| Age | Commit message (Expand) | Author |
|---|
| 2022-07-12 | Include genotypes for F1s/reference/non-reference strains when fetching...sample data for genotype traits
| zsloan |
| 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...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.
| BonfaceKilz |
| 2022-07-04 | wqflask: use the raw user string if value is non-existent in redis...* 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.
| BonfaceKilz |
| 2022-07-04 | wqflask: Use a map over a tuple when fetching case-attributes...* 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.
| BonfaceKilz |
| 2022-06-21 | wqflask: views: Delete noisy logging and dead code...- 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()".
| BonfaceKilz |
| 2022-06-20 | Simplify partial correlation method choices...- Have only `Pearson's r` and `Spearman's rho` as the available
choices for the partial correlations.
| Frederick Muriuki Muriithi |
| 2022-06-15 | templates: base: Update GN2 footer...* 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>
| BonfaceKilz |
| 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 lines... | zsloan |
| 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...ATM, it's hard to by-pass the authentication
decorators, and as such, skip this test for. This
may be deleted later.
| BonfaceKilz |
| 2022-06-10 | Reverse polarity for gemma additive effects in tests...Fixes broken test. See: #89a7868.
| BonfaceKilz |
| 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...dataset_select_menu_orig.js
| zsloan |
| 2022-06-07 | Fix issue that caused Submit Trait page drop-down menus to not work...Also removes a bunch of unnecessary console logging
| zsloan |
| 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...Apparently if a button has an ID called 'submit', trying to submit a
form via JS won't work
| zsloan |
| 2022-05-31 | Check if entered pubmed_id is already associated with a publication, and...set PublishXRef.PublicationId equal to that Id if it exists
| zsloan |
| 2022-05-31 | Reverse polarity for gemma additive effects...This is basically just a quick pseudo-fix to at least get the polarity
right
| zsloan |
| 2022-05-31 | Fix minor bug | Frederick Muriuki Muriithi |
| 2022-05-31 | Fix error rendering...Render the command_id if present in the error report to help with
troubleshooting failures.
| Frederick Muriuki Muriithi |
| 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...* wqflask/wqflask/metadata_edits.py (approve_case_attribute_data): New
end-point.
| BonfaceKilz |
| 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...* wqflask/wqflask/metadata_edits.py (show_case_attribute_columns): Add
"case_attributes_edit_access" and "login_required" decorators.
| BonfaceKilz |
| 2022-05-27 | Make sure user is part of "editors" group to make (case attrs) edits...* 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.
| BonfaceKilz |
| 2022-05-27 | Replace "_get_author" with "gn3.authentication.get_user_info_by_key"...* wqflask/wqflask/metadata_edits.py (_get_author): Delete function.
(show_case_attribute_columns): Use "get_user_info_by_key".
| BonfaceKilz |
| 2022-05-27 | Implement "reject"---for case-attr---endpoint...* 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.
| BonfaceKilz |
| 2022-05-27 | Move the case-attribute id to the button where the event occurs | BonfaceKilz |
| 2022-05-27 | Make approve/reject buttons normal links instead of embedded links | BonfaceKilz |
| 2022-05-27 | Remove unnecessary white space | BonfaceKilz |
| 2022-05-27 | Parse author id into a human readable name...* wqflask/wqflask/metadata_edits.py (_get_author):
New function.
(show_case_attribute_columns): Pass the author
name and id---case-attribute---field into the
template.
* wqflask/wqflask/templates/case_attributes.html:
Add an "author" column when displaying the
modified/deleted/inserted data. Also, add the
case-attribute's id as a data-id element.
| BonfaceKilz |
