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2020-09-17Merge branch 'testing' into build/python3-migrationBonfaceKilz
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.
2020-09-16Add 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.
2020-09-08Changed 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
2020-08-31Remove typo at beginning of lineBonfaceKilz
* wqflask/utility/authentication_tools.py: Remove accidental char at beginning of line.
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
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.
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