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2020-09-01There was a missing quote in one of the javascript imports added by the...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 zsloan
2020-09-01Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-09-01Fixed indent issue that could cause error when showing the haplotype...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 zsloan
2020-09-01Merge pull request #434 from BonfaceKilz/Build/use-md5-js-from-guix...Build/use md5 js from guixBonfaceKilz
2020-09-01Add check for "md5.min.js" library...* test/requests/link_checker.py: Add it. BonfaceKilz
2020-09-01Use "md5.min.js" from guixBonfaceKilz
2020-09-01Merge pull request #433 from BonfaceKilz/Build/remove-cdns...Build/remove cdnsBonfaceKilz
2020-09-01Check availability of several js and css files...* test/requests/link_checker.py: Check availability of: chroma.min.js; d3-tip.js; d3.min.js; underscore.min.js; nv.d3.min.css; and jquery.qtip.min.js BonfaceKilz
2020-09-01Remove commented out script tags that references CDNsBonfaceKilz
2020-09-01Replace CDNs with packages from guixBonfaceKilz
2020-09-01Merge pull request #432 from BonfaceKilz/Fix/add-missing-apostrophe...Add missing apostrophe in url_for argsBonfaceKilz
2020-09-01Add missing apostrophe in url_for argsBonfaceKilz
2020-08-31Remove typo at beginning of line...* wqflask/utility/authentication_tools.py: Remove accidental char at beginning of line. BonfaceKilz
2020-08-31Merge pull request #431 from BonfaceKilz/Build/add-d3-tip...Use d3-tip from guixBonfaceKilz
2020-08-31Fixed text on not_authenticated to use proper grammar...* wqflask/wqflask/templates/new_security/not_authenticated.html - Changed "this" to "these" since "data" is plural zsloan
2020-08-31Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-08-31Fixed issue that was causing updating resource default privileges to not...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). zsloan
2020-08-31Add check for "d3-tip.js" js library...* test/requests/link_checker.py (check_packaged_js_files): Add it. BonfaceKilz
2020-08-31Merge pull request #429 from BonfaceKilz/chore/add-gh-templates...Add github templates for filing bugs, user stories/ features and PRsBonfaceKilz
2020-08-31Use d3-tip from guixBonfaceKilz
2020-08-31Merge pull request #430 from BonfaceKilz/Build/add-chroma-js...Build/add chroma jsBonfaceKilz
2020-08-31Add github templates for filing bugs, user stories/ features and PRs...* .github/ISSUE_TEMPLATE/bug_report.md : Add template for filing bug reports. * .github/ISSUE_TEMPLATE/feature_request.md: Add template for filing a feature. * .github/ISSUE_TEMPLATE/user_story.md: Add a template for creating a user story for a feature. * .github/PULL_REQUEST_TEMPLATE.md: Add a template for filing a PR. BonfaceKilz
2020-08-31Add check for "chroma.js" dataTables extension plugin...* test/requests/link_checker.py (check_packaged_js_files): Add it. BonfaceKilz
2020-08-31Use chroma from guix...* wqflask/wqflask/templates/correlation_matrix.html: Fetch chroma from guix profile BonfaceKilz
2020-08-31Merge pull request #428 from BonfaceKilz/chore/delete-datatables-extensions-f......Delete dataTables and it's extensions from gitBonfaceKilz
2020-08-31Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-08-29Fixed issue where exporting traits would throw an error if a dataset's...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 zsloan
2020-08-29Fixed issue with exporting traits from multiple different groups from...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 zsloan
2020-08-28Delete dataTables and it's extensions from git...* wqflask/wqflask/static/new/packages/DataTables/: Delete folder. BonfaceKilz
2020-08-28Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-08-27Added logic that creates a user account if an e-mail is added to a group...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 zsloan
2020-08-27Added function for sending an invitation e-mail...* wqflask/wqflask/user_login.py - Added send_invitation_email function, which does what it says zsloan
2020-08-27Added manager_user.html because it was missing from gitzsloan
2020-08-27Add check for empty group_code when adding a new resource...* wqflask/utility/authentication_tools.py(add_new_resource): If group_code is "None", an error is thrown when you try to: `group_code + "_" + str(trait_id)` BonfaceKilz
2020-08-27Add a check for a "uuid" object...* wqflask/wqflask/views.py(json_default_handler): Check for "uuid.UUID" instance to avoid TypeError. BonfaceKilz
2020-08-27Update imports...* wqflask/wqflask/api/router.py: Break imports into separate lines and remove unused ones. BonfaceKilz
2020-08-27Remove python2 string processing to utf-8...* wqflask/base/trait.py: Remove python2 codecs.BOM_UTF8 methods. * wqflask/wqflask/search_results.py: Remove utf-8 decode method on string. BonfaceKilz
2020-08-27Remove relative imports...* wqflask/runserver.py: Relative imports leads to import errors. BonfaceKilz
2020-08-27Replace dict.iteritems() with dict.items()..."iteritems()" got omitted in python3.X BonfaceKilz
2020-08-27Convert sibling imports to relative imports...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-import> BonfaceKilz
2020-08-27Import "reduce" without a try block...* wqflask/wqflask/correlation_matrix/show_corr_matrix.py: Import 'reduce' BonfaceKilz
2020-08-27Replace string arguments to "hmac.new" with bytearray...See: <https://stackoverflow.com/questions/31848293/python3-and-hmac-how-to-handle-string-not-being-binary> BonfaceKilz
2020-08-27Fix failing testsBonfaceKilz
2020-08-27Apply pep-8 formattingBonfaceKilz
2020-08-27Remove comment blockBonfaceKilz
2020-08-27Replace mysqldb's "escape" with the one from utils.db_tools...Mysqldb's escape returns a binary string. Use utils.db_tools which adds an extra step of converting the binary string to a string. BonfaceKilz
2020-08-27Remove redundant methods which are defined elsewhere...* wqflask/base/data_set.py: Delete "create_in_clause", and "mescape" which are defined in "utility.db_tools" BonfaceKilz
2020-08-27Add global method to convert binary string to plain string...* wqflask/utility/db_tools.py: escape_string returns a binary string which introduces a bug when composing sql query string. The escaped strings have to be converted to plain text. BonfaceKilz
2020-08-27Remove unused importsBonfaceKilz
2020-08-27Replace "string.split" & "string.join" with python's inbuilt methodsBonfaceKilz
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