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2020-10-29Replace map on strip with a list comprehension that calls strip()BonfaceKilz
* scripts/maintenance/readProbeSetSE_v7.py: In Python3 you can't map string.strip on a list of strings. Instead use a list comprehension and apply strip() on each element of the list. * wqflask/wqflask/marker_regression/plink_mapping.py: Ditto. * wqflask/wqflask/snp_browser/snp_browser.py: Ditto.
2020-10-28Merge pull request #468 from zsloan/export_fixzsloan
Fixed trait page export issue caused by Scroller
2020-10-28Fixed trait page export to work with Scroller + added metadata for ↵zsloan
non-Phenotype traits and column headers * wqflask/wqflask/show_trait/export_trait_data.py - Added metadata for non-Phenotype traits and column headers (which didn't previously exist) * wqflask/wqflask/static/new/javascript/show_trait.js - Changed export_sample_table_data to use DataTables API instead of just selecting from the DOM with JQuery
2020-10-27Merge pull request #467 from zsloan/gsearch_encoding_fixzsloan
Remaining gsearch encoding fix for ProbeSet description
2020-10-27Cast ProbeSet description as binary to fix encoding issue on global search pagezsloan
* wqflask/wqflask/gsearch.py - Cast ProbeSet description as binary
2020-10-27Merge pull request #466 from zsloan/show_trait_attributes_fixzsloan
Fix issue where attribute values were displayed in the wrong columns
2020-10-27Get the "first_attr_start_pos" from a samplelist instead of from each ↵zsloan
individual sample, because it was previously causing problems when only some samples had an N * wqflask/base/webqtlCaseData.py - Removed code getting first_attr_start_pos * wqflask/wqflask/show_trait/SampleList.py - Added code getting first_attr_start_pos and assigning it to all samples + removing one unnecessary sort * wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - Fixed issue that was causing the N column to not be displayed
2020-10-27Cast post and pre-publication descriptions into binaryBonfaceKilz
* wqflask/wqflask/gsearch.py (GSearch): There's an exception thrown when the decode method is called on that description string. If the casting is absent, and the decode statements are removed, the some characters get broken.
2020-10-27Merge pull request #465 from Alexanderlacuna/test-branchBonfaceKilz
add test for trait_data
2020-10-27switch from single quote to double quoteAlexanderlacuna
2020-10-27address failuresAlexanderlacuna
2020-10-27added changes to fileAlexanderlacuna
2020-10-27modified to use pep8 standardsAlexanderlacuna
2020-10-27Merge pull request #422 from BonfaceKilz/build/python3-migrationBonfaceKilz
Build/python3 migration
2020-10-26Merge pull request #463 from BonfaceKilz/feature/add-load-metrics-to-footerBonfaceKilz
Add page load metrics to footer
2020-10-26modified test fileAlexanderlacuna
2020-10-26Add page load metrics to footerBonfaceKilz
* wqflask/wqflask/__init__.py (before_request): New function. Add method for calculating total request_time to global context. * wqflask/wqflask/templates/base.html: - Display total server load time. - Display total page rendering time, and add js functionality to calculate it.
2020-10-23Merge pull request #462 from zsloan/fix_export_errorzsloan
Fixed trait export for situations where there's no authors/title/journal
2020-10-23Fixed trait export for situations where there's no authors/title/journalzsloan
2020-10-22Merge pull request #460 from zsloan/move_styling_to_csszsloan
Move styling to css
2020-10-22Merge pull request #461 from zsloan/mapping_y_axis_fixzsloan
Mapping y axis fix
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 pull request #442 from zsloan/scroller_testingzsloan
Added scroller to trait page and changed sample tables to use it
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
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