| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-07-25 | Change Interval Analyst genome browser link to use mm10 instead of mm9 | zsloan | |
| 2022-07-25 | Return config in app.config or None | Frederick Muriuki Muriithi | |
| Update the code to return the setting already set up in the app.config dictionary if it exists or None if it does not exist. | |||
| 2022-07-14 | Remove column toggle JS from show_trait.html since it's in ↵ | zsloan | |
| initialize_show_trait_tables.js | |||
| 2022-07-14 | Call DataTable() on the table id instead of referring to the_table; not | zsloan | |
| sure why this is necessary, but the search doesn't work otherwise | |||
| 2022-07-12 | Include genotypes for F1s/reference/non-reference strains when fetching | zsloan | |
| sample data for genotype traits | |||
| 2022-07-11 | Increase min-width for div containing tool buttons on search page | zsloan | |
| 2022-07-08 | Add python for exporting case attributes | zsloan | |
| 2022-07-08 | Add JS for exporting case attributes (sample metadata) | zsloan | |
| 2022-07-04 | wqflask: Remove DebugToolbarExtension | BonfaceKilz | |
| This functionality, at least how we use it, is already provided natively in python's pdb. Should someone need this, they can add it manually. * wqflask/runserver.py (app_config): Remove "flask_debugtoolbar" import and instantiation. * wqflask/utility/startup_config.py (app_config): Ditto. | |||
| 2022-07-04 | wqflask: use the raw user string if value is non-existent in redis | BonfaceKilz | |
| * wqflask/wqflask/metadata_edits.py (_get_diffs): If a user---whose value is extracted from Redis and encoded in the file name---doesn't exist in Redis, use the raw string extracted from the file. | |||
| 2022-07-04 | wqflask: Use a map over a tuple when fetching case-attributes | BonfaceKilz | |
| * wqflask/wqflask/metadata_edits.py (update_phenotype): Replace old "get_case_attributes" function call which returned a dict with the new updated version that returns a tuple. | |||
| 2022-06-21 | wqflask: views: Delete noisy logging and dead code | BonfaceKilz | |
| - Remove commented out code-blocks - Remove calls with this pattern: logger.info("Sending ...") logger.info(request.url) Should you want to inspect the local context of an environment when troubleshooting, set a breakpoint() and inspect the environment. To view everything in the local context, use "pp locals()"; and to view everything in the global context, use "pp globals()". | |||
| 2022-06-20 | Simplify partial correlation method choices | Frederick Muriuki Muriithi | |
| - Have only `Pearson's r` and `Spearman's rho` as the available choices for the partial correlations. | |||
| 2022-06-15 | templates: base: Update GN2 footer | BonfaceKilz | |
| * wqflask/wqflask/templates/base: Remove links to non-functioning mailing list. Remove link to "#genenetwork" channel that isn't currently owned/moderated. Co-authored-by: Ethan Willis <elwillis1@gmail.com> | |||
| 2022-06-13 | Check chromosome for 'Un' in search results and print N/A in such cases | zsloan | |
| 2022-06-13 | Check for chromosome of 'Un' and print location as 'Not available' in such cases | zsloan | |
| 2022-06-13 | Increase width threshold for using scroller, to prevent issue with blue ↵ | zsloan | |
| lines at bottom of table | |||
| 2022-06-13 | Limit search result descriptions to 500 characters | zsloan | |
| 2022-06-13 | Add |safe to ensure HTML entites are correctly escaped for trait descriptions | zsloan | |
| 2022-06-10 | Skip failing integration test | BonfaceKilz | |
| ATM, it's hard to by-pass the authentication decorators, and as such, skip this test for. This may be deleted later. | |||
| 2022-06-10 | Reverse polarity for gemma additive effects in tests | BonfaceKilz | |
| Fixes broken test. See: #89a7868. | |||
