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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
2020-08-31Merge 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
2020-08-29Fixed 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
2020-08-27Added 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
2020-08-25Merge 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
2020-08-25Merge 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
2020-08-24Remove non-keyword args...* wqflask/wqflask/marker_regression/display_mapping_results.py (HtmlGenWrapper)[create_image_tag]: Remove "src" and "alt" as function parameters. BonfaceKilz
2020-08-24Replace "HtmlGen" method calls with those from "HtmlGenWrapper"...* wqflask/wqflask/marker_regression/display_mapping_results.py (DisplayMappingResults): Replace direct calls to HtmlGen with methods from the constructed wrapper class "HtmlGenWrapper". BonfaceKilz
2020-08-24Add new wrapper class for HtmlGen method...* wqflask/wqflask/marker_regression/display_mapping_results.py: Add new class BonfaceKilz
2020-08-24Add tests for the HtmlGenWrapper class...* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Add new tests BonfaceKilz
2020-08-24Fix some pylint errors...* wqflask/wqflask/marker_regression/display_mapping_results.py: Remove unused imports and add fix some pylint errors BonfaceKilz
2020-08-24Remove unused imports...* 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. BonfaceKilz
2020-08-24Rename file...* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Rename test_display_marking_results.py to test_display_mapping_results.py BonfaceKilz
2020-08-24Fix failing test...* wqflask/tests/wqflask/api/test_gen_menu.py: Update assertion. Result data introduced in 092212df Signed-off-by: BonfaceKilz <bonfacemunyoki@gmail.com> BonfaceKilz
2020-08-24Fixed issue where im_drawer wasn't being set in drawHaplotypeBand...* wqflask/wqflask/marker_regression/display_mapping_results.py - defined im_drawer in drawHaplotypeBand to fix errror and removed an unused import zsloan
2020-08-24The function draw_rotated_text_ was writing an image to /tmp, which GN2...user apparently doesn't have access to, so I replaced it with a link to the dynamically set TEMPDIR * wqflask/utility/pillow_utils.py - Replaced "/tmp/" in image location with TEMPDIR zsloan
2020-08-22Set min-width for search result table, since the description column...often looks weird if it gets below a certain width * wqflask/wqflask/templates/search_result_page.html - Set min-width of table container div to 1500px since that seems to be a reasonable width that prevents the description column from getting too narrow zsloan
2020-08-20Changed Molecular Trait Datasets to Molecular Traits in the Type...drop-down on the home page * wqflask/wqflask/api_gen_menu.py - Changed where Molecular Trait Datasets was hardcoded to Molecular Traits zsloan
2020-08-20Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-08-20Merge pull request #423 from BonfaceKilz/build/use-datatable-extensions-from-......Build/use datatable extensions from guixzsloan
2020-08-20Check the availability of datatables extension files from guix...* test/requests/link_checker.py (check_packaged_js_files): Add it. * test/requests/test-website.py: Use above method. BonfaceKilz
2020-08-20Use dataTables.colResize.js and naturalSort from guixBonfaceKilz
2020-08-20Use buttons.colVis.min.js from guixBonfaceKilz
2020-08-20Use buttons.bootstrap.css from guixBonfaceKilz
2020-08-20Use scroller.dataTables.min.css from guixBonfaceKilz
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