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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
2020-09-25Fixed 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
2020-09-22Changed JS on trait page that updates basic stats and graphs/figures tozsloan
use the DataTables API to pull sample values * wqflask/wqflask/static/new/javascript/show_trait.js - Changed the way sample name/val/var are pulled from the table to instead use DataTables' API + removed an unused event listener * wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - added "var" before a defined variable for consistency
2020-09-18Made some style changes with whitespace/line-breakszsloan
2020-09-18Made a bunch of changes to move trait page DataTables initialization tozsloan
a separate file (initialize_show_trait_tables.js). The biggest complication was getting the order of attributes in the rows to sync with the order of atribute namees in the column headers. Previously this logic was all in the template. * wqflask/base/webqtlCaseData.py - added attribute first_attr_col as a very awkward solution to passing the column position into the column render function in situations where there are case attribute columns (which can be variable in number) * wqflask/wqflask/show_trait/show_trait.py - Replace "attribute_names" in js_data with "attributes" (which allows the JS access to more information) and also pass new se_exists and has_num_cases variables with js_data, so the javascript has access to whether or not those columns exist in the table * wqflask/wqflask/static/new/javascript/show_trait.js - Change case attribute-related logic to use js_data.attributes instead of js_data.attribute_names * wqflask/wqflask/templates/show_trait.html - Removed table initialization from template * wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - new file that initializes tables and reproduces what the template logic used to do with JS logic
2020-09-16Changed references to se_exists to just get it as a property ofzsloan
SampleList instead of calling the method * wqflask/wqflask/show_trait/show_trait.py - see above * wqflask/wqflask/templates/show_trait.html - see above + removed some commented out code
2020-09-16Changed se_exists to a property so the SampleList instance can includezsloan
that when converted to a dict (which is needed to use it in the javascript) * wqflask/wqflask/show_trait/SampleList.py - Directly set se_exists as a property of SampleList instead of requiring a method be called; I could have set self.se_exists by calling the se_exists method, but that would have resulted in the convoluted line "self.se_exists = self.se_exists()" and the se_exists method only consisted of one line anyways
2020-09-16Applied PEP8 and removed commented out codezsloan
2020-09-15Added scroller to trait page and changed sample tables to use itzsloan
* wqflask/wqflask/templates/show_trait.html - Imported scroller (from the Google cdn temporarily for testing) and activated it for the sample tables, as well as disabled options that conflicted with it (like paging: false)
2020-09-08Changed the Add button color for all the different pages that use itzsloan
* wqflask/wqflask/templates/collections/view.html - changed Add button color * wqflask/wqflask/templates/correlation_matrix.html - changed Add button color * wqflask/wqflask/templates/correlation_page.html - changed Add button color * wqflask/wqflask/templates/mapping_results.html - changed Add button color * wqflask/wqflask/templates/search_result_page.html - changed Add button color
2020-09-08Search code now checks if there are more than 50,000 results beforezsloan
running the code that queries the DB for max LRS locus information (which is what takes the most time to run) and sets a variable that indicates to the template (search_results.html) that it shouldn't show the results * wqflask/wqflask/search_results.py - Check number of results from base query in order to prevent certain searches from running too long
2020-09-08Changed regular and global search results table to use the new sortzsloan
method that always places NAs at bottom, changed the Add to Collection button's color, and added something to the regular search page template to display alternative text if there are more than 50000 results * wqflask/wqflask/templates/gsearch_gene.html - Added natural-minus-na sort to certain columns and changed Add button color * wqflask/wqflask/templates/gsearch_pheno.html - Added natural-minus-na sort to certain columns and changed Add button color * wqflask/wqflask/templates/search_result_page.html - Added natural-minus-na sort to certain columns, changed Add button color, and added template logic that shows alternative text if there are more than 50,000 results
2020-09-08Added a sort function (derived from the natural sort import) that alwayszsloan
places N/As at the bottom regardless of search direction * wqflask/wqflask/static/new/javascript/search_results.js - created "natural-minus-na" sort
2020-09-04Update how static js/ css files are fetchedBonfaceKilz
* wqflask/wqflask/views.p:(css, js) Add "css" router decorator. Also, if "js_alt" is in path, fetch the file from "GUIX_PROFILE/share/javascript" instead of the default directory: "GUIX_PROFILE/share/genenetwork2/javascript" See: <https://github.com/genenetwork/genenetwork2/issues/436>
2020-09-01There was a missing quote in one of the javascript imports added by thezsloan
PR changing them to get fetched from GUIX; I need to check and see if there are other situations like this * wqflask/wqflask/templates/mapping_results.html - Added missing quote
2020-09-01Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-09-01Fixed indent issue that could cause error when showing the haplotypezsloan
analyst in the mapping chromosome view * wqflask/wqflask/marker_regression/display_mapping_results.py - Indented a bit of code that was wrongly indented in such a way that the variable "ind" wasn't set if "plotbxd" is 0
2020-09-01Use "md5.min.js" from guixBonfaceKilz
2020-09-01Remove commented out script tags that references CDNsBonfaceKilz
2020-09-01Replace CDNs with packages from guixBonfaceKilz
2020-09-01Add missing apostrophe in url_for argsBonfaceKilz
2020-08-31Merge pull request #431 from BonfaceKilz/Build/add-d3-tipBonfaceKilz
Use d3-tip from guix
2020-08-31Fixed text on not_authenticated to use proper grammarzsloan
* wqflask/wqflask/templates/new_security/not_authenticated.html - Changed "this" to "these" since "data" is plural
2020-08-31Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-08-31Fixed issue that was causing updating resource default privileges to notzsloan
work * wqflask/utility/redis_tools.py - There was an issue where resources wouldn't be updated if they already existed. This is because the code didn't yet account for the "update" tag (that is meant to give the option of preventing updating resources when running the script to enter all resources into Redis). I changed the logic to add a resource if "update" is True or the resource doesn't already exist (so it won't if update is False and the resource exists).
