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2020-09-29Trait page link-out buttons were previously inside <a> tags, but thiszsloan
caused there to be a small line between buttons when hovering over them (because the <a> tags were wider than the button itself); this was changed to instead just be an "onclick" on the button (which is also a bit more concise) * wqflask/wqflask/templates/show_trait_details.html - Replaced <a> tags with onclick for trait page link-out buttons
2020-09-29Removed "Color By Trait" button from the Bar Chart, because it was meantzsloan
to work with the figure we used before switching to Plotly. This feature will need to be redone to work with Plotly * wqflask/wqflask/templates/show_trait_statistics.html - commented out Color By Trait button until it's reimplemented
2020-09-29Made a variety of changes to table pageszsloan
* wqflask/wqflask/static/new/css/show_trait.css - Adding position relative and a 2px offset for glyphicons to make them better align with button text * wqflask/wqflask/templates/collections/view.html - Added glyphicon to Download button, changed a couple head names (Peak Location and Effect Size), made Location and Peak Location columns the same width, and made the "?" glossary links a little larger and red * wqflask/wqflask/templates/search_result_page.html - same as above * wqflask/wqflask/templates/show_trait_edit_data.html - Added glyphicon to Export button
2020-09-29Remove undefined variableBonfaceKilz
2020-09-29Apply pep 8 to bufferBonfaceKilz
* wqflask/wqflask/user_manager.py: Remove some stale comments. (imports): Apply pep-8 and remove unused imports.
2020-09-29Fixed issue where negative additive effect values weren't beingzsloan
displayed in the "view collection" page * wqflask/wqflask/templates/collections/view.html - Apparently the correct way to check if a value can be cast to a float in Jinja2 is to say "value != 0"; it previous said "value > 0" which exlcuded all negative values
2020-09-29Changed Add (to collection) button color to match other Add buttons andzsloan
changed the text for the GN1 link button * wqflask/wqflask/templates/show_trait_details.html - Changed Add button class to btn-success (to make it green like the other Add buttons) and changed text from "View in GN1" to "Go to GN1"
2020-09-29Changed the DataTables column sort arrows to a different color byzsloan
changing the image they're referencing * wqflask/wqflask/templates/base.html - Added CSS changing the table sort arrow image directly into base.html because it requires using url_for to reference the images in the GUIX profile (so it needs to be in the template and can't just be added to a CSS file)
2020-09-29Add check for bytesBonfaceKilz
* wqflask/wqflask/collect.py (process_traits): Check whether the passed "unprocessed_traits" is a byte otherwise an error is generated when bytes(the default) are passed.
2020-09-29Add test for process_traits from collections.pyBonfaceKilz
* wqflask/tests/wqflask/test_collect.py: Add it.
2020-09-28Changed add to collection to open the collection in a new tab/page sozsloan
the results on the initial page aren't lost * wqflask/wqflask/static/new/javascript/search_results.js - Changed the add to collection method name to "add_to_collection" because it was previously "add" which is a terrible method name * wqflask/wqflask/templates/collections/add.html - Added target="_blank" to the add to collection form so it will open in a new tab/window
2020-09-28Fix failing testBonfaceKilz
* wqflask/tests/base/test_trait.py: Add app_context to test class, otherwise an error related to working outside the app_context is generated. Adding the app_context is required when mocking "Flask.g".
2020-09-28Merge branch 'build/python3-migration' of ↵BonfaceKilz
github.com:BonfaceKilz/genenetwork2 into build/python3-migration
2020-09-28Fix casting errorBonfaceKilz
* wqflask/base/trait.py (retrieve_trait_info): If the description_string or discription_display value return a None object, evaluate to an empty string. Fixes errors related to *len(None)*.
2020-09-28Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-28Fix casting errorBonfaceKilz
* wqflask/base/trait.py (retrieve_trait_info): If the description_string or discription_display value return a None object, evaluate to an empty string. Fixes errors related to *len(None)*.
2020-09-28Merge pull request #446 from BonfaceKilz/Bug/Fix-casting-errorBonfaceKilz
Bug/fix casting error
2020-09-28Convert None to "" in if statementBonfaceKilz
* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork error: float argument required, not NoneType)"
2020-09-28Update trait testsBonfaceKilz
* wqflask/tests/base/test_trait.py (test_retrieve_trait_info_with_non_empty_lrs): Check trait.LRS_score_repr is set correctly if trait.lrs is None. (test_retrieve_trait_info_with_empty_lrs_field): Check trait.LRS_score_repr and test_trait.LRS_location_repr is set correctly if trait.lrs is None. (test_retrieve_trait_info_with_empty_chr_field): Check test_trait.LRS_score_repr and test_trait.LRS_location_repr is set correctly if trait.locus is None.
2020-09-26Fix failing tests by replacing mock with unittest.mockBonfaceKilz
* wqflask/tests/base/test_data_set.py (imports): Run: `find . -type f -name "*py" -print0 | xargs -0 sed -i \ "s|import mock|from unittest import mock|g"` * wqflask/tests/base/test_trait.py(imports): Ditto. * wqflask/tests/utility/test_authentication_tools.py(imports): Ditto. * wqflask/tests/utility/test_hmac.py(imports). Ditto. * wqflask/tests/wqflask/api/test_gen_menu.py: Ditto
2020-09-26Use Python3 image to run testsBonfaceKilz
2020-09-26Fix failing testsBonfaceKilz
* wqflask/tests/base/test_trait.py: Remove decode function call which is no longer supported in python3.
