| Age | Commit message (Expand) | Author |
|---|
| 2020-10-19 | Merge branch 'testing' into scroller_testing | zsloan |
| 2020-10-13 | Merge pull request #456 from zsloan/misc_rob_changes...Some trait page width changes | zsloan |
| 2020-10-13 | Added right-alignment for trait_value_input text fields in sample table to CS... | zsloan |
| 2020-10-13 | Merge pull request #459 from zsloan/table_width_changes...Change some column widths/headers in search and view collection pages | zsloan |
| 2020-10-09 | Change some column and overall table widths for search result table and view ......* 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"
| zsloan |
| 2020-10-09 | Merge pull request #458 from BonfaceKilz/tests/add-extra-tests-for-collections...Tests/add extra tests for collections | BonfaceKilz |
| 2020-10-09 | Apply PEP 8 to buffer...* wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8
* wqflask/wqflask/collect.py: Ditto
* wqflask/base/trait.py: Ditto
| BonfaceKilz |
| 2020-10-09 | Add test for process_traits from collections.py...* wqflask/tests/wqflask/test_collect.py: Add it.
| BonfaceKilz |
| 2020-10-08 | Fixed remaining issue that applies to all dataset types...* 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
| zsloan |
| 2020-10-08 | Fixed issue where new phenotype groups wouldn't be saved to the self.datasets......* 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
| zsloan |
| 2020-10-08 | Allowed mapping method description text to shrink with screen size...* 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
| zsloan |
| 2020-10-08 | Adjusted some widths/classes to allow correlation description text to expand/......* 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
| zsloan |
| 2020-10-08 | Changed the min-width of trait page main div in order to allow trait descript......* wqflask/wqflask/templates/show_trait.html - Changed width of main container div to 700px
| zsloan |
| 2020-10-08 | Merge pull request #452 from zsloan/authentication_bug_fix...Checked if owner_id is "none" to avoid an error when trying to access… | zsloan |
| 2020-10-08 | Merge pull request #455 from zsloan/temp_trait_scatterplot_fix...Temp Trait Scatterplot Error Fix | zsloan |
| 2020-10-08 | When generating links to correlation scatterplots (in corr results and corr m......* 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
| zsloan |
| 2020-10-06 | Merge pull request #454 from zsloan/update_docs_fix...Made change that should fix error when trying to change page text usi… | zsloan |
| 2020-10-06 | Made change that should fix error when trying to change page text using ckeditor...* 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
| zsloan |
| 2020-10-06 | Merge pull request #453 from zsloan/index_page_textarea_fix...Index page dropdown/textarea fix | zsloan |
| 2020-10-06 | Fixed issue where drop-down arrows and textarea corners couldn't be clicked w......* 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
| zsloan |
| 2020-10-05 | Replaced "+" with "and" in transform text...* wqflask/wqflask/static/new/javascript/show_trait.js - Replaced "+" with "and" when Invert and another transform are combined and capitalized "Transform"
| zsloan |
| 2020-10-05 | Changed the way tranform functions work...* 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
| zsloan |
| 2020-10-05 | Simplified if statements...* 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)
| zsloan |
| 2020-10-05 | Changed order of JS imports to both make DataTables objects available to all ......* wqflask/wqflask/templates/show_trait.html - Changed order of JS imports
| zsloan |
| 2020-10-05 | Added square root to the transform functions that are only active if there ar......* wqflask/wqflask/templates/show_trait_transform_and_filter.html - made sqrt option contingent on no negative values
| zsloan |
| 2020-10-05 | Fixed issue that was causing SE column to not show up in the trait page table...* 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
| zsloan |
| 2020-10-02 | Converted transform functions to use DataTables API to work with scroller + f......* 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
| zsloan |
| 2020-10-02 | Added function that pulls input data out of table and inserts it as hidden in......* 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)
| zsloan |
| 2020-10-02 | There were two copies of the "submit_special" function in both show_trait.js ......* 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
| zsloan |
| 2020-10-02 | Checked if owner_id is "none" to avoid an error when trying to access the res......* 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
| zsloan |
