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2020-09-30Apply pep 8 formatting...* wqflask/wqflask/correlation/show_corr_results.py [imports]: Apply pep8 and remove unused imports. BonfaceKilz
2020-09-30Fix StopIteration error thrown in view collections page...* wqflask/wqflask/user_session.py (user_id): Use byte-string when fetching user_id. See: https://github.com/genenetwork/genenetwork2/pull/422#issuecomment-701082458 BonfaceKilz
2020-09-30Fix import in testsBonfaceKilz
2020-09-29Remove undefined variableBonfaceKilz
2020-09-29Apply pep 8 to buffer...* wqflask/wqflask/user_manager.py: Remove some stale comments. (imports): Apply pep-8 and remove unused imports. BonfaceKilz
2020-09-29Add check for bytes...* 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. BonfaceKilz
2020-09-29Add test for process_traits from collections.py...* wqflask/tests/wqflask/test_collect.py: Add it. BonfaceKilz
2020-09-28Fix failing test...* 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". BonfaceKilz
2020-09-28Merge branch 'build/python3-migration' of github.com:BonfaceKilz/genenetwork2...BonfaceKilz
2020-09-28Fix casting error...* 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)*. BonfaceKilz
2020-09-28Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-28Fix casting error...* 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)*. BonfaceKilz
2020-09-28Merge pull request #446 from BonfaceKilz/Bug/Fix-casting-error...Bug/fix casting errorBonfaceKilz
2020-09-28Convert None to "" in if statement...* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork error: float argument required, not NoneType)" BonfaceKilz
2020-09-28Update trait tests...* 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. BonfaceKilz
2020-09-26Fix failing tests by replacing mock with unittest.mock...* 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 BonfaceKilz
2020-09-26Use Python3 image to run testsBonfaceKilz
2020-09-26Fix failing tests...* wqflask/tests/base/test_trait.py: Remove decode function call which is no longer supported in python3. BonfaceKilz
2020-09-26Apply PEP 8 to buffer...* wqflask/wqflask/db_info.py: Run pep8 through buffers. Fixes inconsistent use of tabs and spaces in indentation which trips up unittests. BonfaceKilz
2020-09-26Run 2to3-8 tool through file...* wqflask/wqflask/db_info.py: Run: 2to3-3.8 -w wqflask/wqflask/db_info.py BonfaceKilz
2020-09-26Fix inconsistent line ending in file...* wqflask/wqflask/db_info.py: Replace ^M with proper unix line endings. See <http://ergoemacs.org/emacs/emacs_line_ending_char.html> BonfaceKilz
2020-09-26Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-25Update docs on CI setup with docker...* doc/docker-container.org: Update it. BonfaceKilz
2020-09-25Update github action...* .github/workflows/main.yml: Set up a mariadb and redis within the GH action. (services): Remove mariadb service. BonfaceKilz
2020-09-23Update github action to include mariadb service...* .github/workflows/main.yml: Add mariadb service. This makes the build pass because somewhere(because of cyclic imports), a connection to mariadb is required. BonfaceKilz
2020-09-23Fix failing builds...* wqflask/wqflask/__init__.py: Move imports from views.py to "__init__.py". Fixes failing build. * wqflask/wqflask/views.py: Ditto. BonfaceKilz
2020-09-23Fix failing tests...* wqflask/tests/base/test_trait.py: In python2 it's necessary to decode the utf-8 string. BonfaceKilz
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 when...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 zsloan
2020-09-22Added something to the mapping result page CSS to change the highlight...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") zsloan
2020-09-22Fixed a couple mistakes in the previous commit and changed the position...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 zsloan
2020-09-22Replaced Chr and Mb/cM columns with a single position column in mapping...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 zsloan
2020-09-22Merge pull request #445 from BonfaceKilz/buid/add-ci...Buid/add ciBonfaceKilz
2020-09-22Add testing badge on README...* README.md: Badge becomes green on successful runs. BonfaceKilz
2020-09-22Update documentation on testing and CI...* README.md: Update section on testing. * doc/docker-container.org: Add it. BonfaceKilz
2020-09-22Add unittesting github action...* .github/workflows/main.yml: Add it. BonfaceKilz
2020-09-22Update Mechanical Rob...* test/requests/main_web_functionality.py (check_search_page): Breaking change introduced by updating text in search page. See: 9f76abc95 BonfaceKilz
2020-09-22Update bug_report template...* .github/ISSUE_TEMPLATE/bug_report.md: Update environment setup section BonfaceKilz
2020-09-18Apply pep8 formattingBonfaceKilz
2020-09-17Update Mechanical Rob...* 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. BonfaceKilz
2020-09-17Convert "target_string" to a str type...* wqflask/base/trait.py (retrieve_trait_info): Convert "target_string" to a str, otherwise an exception will be thrown if it's None. BonfaceKilz
2020-09-17Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-17Mock "SECRET_HMAC_CODE"...* wqflask/tests/utility/test_hmac.py: Mock app.config's "SECRET_HMAC_CODE" value. BonfaceKilz
2020-09-17Replace string arguments to "hmac.new" with bytearray...Same as: https://github.com/genenetwork/genenetwork2/pull/422/commits/46443ec8d2cdfd7c60358a889d90a90e4f7daaf4 BonfaceKilz
2020-09-17Fix errors in tests...* 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. BonfaceKilz
2020-09-17Apply pep8...* wqflask/base/trait.py: Apply pep8. * wqflask/utility/authentication_tools.py: Ditto. BonfaceKilz
2020-09-17Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-17Merge pull request #443 from BonfaceKilz/tests/test-auth-and-utf8...Tests/test auth and utf8BonfaceKilz
2020-09-17Apply pep8...* wqflask/utility/hmac.py: Apply pep8 and fix typo. BonfaceKilz
2020-09-17Add tests for hmac utility...* wqflask/tests/utility/test_hmac.py: New tests. BonfaceKilz
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