| 2022-06-07 | Define gn_server_url before running the drop-down menu JS code | zsloan | |
| 2022-06-07 | Make indentation and spacing more consistent for | zsloan | |
| dataset_select_menu_orig.js | |||
| 2022-06-07 | Fix issue that caused Submit Trait page drop-down menus to not work | zsloan | |
| Also removes a bunch of unnecessary console logging | |||
| 2022-06-01 | Fix the way R/qtl is called in the GN2 REST API | zsloan | |
| 2022-06-01 | Remove IDs called 'submit' to prevent forms from breaking | zsloan | |
| Apparently if a button has an ID called 'submit', trying to submit a form via JS won't work | |||
| 2022-05-31 | Check if entered pubmed_id is already associated with a publication, and | zsloan | |
| set PublishXRef.PublicationId equal to that Id if it exists | |||
| 2022-05-31 | Reverse polarity for gemma additive effects | zsloan | |
| This is basically just a quick pseudo-fix to at least get the polarity right | |||
| 2022-05-31 | Fix minor bug | Frederick Muriuki Muriithi | |
| 2022-05-31 | Fix error rendering | Frederick Muriuki Muriithi | |
| Render the command_id if present in the error report to help with troubleshooting failures. | |||
| 2022-05-27 | Apply python-black on file | BonfaceKilz | |
| 2022-05-27 | Don't make a POST if there's a blank form-element | BonfaceKilz | |
| 2022-05-27 | Move SQL queries to GN3 | BonfaceKilz | |
| 2022-05-27 | Strip data before storing it | BonfaceKilz | |
| 2022-05-27 | Make sure the user is logged in when approving data | BonfaceKilz | |
| 2022-05-27 | Pass secend arg to cursor.execute as a tuple | BonfaceKilz | |
| 2022-05-27 | Add sensible styling to "reject"/"approve" buttons | BonfaceKilz | |
| 2022-05-27 | Align "Add New" button with the actions column | BonfaceKilz | |
| 2022-05-27 | Add js logic to POST to "approval" endpoint | BonfaceKilz | |
| 2022-05-27 | Assign the correct value to key | BonfaceKilz | |
| 2022-05-27 | Display description diff-data if it exists | BonfaceKilz | |
| 2022-05-27 | Ony show the title if there are any changes to be approved/rejected | BonfaceKilz | |
| 2022-05-27 | Cosmetic changes in Jinja template | BonfaceKilz | |
| 2022-05-27 | Add new endpoint for "approving" case-attributes modifications | BonfaceKilz | |
| * wqflask/wqflask/metadata_edits.py (approve_case_attribute_data): New end-point. | |||
| 2022-05-27 | Remove dead comment | BonfaceKilz | |
| 2022-05-27 | Append to "modifications" if "description"/"name" exist | BonfaceKilz | |
| 2022-05-27 | Make sure is in editor's group to view the case-attributes | BonfaceKilz | |
| * wqflask/wqflask/metadata_edits.py (show_case_attribute_columns): Add "case_attributes_edit_access" and "login_required" decorators. | |||
| 2022-05-27 | Make sure user is part of "editors" group to make (case attrs) edits | BonfaceKilz | |
| * wqflask/wqflask/decorators.py: Import "gn3.authentication.get_groups_by_user_uid". (case_attributes_edit_access): New decorator. Checks which users are in the "editors" group in Redis. * wqflask/wqflask/metadata_edits.py: Import "wqflask.decorators.case_attributes_edit_access" (update_case_attributes): Use "@update_case_attributes" decorator. (reject_case_attribute_data): Ditto. | |||
| 2022-05-27 | Replace "_get_author" with "gn3.authentication.get_user_info_by_key" | BonfaceKilz | |
| * wqflask/wqflask/metadata_edits.py (_get_author): Delete function. (show_case_attribute_columns): Use "get_user_info_by_key". | |||
| 2022-05-27 | Implement "reject"---for case-attr---endpoint | BonfaceKilz | |
| * wqflask/wqflask/metadata_edits.py (show_case_attribute_columns): Fetch id---this is already passed in the template---when getting case attributes. (reject_case_attribute_data): New endpoint for rejecting data. * wqflask/wqflask/templates/case_attributes.html: Add JS logic for rejecting data. | |||
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