| 2020-10-01 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into corr_matri... | zsloan |
| 2020-09-30 | Changed the logic for adding 0 to the PCA results to do so when the...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)
| zsloan |
| 2020-09-30 | Added "natural-minus-na" sorting for relevant columns in the correlation...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
| zsloan |
| 2020-09-30 | Fixed issue where columns sorted by inner text (text inside link tags)...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
| zsloan |
| 2020-09-30 | Removed unused code from TempDataSet class...* 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
| zsloan |
| 2020-09-29 | Trait page link-out buttons were previously inside <a> tags, but this...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
| zsloan |
| 2020-09-29 | Removed "Color By Trait" button from the Bar Chart, because it was meant...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
| zsloan |
| 2020-09-29 | Made a variety of changes to table pages...* 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
| zsloan |
| 2020-09-29 | Fixed issue where negative additive effect values weren't being...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
| zsloan |
| 2020-09-29 | Changed Add (to collection) button color to match other Add buttons and...changed the text for the GN1 link button
* wqflask/wqflask/templates/show_trait_details.html - Changed Add button
class to btn-success (to make it green like the other Add buttons) and
changed text from "View in GN1" to "Go to GN1"
| zsloan |
| 2020-09-29 | Changed the DataTables column sort arrows to a different color by...changing the image they're referencing
* wqflask/wqflask/templates/base.html - Added CSS changing the table
sort arrow image directly into
base.html because it requires using url_for to reference the images in
the GUIX profile (so it needs to be in the template and can't just be
added to a CSS file)
| zsloan |
| 2020-09-28 | Changed add to collection to open the collection in a new tab/page so...the results on the initial page aren't lost
* wqflask/wqflask/static/new/javascript/search_results.js - Changed the
add to collection method name to "add_to_collection" because it was
previously "add" which is a terrible method name
* wqflask/wqflask/templates/collections/add.html - Added target="_blank"
to the add to collection form so it will open in a new tab/window
| zsloan |
| 2020-09-28 | Fix casting error...* wqflask/base/trait.py (retrieve_trait_info): If the
description_string or discription_display value return a None object,
evaluate to an empty string. Fixes errors related to *len(None)*.
| BonfaceKilz |
| 2020-09-28 | Convert None to "" in if statement...* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork
error: float argument required, not NoneType)"
| BonfaceKilz |
| 2020-09-28 | Update trait tests...* wqflask/tests/base/test_trait.py
(test_retrieve_trait_info_with_non_empty_lrs): Check
trait.LRS_score_repr is set correctly if trait.lrs is None.
(test_retrieve_trait_info_with_empty_lrs_field): Check
trait.LRS_score_repr and test_trait.LRS_location_repr is set correctly
if trait.lrs is None.
(test_retrieve_trait_info_with_empty_chr_field): Check
test_trait.LRS_score_repr and test_trait.LRS_location_repr is set
correctly if trait.locus is None.
| BonfaceKilz |
| 2020-09-25 | Fixed issue where attribute columns' alignment was offset by 1...* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
- attribute cells' alignment and column names were wrong because they were referring to an attribute offset by 1 in the attribute list
-
| zsloan |
| 2020-09-25 | Changed edit_data_change and block_by_index to use DataTables API...* wqflask/wqflask/static/new/javascript/show_trait.js - Changed
edit_data_change to use DataTables API to fetch the list of names,
values, and (where applicable) standard errors in a way that just looks
at those columns (previously it iterated through all rows).
block_by_index was also changed to look just at columns
| zsloan |
| 2020-09-24 | Changed logic that defines the primary/other samplelists to be much more...efficient
* wqflask/wqflask/show_trait/show_trait.py - Add an "if" statement to
avoid unnecessarily running some code and changed a list to a set for
the purposes of searching if it contains an element
| zsloan |
| 2020-09-23 | Fix failing builds...* wqflask/wqflask/__init__.py: Move imports from views.py to
"__init__.py". Fixes failing build.
* wqflask/wqflask/views.py: Ditto.
| BonfaceKilz |
| 2020-09-23 | Fix failing tests...* wqflask/tests/base/test_trait.py: In python2 it's necessary to
decode the utf-8 string.
| BonfaceKilz |
