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2020-09-25Fixed issue where attribute columns' alignment was offset by 1...* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - attribute cells' alignment and column names were wrong because they were referring to an attribute offset by 1 in the attribute list - zsloan
2020-09-25Changed edit_data_change and block_by_index to use DataTables API...* wqflask/wqflask/static/new/javascript/show_trait.js - Changed edit_data_change to use DataTables API to fetch the list of names, values, and (where applicable) standard errors in a way that just looks at those columns (previously it iterated through all rows). block_by_index was also changed to look just at columns zsloan
2020-09-24Changed logic that defines the primary/other samplelists to be much more...efficient * wqflask/wqflask/show_trait/show_trait.py - Add an "if" statement to avoid unnecessarily running some code and changed a list to a set for the purposes of searching if it contains an element zsloan
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
2020-09-22Changed JS on trait page that updates basic stats and graphs/figures to...use the DataTables API to pull sample values * wqflask/wqflask/static/new/javascript/show_trait.js - Changed the way sample name/val/var are pulled from the table to instead use DataTables' API + removed an unused event listener * wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - added "var" before a defined variable for consistency 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
2020-09-18Made some style changes with whitespace/line-breakszsloan
2020-09-18Made a bunch of changes to move trait page DataTables initialization to...a separate file (initialize_show_trait_tables.js). The biggest complication was getting the order of attributes in the rows to sync with the order of atribute namees in the column headers. Previously this logic was all in the template. * wqflask/base/webqtlCaseData.py - added attribute first_attr_col as a very awkward solution to passing the column position into the column render function in situations where there are case attribute columns (which can be variable in number) * wqflask/wqflask/show_trait/show_trait.py - Replace "attribute_names" in js_data with "attributes" (which allows the JS access to more information) and also pass new se_exists and has_num_cases variables with js_data, so the javascript has access to whether or not those columns exist in the table * wqflask/wqflask/static/new/javascript/show_trait.js - Change case attribute-related logic to use js_data.attributes instead of js_data.attribute_names * wqflask/wqflask/templates/show_trait.html - Removed table initialization from template * wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - new file that initializes tables and reproduces what the template logic used to do with JS logic zsloan
2020-09-18Apply pep8 formattingBonfaceKilz
2020-09-17Mock "SECRET_HMAC_CODE"...* wqflask/tests/utility/test_hmac.py: Mock app.config's "SECRET_HMAC_CODE" value. BonfaceKilz
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
2020-09-16Changed references to se_exists to just get it as a property of...SampleList instead of calling the method * wqflask/wqflask/show_trait/show_trait.py - see above * wqflask/wqflask/templates/show_trait.html - see above + removed some commented out code zsloan
2020-09-16Changed se_exists to a property so the SampleList instance can include...that when converted to a dict (which is needed to use it in the javascript) * wqflask/wqflask/show_trait/SampleList.py - Directly set se_exists as a property of SampleList instead of requiring a method be called; I could have set self.se_exists by calling the se_exists method, but that would have resulted in the convoluted line "self.se_exists = self.se_exists()" and the se_exists method only consisted of one line anyways zsloan
2020-09-16Applied PEP8 and removed commented out codezsloan
2020-09-16Add new tests for "base/trait.py"...* wqflask/tests/base/test_trait.py: New tests. BonfaceKilz
2020-09-16Apply pep8...* wqflask/utility/authentication_tools.py: Apply pep8 formatting to file. BonfaceKilz
2020-09-16Add tests for "add_new_resource" method...* wqflask/tests/utility/test_authentication_tools.py: Add them. BonfaceKilz
2020-09-16Remove unnecessary if branch...* wqflask/utility/authentication_tools.py (check_resource_availability): Combine if statements into one boolean check in one if branch. BonfaceKilz
2020-09-16Add tests for authentication tools...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". BonfaceKilz
2020-09-15Fix failing tests...* wqflask/tests/base/test_data_set.py: Update failing tests introduced by the change in 301bdd2f4. BonfaceKilz
2020-09-15Added scroller to trait page and changed sample tables to use it...* wqflask/wqflask/templates/show_trait.html - Imported scroller (from the Google cdn temporarily for testing) and activated it for the sample tables, as well as disabled options that conflicted with it (like paging: false) zsloan
2020-09-14Merge branch 'scroller_testing' of github.com:zsloan/genenetwork2 into testingzsloan
2020-09-13Added in-progress info-page to views.py as well as in-progress...authorization/security guide * wqflask/wqflask/views.py - Added endpoint for info page and authorization/security tutorial zsloan
2020-09-11Wrote code and template for reproducing GN1's Info Page (page that...displays info about a dataset + download links for its data) * wqflask/wqflask/db_info.py - Python that pulls the info out of the DB and parses the download links from the ipfs response * wqflask/wqflask/templates/info_page.html - template for displaying db info; need to make a lot of changes to its format/aesthetics zsloan
2020-09-10Modified "natural-minus-na" sort function to treat an array of values...as equivalent to "N/A" (since different tables sometimes include other values that imply there's no value) and applied it to some extra columns in the Interval Analyst table * wqflask/wqflask/static/new/javascript/search_results.js - Modified sort_NAs function to take an array of "N/A"-equivalent values instead of just comparing against the string "N/A" * wqflask/wqflask/templates/mapping_results.html - Applied "natural-minus-na" sort method to several columns that include "--" in the Interval Analyst table zsloan
2020-09-10Fixed several sorting issues and moved orderDataType definitions into...search_results.js since all the tables that use them import that file (that file's name needs to be changed, though) * wqflask/wqflask/static/new/javascript/search_results.js - Added the dom-checkbox and dom-inner-text order types into this file; they were previously duplicated across several template files * wqflask/wqflask/templates/gsearch_gene.html - Added dom-inner-text order type to relevant columns with hyperlink contents and disabled deferRender since it conflicted with use of both pagination and orderDataType for sorting * wqflask/wqflask/templates/gsearch_pheno.html - Same as above * wqflask/wqflask/templates/mapping_results.html - Added dom-inner-text for a few columns that have hyperlink values - still need to modify natural-minus-na to also include other "N/A"-equivalent values like "--" * wqflask/wqflask/templates/search_result_page.html Removed the dom-checkbox and dom-inner-text order types from this file since they were moved to search_results.js zsloan
2020-09-08Changed the Add button color for all the different pages that use it...* 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 zsloan
2020-09-08Search code now checks if there are more than 50,000 results before...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 zsloan
2020-09-08Changed regular and global search results table to use the new sort...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 zsloan
2020-09-08Added a sort function (derived from the natural sort import) that always...places N/As at the bottom regardless of search direction * wqflask/wqflask/static/new/javascript/search_results.js - created "natural-minus-na" sort zsloan
2020-09-04Merge pull request #437 from BonfaceKilz/fix/use-correct-path-give-a-path-loc......Fix/use correct path give a path locationBonfaceKilz
2020-09-04Update how static js/ css files are fetched...* 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> BonfaceKilz
2020-09-04Fix false positive tests...* test/requests/link_checker.py: (verify_static_file): Add it. Verify that a static link is fetched by checking for the message "Error: 404 not Found" in page. (check_package_js_files): Add appropriate 'js' or 'css' prefix. BonfaceKilz
2020-09-01There was a missing quote in one of the javascript imports added by the...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 zsloan