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2020-09-26Run 2to3-8 tool through fileBonfaceKilz
* wqflask/wqflask/db_info.py: Run: 2to3-3.8 -w wqflask/wqflask/db_info.py
2020-09-26Fix inconsistent line ending in fileBonfaceKilz
* wqflask/wqflask/db_info.py: Replace ^M with proper unix line endings. See <http://ergoemacs.org/emacs/emacs_line_ending_char.html>
2020-09-26Merge branch 'testing' into build/python3-migrationBonfaceKilz
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
2020-09-25Update docs on CI setup with dockerBonfaceKilz
* doc/docker-container.org: Update it.
2020-09-25Update github actionBonfaceKilz
* .github/workflows/main.yml: Set up a mariadb and redis within the GH action. (services): Remove mariadb service.
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
2020-09-23Update github action to include mariadb serviceBonfaceKilz
* .github/workflows/main.yml: Add mariadb service. This makes the build pass because somewhere(because of cyclic imports), a connection to mariadb is required.
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
2020-09-22Merge pull request #445 from BonfaceKilz/buid/add-ciBonfaceKilz
Buid/add ci
2020-09-22Add testing badge on READMEBonfaceKilz
* README.md: Badge becomes green on successful runs.
2020-09-22Update documentation on testing and CIBonfaceKilz
* README.md: Update section on testing. * doc/docker-container.org: Add it.
2020-09-22Add unittesting github actionBonfaceKilz
* .github/workflows/main.yml: Add it.
2020-09-22Update Mechanical RobBonfaceKilz
* test/requests/main_web_functionality.py (check_search_page): Breaking change introduced by updating text in search page. See: 9f76abc95
2020-09-22Update bug_report templateBonfaceKilz
* .github/ISSUE_TEMPLATE/bug_report.md: Update environment setup section
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
2020-09-17Update Mechanical RobBonfaceKilz
* test/requests/link_checker.py (verify_static_file): Cast result.content.find's args to bytes. * test/requests/main_web_functionality.py (check_search_page): Update text to search for in a successful result. This value changed in 2aac6a06.
2020-09-17Convert "target_string" to a str typeBonfaceKilz
* wqflask/base/trait.py (retrieve_trait_info): Convert "target_string" to a str, otherwise an exception will be thrown if it's None.
2020-09-17Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-17Mock "SECRET_HMAC_CODE"BonfaceKilz
* wqflask/tests/utility/test_hmac.py: Mock app.config's "SECRET_HMAC_CODE" value.
2020-09-17Replace string arguments to "hmac.new" with bytearrayBonfaceKilz
Same as: https://github.com/genenetwork/genenetwork2/pull/422/commits/46443ec8d2cdfd7c60358a889d90a90e4f7daaf4
2020-09-17Fix errors in testsBonfaceKilz
* wqflask/tests/utility/test_authentication_tools.py test_check_resource_availability_non_default_mask): Mock flask's global 'g' variable properly. * wqflask/tests/base/test_trait.py: Ditto. * wqflask/tests/utility/test_authentication_tools.py: Ditto.
2020-09-17Apply pep8BonfaceKilz
* wqflask/base/trait.py: Apply pep8. * wqflask/utility/authentication_tools.py: Ditto.
2020-09-17Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-17Merge pull request #443 from BonfaceKilz/tests/test-auth-and-utf8BonfaceKilz
Tests/test auth and utf8
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
generated by cgit v1.2.3 (git 2.44.0) at 2024-12-03 11:29:15 +0000