Y Axis Fix
2020-10-30Removed a line adding the ceiling of the Max LRS to the Y axis, since it has ↵zsloan
the potential to cause an axis tick to appear above the figure * wqflask/wqflask/marker_regression/display_mapping_results.py - Removed a line adding the ceiling of the max LRS/LOD value to the Y axis
2020-10-30add test for get_export_metadataAlexanderlacuna
2020-10-30Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵Alexanderlacuna
test-branch
2020-10-29Merge pull request #473 from zsloan/reaper_bootstrap_fixzsloan
Reaper bootstrap fix
2020-10-29Fixed issue with single-chromosome mapping after the bootstrap fix and fixed ↵zsloan
error that occurred if either bootstrap or permutations were set to 0 * wqflask/wqflask/marker_regression/display_mapping_results.py - Cast self.qtlresults 'chr' as a string since the comparison between it and the chromosome names was faililng due to numeric chromosomes being int type + used a list comprehension that converts None to an empty string when creating a comma-joined string from the list of mapping output files
2020-10-29Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵zsloan
reaper_bootstrap_fix
2020-10-29add test for show_traitAlexanderlacuna
2020-10-29Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵Alexanderlacuna
test-branch
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