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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
2020-08-31Merge branch 'testing' into build/python3-migrationBonfaceKilz
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.
2020-08-28Merge branch 'testing' into build/python3-migrationBonfaceKilz
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
2020-08-27Add check for empty group_code when adding a new resourceBonfaceKilz
* 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)`
2020-08-27Add a check for a "uuid" objectBonfaceKilz
* wqflask/wqflask/views.py(json_default_handler): Check for "uuid.UUID" instance to avoid TypeError.
2020-08-27Update importsBonfaceKilz
* wqflask/wqflask/api/router.py: Break imports into separate lines and remove unused ones.
2020-08-27Remove python2 string processing to utf-8BonfaceKilz
* wqflask/base/trait.py: Remove python2 codecs.BOM_UTF8 methods. * wqflask/wqflask/search_results.py: Remove utf-8 decode method on string.
2020-08-27Remove relative importsBonfaceKilz
* wqflask/runserver.py: Relative imports leads to import errors.
2020-08-27Replace dict.iteritems() with dict.items()BonfaceKilz
"iteritems()" got omitted in python3.X
2020-08-27Convert sibling imports to relative importsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-import>
2020-08-27Import "reduce" without a try blockBonfaceKilz
* wqflask/wqflask/correlation_matrix/show_corr_matrix.py: Import 'reduce'
2020-08-27Replace string arguments to "hmac.new" with bytearrayBonfaceKilz
See: <https://stackoverflow.com/questions/31848293/python3-and-hmac-how-to-handle-string-not-being-binary>
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_toolsBonfaceKilz
Mysqldb's escape returns a binary string. Use utils.db_tools which adds an extra step of converting the binary string to a string.
2020-08-27Remove redundant methods which are defined elsewhereBonfaceKilz
* wqflask/base/data_set.py: Delete "create_in_clause", and "mescape" which are defined in "utility.db_tools"
2020-08-27Add global method to convert binary string to plain stringBonfaceKilz
* 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.
2020-08-27Remove unused importsBonfaceKilz
2020-08-27Replace "string.split" & "string.join" with python's inbuilt methodsBonfaceKilz
2020-08-26Remove debug statementBonfaceKilz
* wqflask/wqflask/views.py(search_page): "debugf" raises an error since the first arg is expected to be an int
2020-08-26Remove "from __future__ import new_feature" statementsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
2020-08-26Replace "__cmp__" with "__eq__" magic methodBonfaceKilz
* 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>
2020-08-26Rename "unicode" to "str"BonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-unicode>
2020-08-26Replace calls to "basestring with "str""BonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-basestring>
2020-08-26Fix failing tests that use python2-htmlgenBonfaceKilz
* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Fix tests.
2020-08-26Replace python2-htmlgen with python-htmlgenBonfaceKilz
* wqflask/wqflask/marker_regression/display_mapping_results.py: Use python-htmlgen
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
2020-08-26Update corestats importBonfaceKilz
* wqflask/utility/Plot.py: import corestats from the utility module.
2020-08-26Remove unused importsBonfaceKilz
2020-08-26Merge branch 'testing' into build/python3-migrationBonfaceKilz
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
2020-08-24Add tests for the HtmlGenWrapper classBonfaceKilz
* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Add new tests
2020-08-24Fix some pylint errorsBonfaceKilz
* wqflask/wqflask/marker_regression/display_mapping_results.py: Remove unused imports and add fix some pylint errors
2020-08-24Remove unused importsBonfaceKilz
* wqflask/utility/Plot.py: Remove unused imports like "numarray". "numarray" is does not have py3 support so it's important to remove references to it.
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