Age | Commit message (Collapse) | Author |
|
permutations aren't used
|
|
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.
|
|
|
|
|
|
Added scroller to trait page and changed sample tables to use it
|
|
|
|
Some trait page width changes
|
|
CSS file instead of setting it as a style in initialize_show_trait_tables.js
|
|
Change some column widths/headers in search and view collection pages
|
|
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"
|
|
Tests/add extra tests for collections
|
|
* wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8
* wqflask/wqflask/collect.py: Ditto
* wqflask/base/trait.py: Ditto
|
|
* wqflask/tests/wqflask/test_collect.py: Add it.
|
|
Fixed issue where new phenotype groups wouldn't be saved to the self.…
|
|
* 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
|
|
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
|
|
* 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
|
|
expand/shrink with screen size and make drop-downs a better width
* wqflask/wqflask/templates/show_trait_calculate_correlations.html - Adjusted widths of drop-down divs and removed the col-width class from the description div (the right side) so it can shrink wqwith screen size
|
|
descriptions to shrink to a smaller width (but not too small)
* wqflask/wqflask/templates/show_trait.html - Changed width of main container div to 700px
|
|
|
|
Checked if owner_id is "none" to avoid an error when trying to access…
|
|
|
|
Temp Trait Scatterplot Error Fix
|
|
matrix), append the group name to Temp dataset names so temp traits can be used in scatterplot
* wqflask/wqflask/correlation/corr_scatter_plot.py - Create the dataset object using the group name included with Temp dataset names (which take the form "Temp_(group_name)")
* wqflask/wqflask/templates/correlation_matrix.html - Change scatterplot links to include the group name if the dataset name is "Temp"
* wqflask/wqflask/templates/correlation_page.html - Change scatterplot links to include the group name if the dataset name is "Temp" + a couple minor style changes
|
|
Made change that should fix error when trying to change page text usi…
|
|
* wqflask/wqflask/docs.py - Changed query to include casting as binary to deal with certain unicode characters in ckeditor pages
* wqflask/wqflask/views.py - Imported update_text from Docs since it previously wasn't updated, causing an error when attempting to update text
|
|
Index page dropdown/textarea fix
|
|
with certain window widths
* wqflask/wqflask/templates/index_page_orig.html - Changed the left/right div's padding to prevent them from overlapping and changed the textareas' styles to make them only expandable vertically
|
|
* wqflask/wqflask/static/new/javascript/show_trait.js - Replaced "+" with "and" when Invert and another transform are combined and capitalized "Transform"
|
|
* wqflask/wqflask/static/new/javascript/show_trait.js
- Changed transform options to only apply to original values, with the exception of the "invert" transform and rows where the value was set to "x"
- Only run "check_if_zero_to_one_vals" once on page load instead of running it every time a transform is run
- Changed Transform text to reflect when there's a combination of Invert and some other transform
- Updated Reset function to use DataTables API
|
|
* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - simplified if statements to just say if(js_data.se_exists) instead of if(js_data.se_exists === true)
|
|
other JS code and move all local JS code below third-party libraries
* wqflask/wqflask/templates/show_trait.html - Changed order of JS imports
|
|
are no negative values
* wqflask/wqflask/templates/show_trait_transform_and_filter.html - made sqrt option contingent on no negative values
|
|
* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - Apparently "true" in js_data was a boolean instead of a string, so the previous if statements weren't working properly
|
|
fixed them to take into account blocked samples
* wqflask/wqflask/static/new/javascript/show_trait.js - Changed transform/normalize functions to use DataTables API to fetch and change values and also changed the way that code is structured to avoid a lot of duplicated code
|
|
input elements in the form (so form submission can work with Scroller)
* wqflask/wqflask/static/new/javascript/show_trait.js - Added function "get_table_contents_for_form_submit" that is called with submit_special (that is called for correlations and mapping from the trait page)
|
|
and show_trait_mapping_tools.js. The latter now just calls the function from the former
* wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js - Everything in this file was previously inside its own function, which made its functions unable to access the functions from show_trait.js (and necessitated it having its own "copy" of the submit_special function
|
|
resource manager page with newly added datasets
* wqflask/wqflask/resource_manager.py - Only get owner user info conditional on owner_id not being "none" (which it will be by default for newly added datasets). Previously it would throw an error due to "owner_info" being None
|
|
Corr matrix error fix
|
|
corr_matrix_error_fix
|
|
Table sort error fix
|
|
shared samples are < 2 instead of 0; this fixed the error when running
the correlation matrix, but results in the PCA traits having no values
* wqflask/wqflask/correlation_matrx/show_corr_matrix.py - changed
"if num_overlap == 0" to "if num_overlap < 2" because correlations can't
be run if there are fewer than 2 shared samples (and previously would
throw an error if there was exactly 1 shared sample)
|
|
page
* wqflask/wqflask/templates/correlation_page.html - Added
natural-minus-na type to columns that can contain N/A values, since I
apparently forgot to add it to this table before
|
|
didn't sort all rows when a table is paginated and has more than one
page
* wqflask/wqflask/static/new/javascript/search_results.js - Added
"extract_inner_text" function for getting the inner text from a string
containing HTML in order to avoid using DataTables' orderDataType (which
can only fetch values directly from the DOM, which is why sorting wasn't
working with multiple pages), and also included this function in the
"natural-minus-na" data type (so columns can be sorted that contain both
HTML/links and N/A values)
* wqflask/wqflask/templates/collections/view.html - Changed record column
to use "natural-minus-na" sort method in order to fix the inner-text
sorting issue + added sorting to the checkbox column (in the same way as
it already works in the search result page)
* wqflask/wqflask/templates/search_results_page.html - Replaced the
columns that used orderDataType with using the updated
"natural-minus-na" data type
* wqflask/wqflask/templates/correlation_page.html - Fixed issue where
N/As in the Year column (for phenotype correlations) were still displayed as links
|
|
* wqflask/base/data_set.py - TempDataSet class contained some code
referring to the SQL DB, but temp traits aren't stored in the SQL DB anymore
|
|
Misc rob changes
|
|
caused there to be a small line between buttons when hovering over them
(because the <a> tags were wider than the button itself); this was
changed to instead just be an "onclick" on the button (which is also a
bit more concise)
* wqflask/wqflask/templates/show_trait_details.html - Replaced <a> tags
with onclick for trait page link-out buttons
|
|
to work with the figure we used before switching to Plotly. This feature
will need to be redone to work with Plotly
* wqflask/wqflask/templates/show_trait_statistics.html - commented out
Color By Trait button until it's reimplemented
|
|
* wqflask/wqflask/static/new/css/show_trait.css - Adding position
relative and a 2px offset for glyphicons to make them better align with
button text
* wqflask/wqflask/templates/collections/view.html - Added glyphicon to
Download button, changed a couple head names (Peak Location and Effect
Size), made Location and Peak Location columns the same width, and made
the "?" glossary links a little larger and red
* wqflask/wqflask/templates/search_result_page.html - same as above
* wqflask/wqflask/templates/show_trait_edit_data.html - Added glyphicon
to Export button
|
|
displayed in the "view collection" page
* wqflask/wqflask/templates/collections/view.html - Apparently the
correct way to check if a value can be cast to a float in Jinja2 is to
say "value != 0"; it previous said "value > 0" which exlcuded all
negative values
|