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2020-10-19Merge branch 'testing' into scroller_testingzsloan
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
2020-10-09Change 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.
2020-10-08Fixed 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
2020-10-08Adjusted some widths/classes to allow correlation description text to ↵zsloan
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
2020-10-08Changed the min-width of trait page main div in order to allow trait ↵zsloan
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
2020-10-08Merge pull request #452 from zsloan/authentication_bug_fixzsloan
Checked if owner_id is "none" to avoid an error when trying to access…
2020-10-08Merge pull request #455 from zsloan/temp_trait_scatterplot_fixzsloan
Temp Trait Scatterplot Error Fix
2020-10-08When generating links to correlation scatterplots (in corr results and corr ↵zsloan
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
2020-10-06Merge pull request #454 from zsloan/update_docs_fixzsloan
Made change that should fix error when trying to change page text usi…
2020-10-06Made change that should fix error when trying to change page text using ckeditorzsloan
* 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
2020-10-06Merge pull request #453 from zsloan/index_page_textarea_fixzsloan
Index page dropdown/textarea fix
2020-10-06Fixed issue where drop-down arrows and textarea corners couldn't be clicked ↵zsloan
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
2020-10-05Replaced "+" with "and" in transform textzsloan
* wqflask/wqflask/static/new/javascript/show_trait.js - Replaced "+" with "and" when Invert and another transform are combined and capitalized "Transform"
2020-10-05Changed the way tranform functions workzsloan
* 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
2020-10-05Simplified if statementszsloan
* 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)
2020-10-05Changed order of JS imports to both make DataTables objects available to all ↵zsloan
other JS code and move all local JS code below third-party libraries * wqflask/wqflask/templates/show_trait.html - Changed order of JS imports
2020-10-05Added square root to the transform functions that are only active if there ↵zsloan
are no negative values * wqflask/wqflask/templates/show_trait_transform_and_filter.html - made sqrt option contingent on no negative values
2020-10-05Fixed issue that was causing SE column to not show up in the trait page tablezsloan
* 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
2020-10-02Converted transform functions to use DataTables API to work with scroller + ↵zsloan
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
2020-10-02Added function that pulls input data out of table and inserts it as hidden ↵zsloan
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)
2020-10-02There were two copies of the "submit_special" function in both show_trait.js ↵zsloan
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
2020-10-02Checked if owner_id is "none" to avoid an error when trying to access the ↵zsloan
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
2020-10-01Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵zsloan
corr_matrix_error_fix
2020-09-30Changed the logic for adding 0 to the PCA results to do so when thezsloan
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)
2020-09-30Added "natural-minus-na" sorting for relevant columns in the correlationzsloan
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
2020-09-30Fixed issue where columns sorted by inner text (text inside link tags)zsloan
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
2020-09-30Removed unused code from TempDataSet classzsloan
* 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
2020-09-29Trait page link-out buttons were previously inside <a> tags, but thiszsloan
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
2020-09-29Removed "Color By Trait" button from the Bar Chart, because it was meantzsloan
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
2020-09-29Made a variety of changes to table pageszsloan
* 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
2020-09-29Fixed issue where negative additive effect values weren't beingzsloan
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
2020-09-29Changed Add (to collection) button color to match other Add buttons andzsloan
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"
2020-09-29Changed the DataTables column sort arrows to a different color byzsloan
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)
2020-09-28Changed add to collection to open the collection in a new tab/page sozsloan
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
2020-09-28Fix casting errorBonfaceKilz
* 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)*.
2020-09-28Convert None to "" in if statementBonfaceKilz
* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork error: float argument required, not NoneType)"
2020-09-28Update trait testsBonfaceKilz
* 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.
2020-09-25Fixed issue where attribute columns' alignment was offset by 1zsloan
* 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 -
2020-09-25Changed edit_data_change and block_by_index to use DataTables APIzsloan
* 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
2020-09-24Changed logic that defines the primary/other samplelists to be much morezsloan
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
2020-09-23Fix failing buildsBonfaceKilz
* wqflask/wqflask/__init__.py: Move imports from views.py to "__init__.py". Fixes failing build. * wqflask/wqflask/views.py: Ditto.
2020-09-23Fix failing testsBonfaceKilz
* wqflask/tests/base/test_trait.py: In python2 it's necessary to decode the utf-8 string.
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