Age | Commit message (Collapse) | Author |
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Fixed error when zooming into a chromosome when mapping
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Python3 switchover, so I converted it to a string
* wqflask/wqflask/marker_regression/display_mapping_results.py - cast theGO["snpCount"] as a string
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Fixed trait page export issue caused by Scroller
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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
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* wqflask/wqflask/gsearch.py - Cast ProbeSet description as binary
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Fix issue where attribute values were displayed in the wrong columns
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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
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* 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.
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add test for trait_data
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Build/python3 migration
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* 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.
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Fixed trait export for situations where there's no authors/title/journal
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Move styling to css
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permutations aren't used
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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.
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merging (there are a lot of conflicts between this and the changes that integrated Scroller)
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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
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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
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other divs that only have the styling of being inline
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* wqflask/wqflask/templates/show_trait_edit_data.html - replaced underscores with -
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* wqflask/wqflask/user_login.py (encode_password):
- Remove unused local variable "salt".
- Pass "hashfunc" as a string.
- Apply Pep-8.
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* wqflask/tests/wqflask/test_user_login.py: New tests.
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* 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.
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* wqflask/tests/wqflask/test_pbkdf2.py: New tests.
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* wqflask/wqflask/marker_regression/display_mapping_results.py:
Replace "%" strings with f-strings. Also, replace old "Href" with new
htmlgen "Link" method.
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reaper mapping
* wqflask/wqflask/templates/show_trait_mapping_tools.html - Mistakenly reversed true/false in the reaper Interval Map option
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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
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their width set in the same way as other sections of the correlation/mapping options
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* 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
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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
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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
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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
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* 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
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* 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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Some trait page width changes
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CSS file instead of setting it as a style in initialize_show_trait_tables.js
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