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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
2020-09-23Aligned relevant columns to right in mapping results tablezsloan
* wqflask/wqflask/templates/mapping_results.html - aligned score, position, additive effect, and dominance column headers to the right
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.
2020-09-22Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-09-22Fixed a pretty big mistake where user accounts would be saved even whenzsloan
there was some mistake/error during registration * wqflask/wqflask/user_login.py - Previously it would still save a user even if there was some problem like their e-mail already being associated with an account. It would display the error, but still run save_user. I fixed this so that it no longer saves the user if there are any errors
2020-09-22Added something to the mapping result page CSS to change the highlightzsloan
color to match the high color in other tables * wqflask/wqflask/static/new/css/marker_regression.css - changed background color when selecting a row (i.e. "highlight color")
2020-09-22Fixed a couple mistakes in the previous commit and changed the positionzsloan
header on the mapping results page to include the mapping scale * wqflask/wqflask/marker_regression/run_mapping.py - changed how "display_pos" is defined for marker obs * wqflask/wqflask/templates/mapping_results.html - Fixed issues with last commit and changed position header name to include mapping scale
2020-09-22Replaced Chr and Mb/cM columns with a single position column in mappingzsloan
results and also changes the -log(p) to use an endash instead * wqflask/wqflask/marker_regression/run_mapping.py - added "display_pos" to each marker object that is a combination of Chr and Mb/cM * wqflask/wqflask/templates/mapping_results.html - Included "display_pos" in results table and replaced -log(p) with using an endash
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
2020-09-18Apply pep8 formattingBonfaceKilz
2020-09-17Mock "SECRET_HMAC_CODE"BonfaceKilz
* wqflask/tests/utility/test_hmac.py: Mock app.config's "SECRET_HMAC_CODE" value.
2020-09-17Apply pep8BonfaceKilz
* wqflask/utility/hmac.py: Apply pep8 and fix typo.
2020-09-17Add tests for hmac utilityBonfaceKilz
* wqflask/tests/utility/test_hmac.py: New tests.
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
2020-09-16Add new tests for "base/trait.py"BonfaceKilz
* wqflask/tests/base/test_trait.py: New tests.
2020-09-16Apply pep8BonfaceKilz
* wqflask/utility/authentication_tools.py: Apply pep8 formatting to file.
2020-09-16Add tests for "add_new_resource" methodBonfaceKilz
* wqflask/tests/utility/test_authentication_tools.py: Add them.
2020-09-16Remove unnecessary if branchBonfaceKilz
* wqflask/utility/authentication_tools.py (check_resource_availability): Combine if statements into one boolean check in one if branch.
2020-09-16Add tests for authentication toolsBonfaceKilz
Catches bugs in: - https://github.com/genenetwork/genenetwork2/pull/422/commits/70dbeeb5832711ed5271434e482c18bc7ea095b8 * wqflask/tests/utility/test_authentication_tools.py: New file. Add tests for "check_resource_availability".
2020-09-15Fix failing testsBonfaceKilz
* wqflask/tests/base/test_data_set.py: Update failing tests introduced by the change in 301bdd2f4.
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)
2020-09-14Merge branch 'scroller_testing' of github.com:zsloan/genenetwork2 into testingzsloan
2020-09-13Added in-progress info-page to views.py as well as in-progresszsloan
authorization/security guide * wqflask/wqflask/views.py - Added endpoint for info page and authorization/security tutorial
2020-09-11Wrote code and template for reproducing GN1's Info Page (page thatzsloan
displays info about a dataset + download links for its data) * wqflask/wqflask/db_info.py - Python that pulls the info out of the DB and parses the download links from the ipfs response * wqflask/wqflask/templates/info_page.html - template for displaying db info; need to make a lot of changes to its format/aesthetics
2020-09-10Modified "natural-minus-na" sort function to treat an array of valueszsloan
as equivalent to "N/A" (since different tables sometimes include other values that imply there's no value) and applied it to some extra columns in the Interval Analyst table * wqflask/wqflask/static/new/javascript/search_results.js - Modified sort_NAs function to take an array of "N/A"-equivalent values instead of just comparing against the string "N/A" * wqflask/wqflask/templates/mapping_results.html - Applied "natural-minus-na" sort method to several columns that include "--" in the Interval Analyst table
2020-09-10Fixed several sorting issues and moved orderDataType definitions intozsloan
search_results.js since all the tables that use them import that file (that file's name needs to be changed, though) * wqflask/wqflask/static/new/javascript/search_results.js - Added the dom-checkbox and dom-inner-text order types into this file; they were previously duplicated across several template files * wqflask/wqflask/templates/gsearch_gene.html - Added dom-inner-text order type to relevant columns with hyperlink contents and disabled deferRender since it conflicted with use of both pagination and orderDataType for sorting * wqflask/wqflask/templates/gsearch_pheno.html - Same as above * wqflask/wqflask/templates/mapping_results.html - Added dom-inner-text for a few columns that have hyperlink values - still need to modify natural-minus-na to also include other "N/A"-equivalent values like "--" * wqflask/wqflask/templates/search_result_page.html Removed the dom-checkbox and dom-inner-text order types from this file since they were moved to search_results.js
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
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