2020-08-31Use d3-tip from guixBonfaceKilz
2020-08-31Use chroma from guixBonfaceKilz
* wqflask/wqflask/templates/correlation_matrix.html: Fetch chroma from guix profile
2020-08-31Merge pull request #428 from ↵BonfaceKilz
BonfaceKilz/chore/delete-datatables-extensions-from-guix Delete dataTables and it's extensions from git
2020-08-29Fixed issue where exporting traits would throw an error if a dataset'szsloan
group didn't have an InbredSetCode set in the DB * wqflask/utility/authentication_tools.py - Changed get_group_code to return an empty string instead of None if InbredSetCode doesn't exist for a dataset group * wqflask/wqflask/views.py - Changed zipped export filename to "export_(datetime)" instead of "collection_(datetime)" since this export can occur from both the collection page and the global search page
2020-08-29Fixed issue with exporting traits from multiple different groups fromzsloan
the collection page (the filename wasn't being set) * wqflask/wqflask/views.py - Set filename to "collection_(datetime)" in export_traits_csv because it wasn't being set before
2020-08-28Delete dataTables and it's extensions from gitBonfaceKilz
* wqflask/wqflask/static/new/packages/DataTables/: Delete folder.
2020-08-27Added logic that creates a user account if an e-mail is added to a groupzsloan
that isn't already associated with a GN2 account and sends the user an e-mail; still need to test * wqflask/wqflask/group_manager.py - Added logic sending an invitation e-mail if user_details aren't found for any of the e-mails provided when adding users to a group
2020-08-27Added function for sending an invitation e-mailzsloan
* wqflask/wqflask/user_login.py - Added send_invitation_email function, which does what it says
2020-08-27Added manager_user.html because it was missing from gitzsloan
2020-08-25Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-08-25Fixed issue in DatasetType that caused an error when trying to load newzsloan
datasets * wqflask/base/data_set.py - Added fetchone() to g.db.execute() which is what was causing the error
2020-08-25Merge pull request #427 from ↵zsloan
BonfaceKilz/Build/add-scientific-js-datatables-plugin Build/add scientific js datatables plugin
2020-08-25This should fix an issue where the new qtlreaper wouldn't work properltyzsloan
with genotypes that only have cM positions * wqflask/wqflask/marker_regression/qtlreaper_mapping.py - parse_reaper_output is changed to check if cM and Mb exist in output when creating marker obs * wqflask/wqflask/marker_regression/run_mapping.py - Changed export_mapping_results to properly deal with all combinations of cM and Mb positions (both and either/or)
2020-08-25Merge pull request #425 from ↵zsloan
BonfaceKilz/refactor/extract-htmlgen-methods-to-wrapper-class Refactor/extract htmlgen methods to wrapper class
2020-08-25Use scientific.js dataTables extension plugin from guixBonfaceKilz
2020-08-24Use natural.js dataTables extension plugin from guixBonfaceKilz
2020-08-24Remove non-keyword argsBonfaceKilz
* wqflask/wqflask/marker_regression/display_mapping_results.py (HtmlGenWrapper)[create_image_tag]: Remove "src" and "alt" as function parameters.
2020-08-24Replace "HtmlGen" method calls with those from "HtmlGenWrapper"BonfaceKilz
* wqflask/wqflask/marker_regression/display_mapping_results.py (DisplayMappingResults): Replace direct calls to HtmlGen with methods from the constructed wrapper class "HtmlGenWrapper".
2020-08-24Add new wrapper class for HtmlGen methodBonfaceKilz
* wqflask/wqflask/marker_regression/display_mapping_results.py: Add new class
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