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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).
2020-08-31Merge pull request #429 from BonfaceKilz/chore/add-gh-templatesBonfaceKilz
Add github templates for filing bugs, user stories/ features and PRs
2020-08-31Merge pull request #430 from BonfaceKilz/Build/add-chroma-jsBonfaceKilz
Build/add chroma js
2020-08-31Add github templates for filing bugs, user stories/ features and PRsBonfaceKilz
* .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.
2020-08-31Add check for "chroma.js" dataTables extension pluginBonfaceKilz
* test/requests/link_checker.py (check_packaged_js_files): Add it.
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
2020-08-29Fixed 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.
2020-08-27Added 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
2020-08-25Merge 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
2020-08-25Merge pull request #427 from ↵zsloan
BonfaceKilz/Build/add-scientific-js-datatables-plugin Build/add scientific js datatables plugin
2020-08-26Add check for "scientific.js" dataTables extension pluginBonfaceKilz
* test/requests/link_checker.py (check_packaged_file): Add it.
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
2020-08-25Merge pull request #426 from ↵zsloan
BonfaceKilz/Build/use-naturaljs-datatables-extensions Build/use naturaljs datatables extensions
2020-08-24Add check for "natural.js" in Mechanical RobBonfaceKilz
* test/requests/link_checker.py (check_packaged_file): Add it.
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.
2020-08-24Rename fileBonfaceKilz
* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Rename test_display_marking_results.py to test_display_mapping_results.py
2020-08-24Fix failing testBonfaceKilz
* wqflask/tests/wqflask/api/test_gen_menu.py: Update assertion. Result data introduced in 092212df Signed-off-by: BonfaceKilz <bonfacemunyoki@gmail.com>
2020-08-24Fixed issue where im_drawer wasn't being set in drawHaplotypeBandzsloan
* wqflask/wqflask/marker_regression/display_mapping_results.py - defined im_drawer in drawHaplotypeBand to fix errror and removed an unused import
2020-08-24The function draw_rotated_text_ was writing an image to /tmp, which GN2zsloan
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
2020-08-22Set min-width for search result table, since the description columnzsloan
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
2020-08-20Changed Molecular Trait Datasets to Molecular Traits in the Typezsloan
drop-down on the home page * wqflask/wqflask/api_gen_menu.py - Changed where Molecular Trait Datasets was hardcoded to Molecular Traits
2020-08-20Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-08-20Merge pull request #423 from ↵zsloan
BonfaceKilz/build/use-datatable-extensions-from-guix Build/use datatable extensions from guix
2020-08-20Check the availability of datatables extension files from guixBonfaceKilz
* test/requests/link_checker.py (check_packaged_js_files): Add it. * test/requests/test-website.py: Use above method.
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
2020-08-20Use dataTables.colReorder.js from guixBonfaceKilz
2020-08-20Use jquery.dataTables.js from guixBonfaceKilz
2020-08-20Use dataTables.buttons.min.js from guixBonfaceKilz
2020-08-20Use buttons.dataTables.min.css from guixBonfaceKilz
2020-08-19Added Invert button to collection pagezsloan
* wqflask/wqflask/templates/collections/view.html - Added the Invert button back to the collection page; it was removed in the past but Rob decided it should be re-added
2020-08-19Tools used from the collection page now use all traits if no rows arezsloan
checked and there are fewer than 100 traits in the table * wqflask/wqflask/static/new/javascript/search_results.js - Created get_traits_from_table function to get the list of traits and check if none are selected, and also renamed the previous function also called get_traits_from_table to submit_traits_to_export_or_bnw since that better describes what the function does
2020-08-19Show short labels by default in Correlation Matrixzsloan
* wqflask/wqflask/templates/correlation_matrix.html - remove display: none for short label div
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