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2020-10-22Merge pull request #460 from zsloan/move_styling_to_csszsloan
Move styling to css
2020-10-21Removed code setting the maximum tick value to 1.15* the max LRS/LOD if ↵zsloan
permutations aren't used
2020-10-21Ensured all Y axis ticks in the mapping figure are below the top of the ↵zsloan
figure, but it would probably be ideal to scale things such that the top tick is at the top of the figure * wqflask/wqflask/marker_regression/display_mapping_results.py - Set LRS_LOD_Max (the top tick value) as the maximum value between the significant value (if permutations are used) and the max LRS/LOD value; previously it would set it as the significant value * 1.1 if the significant value exists and is higher than the max LRS/LOD value.
2020-10-20Fixing typo in JS code where "attribute_start_pos" said "attribute_start_post"zsloan
2020-10-20Fixed some problems with the previous attempt at resolving conflicts before ↵zsloan
merging (there are a lot of conflicts between this and the changes that integrated Scroller)
2020-10-20Merge branch 'testing' into move_styling_to_csszsloan
2020-10-20Added classes to replace styling in show_trait_edit_data.html to ↵zsloan
show_trait.css, replaced _ with - in class names, and changed the checkbox table cell styling to better center it * wqflask/wqflask/static/new/css/show_trait.css - Moved show_trait_edit_data.html styling to this file and changes padding for the checkbox table cell to better center it; for some reason text-align: center wasn't working and it specifically needed left-padding * wqflask/wqflask/static/new/javascript/show_trait.js - Replaced underscores with - in class names * wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js - Replaced underscores with - in class names
2020-10-20Replaced _ with - in class names (though this change will end up being ↵zsloan
unnecessary with the scroller changes that move the table initialization to a separate file) * wqflask/wqflask/templates/show_trait.html - Replaced underscores with - in class names
2020-10-20Replaced one class name with a more generic "inline-div" since there are ↵zsloan
other divs that only have the styling of being inline
2020-10-20Made class names consistently use - instead of _ in show_trait_edit_data.htmlzsloan
* wqflask/wqflask/templates/show_trait_edit_data.html - replaced underscores with -
2020-10-20Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-10-20Update how pbkdf2.pbkdf2_hex is used when encrypting passBonfaceKilz
* wqflask/wqflask/user_login.py (encode_password): - Remove unused local variable "salt". - Pass "hashfunc" as a string. - Apply Pep-8.
2020-10-20Add tests for encoding passwordBonfaceKilz
* wqflask/tests/wqflask/test_user_login.py: New tests.
2020-10-20Update pbkdf2BonfaceKilz
* wqflask/wqflask/pbkdf2.py: Remove unnecessary pbkdf2 usage docs--- it already exists in python3 stdlib--- and "__main__" section which runs the test. (imports): Delete unused imports. Add safe_str_cmp. (pbkdf2_hex): Use hashlib.pbkdf2_hmac. (safe_str_cmp): Replace with werkzeug.security.safe_str_cmp (test): Delete it. Tests moved to test_pbkdf2.py.
2020-10-20Add pbkdf2 testsBonfaceKilz
* wqflask/tests/wqflask/test_pbkdf2.py: New tests.
2020-10-20Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-10-19Merge branch 'testing' into scroller_testingzsloan
2020-10-19Update snpString linkBonfaceKilz
* wqflask/wqflask/marker_regression/display_mapping_results.py: Replace "%" strings with f-strings. Also, replace old "Href" with new htmlgen "Link" method.
2020-10-19Delete stale commentBonfaceKilz
2020-10-15Fixed issue that caused interval map setting to not work correctly for ↵zsloan
reaper mapping * wqflask/wqflask/templates/show_trait_mapping_tools.html - Mistakenly reversed true/false in the reaper Interval Map option
2020-10-15Replaced the styling in show_trait_mapping_tools.html with CSS and changed ↵zsloan
some styling to be more simple/consistent and deal better with different screen sizes * wqflask/wqflask/marker_regression/run_mapping.py - "manhattan_plot" is now passed as lower-case "true"/"false" to match the case of other boolean options * wqflask/wqflask/static/new/css/show_trait.css - Added classes for the styling in show_trait_mapping_tools.html * wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js - Changed class name "selected_covariates" to "selected-covariates" to match class naming scheme * wqflask/wqflask/static/new/javascript/show_trait.js - Changed class name "selected_covariates" to "selected-covariates" to match class naming scheme * wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js - Changed class names from using underscore to useing "-" to match class naming scheme * wqflask/wqflask/templates/show_trait_mapping_tools.html - Replaced styling with class names and changed some styling to be more simple/consistent
2020-10-15Put the correlation descriptions inside of a div so that they could have ↵zsloan
their width set in the same way as other sections of the correlation/mapping options
2020-10-15Replaced styling from show_trait_transform_and_filter.html with CSSzsloan
* wqflask/wqflask/static/new/css/show_trait.css - Added styles for elements in show_trait_transform_and_filter.html * wqflask/wqflask/templates/show_trait_transform_and_filter.html - Replaced styling in template with classes
2020-10-14Removed some commented out HTMLzsloan
2020-10-14Converted show_trait_calculate_correlations.html to use CSS instead of ↵zsloan