2020-09-26Apply PEP 8 to bufferBonfaceKilz
* wqflask/wqflask/db_info.py: Run pep8 through buffers. Fixes inconsistent use of tabs and spaces in indentation which trips up unittests.
2020-09-26Run 2to3-8 tool through fileBonfaceKilz
* wqflask/wqflask/db_info.py: Run: 2to3-3.8 -w wqflask/wqflask/db_info.py
2020-09-26Fix inconsistent line ending in fileBonfaceKilz
* wqflask/wqflask/db_info.py: Replace ^M with proper unix line endings. See <http://ergoemacs.org/emacs/emacs_line_ending_char.html>
2020-09-26Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-25Update docs on CI setup with dockerBonfaceKilz
* doc/docker-container.org: Update it.
2020-09-25Update github actionBonfaceKilz
* .github/workflows/main.yml: Set up a mariadb and redis within the GH action. (services): Remove mariadb service.
2020-09-23Update github action to include mariadb serviceBonfaceKilz
* .github/workflows/main.yml: Add mariadb service. This makes the build pass because somewhere(because of cyclic imports), a connection to mariadb is required.
2020-09-23Fix failing buildsBonfaceKilz
* wqflask/wqflask/__init__.py: Move imports from views.py to "__init__.py". Fixes failing build. * wqflask/wqflask/views.py: Ditto.
2020-09-23Fix failing testsBonfaceKilz
* wqflask/tests/base/test_trait.py: In python2 it's necessary to decode the utf-8 string.
2020-09-22Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-09-22Fixed a pretty big mistake where user accounts would be saved even whenzsloan
there was some mistake/error during registration * wqflask/wqflask/user_login.py - Previously it would still save a user even if there was some problem like their e-mail already being associated with an account. It would display the error, but still run save_user. I fixed this so that it no longer saves the user if there are any errors
2020-09-22Added something to the mapping result page CSS to change the highlightzsloan
color to match the high color in other tables * wqflask/wqflask/static/new/css/marker_regression.css - changed background color when selecting a row (i.e. "highlight color")
2020-09-22Fixed a couple mistakes in the previous commit and changed the positionzsloan
header on the mapping results page to include the mapping scale * wqflask/wqflask/marker_regression/run_mapping.py - changed how "display_pos" is defined for marker obs * wqflask/wqflask/templates/mapping_results.html - Fixed issues with last commit and changed position header name to include mapping scale
2020-09-22Replaced Chr and Mb/cM columns with a single position column in mappingzsloan
results and also changes the -log(p) to use an endash instead * wqflask/wqflask/marker_regression/run_mapping.py - added "display_pos" to each marker object that is a combination of Chr and Mb/cM * wqflask/wqflask/templates/mapping_results.html - Included "display_pos" in results table and replaced -log(p) with using an endash
2020-09-22Merge pull request #445 from BonfaceKilz/buid/add-ciBonfaceKilz
Buid/add ci
2020-09-22Add testing badge on READMEBonfaceKilz
* README.md: Badge becomes green on successful runs.
2020-09-22Update documentation on testing and CIBonfaceKilz
* README.md: Update section on testing. * doc/docker-container.org: Add it.
2020-09-22Add unittesting github actionBonfaceKilz
* .github/workflows/main.yml: Add it.
2020-09-22Update Mechanical RobBonfaceKilz
* test/requests/main_web_functionality.py (check_search_page): Breaking change introduced by updating text in search page. See: 9f76abc95
2020-09-22Update bug_report templateBonfaceKilz
* .github/ISSUE_TEMPLATE/bug_report.md: Update environment setup section
2020-09-18Apply pep8 formattingBonfaceKilz
2020-09-17Update Mechanical RobBonfaceKilz
* test/requests/link_checker.py (verify_static_file): Cast result.content.find's args to bytes. * test/requests/main_web_functionality.py (check_search_page): Update text to search for in a successful result. This value changed in 2aac6a06.
2020-09-17Convert "target_string" to a str typeBonfaceKilz
* wqflask/base/trait.py (retrieve_trait_info): Convert "target_string" to a str, otherwise an exception will be thrown if it's None.
2020-09-17Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-17Mock "SECRET_HMAC_CODE"BonfaceKilz
* wqflask/tests/utility/test_hmac.py: Mock app.config's "SECRET_HMAC_CODE" value.
2020-09-17Replace string arguments to "hmac.new" with bytearrayBonfaceKilz
Same as: https://github.com/genenetwork/genenetwork2/pull/422/commits/46443ec8d2cdfd7c60358a889d90a90e4f7daaf4
2020-09-17Fix errors in testsBonfaceKilz
* wqflask/tests/utility/test_authentication_tools.py test_check_resource_availability_non_default_mask): Mock flask's global 'g' variable properly. * wqflask/tests/base/test_trait.py: Ditto. * wqflask/tests/utility/test_authentication_tools.py: Ditto.
2020-09-17Apply pep8BonfaceKilz
* wqflask/base/trait.py: Apply pep8. * wqflask/utility/authentication_tools.py: Ditto.
generated by cgit v1.2.3 (git 2.44.0) at 2024-12-02 15:45:35 +0000