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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
2020-08-26Replace tabs with spaces...* scripts/maintenance/readProbeSetMean_v7.py: Run python-autopep8 on this file. BonfaceKilz
2020-08-26Remove debug statement...* wqflask/wqflask/views.py(search_page): "debugf" raises an error since the first arg is expected to be an int BonfaceKilz
2020-08-26Remove "from __future__ import new_feature" statements...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future> BonfaceKilz
2020-08-26Replace "__cmp__" with "__eq__" magic method...* wqflask/base/GeneralObject.py: "__cmp__" is no longer used in python3. See: <https://stackoverflow.com/questions/8276983/why-cant-i-use-the-method-cmp-in-python-3-as-for-python-2> BonfaceKilz
2020-08-26Rename "unicode" to "str"...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-unicode> BonfaceKilz
2020-08-26Replace calls to "basestring with "str""...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-basestring> BonfaceKilz
2020-08-26Fix failing tests that use python2-htmlgen...* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Fix tests. BonfaceKilz
2020-08-26Replace python2-htmlgen with python-htmlgen...* wqflask/wqflask/marker_regression/display_mapping_results.py: Use python-htmlgen BonfaceKilz
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 new...datasets * wqflask/base/data_set.py - Added fetchone() to g.db.execute() which is what was causing the error zsloan
2020-08-26Update corestats import...* wqflask/utility/Plot.py: import corestats from the utility module. BonfaceKilz
2020-08-26Remove unused importsBonfaceKilz
2020-08-26Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-08-25Merge pull request #427 from BonfaceKilz/Build/add-scientific-js-datatables-p......Build/add scientific js datatables pluginzsloan
2020-08-26Add check for "scientific.js" dataTables extension plugin...* test/requests/link_checker.py (check_packaged_file): Add it. BonfaceKilz
2020-08-25This should fix an issue where the new qtlreaper wouldn't work properlty...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) zsloan
2020-08-25Merge pull request #425 from BonfaceKilz/refactor/extract-htmlgen-methods-to-......Refactor/extract htmlgen methods to wrapper classzsloan
2020-08-25Use scientific.js dataTables extension plugin from guixBonfaceKilz
2020-08-25Merge pull request #426 from BonfaceKilz/Build/use-naturaljs-datatables-exten......Build/use naturaljs datatables extensionszsloan
2020-08-24Add check for "natural.js" in Mechanical Rob...* test/requests/link_checker.py (check_packaged_file): Add it. BonfaceKilz
2020-08-24Use natural.js dataTables extension plugin from guixBonfaceKilz
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