styling in the template * wqflask/wqflask/static/new/css/show_trait.css - Added styling for elements in show_trait_calculate_correlations.html and changed a few existing class names to be more reasonable * wqflask/wqflask/templates/show_trait.html - Changed the class name for the main div * wqflask/wqflask/templates/show_trait_calculate_correlations.html - Substituted direct styling with CSS and changing some styling to make the correlation method descriptions keep a reasonable width and position * wqflask/wqflask/templates/show_trait_statistics.html - Changed some class names to be better
2020-10-14Changed a couple class names because it's probably dumb to include the ↵zsloan
pixels in the name since that might change later * wqflask/wqflask/static/new/css/show_trait.css - Changed a couple class names * wqflask/wqflask/templates/show_trait_statistics.html - Changed a couple class names
2020-10-14Moved show_trait_statistics.html styling to show_trait.css and fixed a minor ↵zsloan
issue where not all figures had "Select Group:" before the group selection drop-down * wqflask/wqflask/static/new/css/show_trait.css - Moved styling from show_trait_statistic.html here * wqflask/wqflask/templates/show_trait_statistics.html - Replaced styling with classes, removed some unnecessary/unused styling, and added some missing label text
2020-10-13Added styling from show_trait_details.html to show_trait.csszsloan
* wqflask/wqflask/static/new/css/show_trait.css - Added the bottom margin styling for the div containing the buttons * wqflask/wqflask/templates/show_trait_details.html - Removed some unnecessary styling and moved the styling for .btn_toolbar to show_trait.css
2020-10-13Changed styling in show_trait.html to use CSS insteadzsloan
* wqflask/wqflask/static/new/css/main.css - Added CSS for min-height in table cells with checkboxes, since this would apply to all tables throughout the site * wqflask/wqflask/static/new/css/show_trait.css - Added CSS for styling that was previous in show_trait.html * wqflask/wqflask/templates/show_trait.html - Replaced directly styling with classes
2020-10-13Merge branch 'testing', remote-tracking branch 'origin' into move_styling_to_csszsloan
2020-10-13Merge pull request #456 from zsloan/misc_rob_changeszsloan
Some trait page width changes
2020-10-13Added right-alignment for trait_value_input text fields in sample table to ↵zsloan
CSS file instead of setting it as a style in initialize_show_trait_tables.js
2020-10-13Merge pull request #459 from zsloan/table_width_changeszsloan
Change some column widths/headers in search and view collection pages
2020-10-12Wrap args of print statements correctly using bracesBonfaceKilz
* wqflask/wqflask/wgcna/wgcna_analysis.py: Update print statements by wrapping then in "()". Run: "2to3-3.8 -w wqflask/wqflask/wgcna/wgcna_analysis.py"
2020-10-12Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-10-09Change some column and overall table widths for search result table and view ↵zsloan
collections table + changed "Max LRS" column header to "High P" * wqflask/wqflask/templates/collections/view.html - changed column widths and "Max LRS" header to "High P" * wqflask/wqflask/templates/search_result_page.html - changed column widths and "Max LRS" header to "High P"
2020-10-09Merge pull request #458 from BonfaceKilz/tests/add-extra-tests-for-collectionsBonfaceKilz
Tests/add extra tests for collections
2020-10-09Apply PEP 8 to bufferBonfaceKilz
* wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8 * wqflask/wqflask/collect.py: Ditto * wqflask/base/trait.py: Ditto
2020-10-09Add test for process_traits from collections.pyBonfaceKilz
* wqflask/tests/wqflask/test_collect.py: Add it.
2020-10-09Fix export function on traits and analysis pageBonfaceKilz
* wqflask/wqflask/views.py (export_trait_excel): Write data as bytes instead of strings. See: https://stackoverflow.com/questions/32075135/python-3-in-memory-zipfile-error-string-argument-expected-got-bytes * wqflask/wqflask/show_trait/export_trait_data.py: Convert cmp function into a key function.
2020-10-09Update base64 conversionBonfaceKilz
2020-10-09Replace string concat("+") with python3's f-stringBonfaceKilz
2020-10-09Replace "ncores" with "nthreads" param to r_CTLscanBonfaceKilz
2020-10-09Use built-in array as a named importBonfaceKilz
* wqflask/wqflask/wgcna/wgcna_analysis.py (WGCNA.render_image): Use named import method. This is a workaround for using explicitly using "array" which conflicts with something else in the namespace.
2020-10-09Update base64 conversionBonfaceKilz
* wqflask/wqflask/wgcna/wgcna_analysis.py (WGCNA.render_image): Use Python3's base64 library from the stdlib to perform conversion. * wqflask/wqflask/ctl/ctl_analysis.py (CTL.loadImage): Ditto.
2020-10-09Convert cmp function into a key functionBonfaceKilz
* wqflask/wqflask/correlation_matrix/show_corr_matrix.py (sortEigenVectors): Convert the comparison function into a key function. See: https://docs.python.org/3/howto/sorting.html#the-old-way-using-the-cmp-parameter
2020-10-09Apply PEP-8 formattingBonfaceKilz
2020-10-08Fixed remaining issue that applies to all dataset typeszsloan
* wqflask/base/data_set.py - Fixed issue where there was an error when trying to take the len of the query results when there were no results
2020-10-08Fixed issue where new phenotype groups wouldn't be saved to the ↵zsloan
self.datasets property because the group name was used as the key (instead of the group name + "Publish", which is the full dataset name for phenotypes) * wqflask/base/data_set.py - Set "group_name" as a separate variable from "name" to avoid it being used as the key in self.datasets
2020-10-08Allowed mapping method description text to shrink with screen sizezsloan
* wqflask/wqflask/templates/show_trait_mapping_tools.html - Removed the "col-xs-_" class to allow the div containing mapping description text to shrink with screen size
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