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2022-06-01Fix the way R/qtl is called in the GN2 REST APIzsloan
2022-06-01Remove IDs called 'submit' to prevent forms from breakingzsloan
Apparently if a button has an ID called 'submit', trying to submit a form via JS won't work
2022-05-31Check if entered pubmed_id is already associated with a publication, andzsloan
set PublishXRef.PublicationId equal to that Id if it exists
2022-05-31Reverse polarity for gemma additive effectszsloan
This is basically just a quick pseudo-fix to at least get the polarity right
2022-05-31Fix minor bugFrederick Muriuki Muriithi
2022-05-31Fix error renderingFrederick Muriuki Muriithi
Render the command_id if present in the error report to help with troubleshooting failures.
2022-05-27Apply python-black on fileBonfaceKilz
2022-05-27Don't make a POST if there's a blank form-elementBonfaceKilz
2022-05-27Move SQL queries to GN3BonfaceKilz
2022-05-27Strip data before storing itBonfaceKilz
2022-05-27Make sure the user is logged in when approving dataBonfaceKilz
2022-05-27Pass secend arg to cursor.execute as a tupleBonfaceKilz
2022-05-27Add sensible styling to "reject"/"approve" buttonsBonfaceKilz
2022-05-27Align "Add New" button with the actions columnBonfaceKilz
2022-05-27Add js logic to POST to "approval" endpointBonfaceKilz
2022-05-27Assign the correct value to keyBonfaceKilz
2022-05-27Display description diff-data if it existsBonfaceKilz
2022-05-27Ony show the title if there are any changes to be approved/rejectedBonfaceKilz
2022-05-27Cosmetic changes in Jinja templateBonfaceKilz
2022-05-27Add new endpoint for "approving" case-attributes modificationsBonfaceKilz
* wqflask/wqflask/metadata_edits.py (approve_case_attribute_data): New end-point.
2022-05-27Remove dead commentBonfaceKilz
2022-05-27Append to "modifications" if "description"/"name" existBonfaceKilz
2022-05-27Make sure is in editor's group to view the case-attributesBonfaceKilz
* wqflask/wqflask/metadata_edits.py (show_case_attribute_columns): Add "case_attributes_edit_access" and "login_required" decorators.
2022-05-27Make sure user is part of "editors" group to make (case attrs) editsBonfaceKilz
* 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.
2022-05-27Replace "_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".
2022-05-27Implement "reject"---for case-attr---endpointBonfaceKilz
* 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.
2022-05-27Move the case-attribute id to the button where the event occursBonfaceKilz
2022-05-27Make approve/reject buttons normal links instead of embedded linksBonfaceKilz
2022-05-27Remove unnecessary white spaceBonfaceKilz
2022-05-27Parse author id into a human readable nameBonfaceKilz
* 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.
2022-05-27Narrow the case-attribute columnBonfaceKilz
2022-05-27Add extra sections for displaying delete/insert dataBonfaceKilz
2022-05-27Fetch diff data from SQLBonfaceKilz
* wqflask/wqflask/metadata_edits.py (show_case_attribute_columns): Replace the redis fetch with SQL for retrieving diff data.
2022-05-27POST deletionsBonfaceKilz
2022-05-27POST new insertsBonfaceKilz
2022-05-27Delete buggy js lineBonfaceKilz
This generates a js error in the console log.
2022-05-27Put the correct class names when appending the name & desc. fieldsBonfaceKilz
2022-05-27Add js logic to make a POST request on DeletionBonfaceKilz
* wqflask/wqflask/templates/case_attributes.html: When deleting a case-attribute, make a POST request.
2022-05-27Store the data in SQL instead of RedisBonfaceKilz
* wqflask/wqflask/metadata_edits.py (show_case_attribute_columns): Store the diff data on a POST in SQL.
2022-05-27Require edit rights to access the case-attributes pageBonfaceKilz
* wqflask/wqflask/metadata_edits.py (update_case_attributes): Add "login_required" and "edit_admins_access_required" decorators.
2022-05-27Display diffs from editing in a nice table.BonfaceKilz
2022-05-27Remove case-attributes list from the metadata edit pageBonfaceKilz
* wqflask/wqflask/metadata_edits.py (display_phenotype_metadata): Delete "headers" variable when passing it to the template. *wqflask/wqflask/templates/edit_phenotype.html: Remove special not that lists the case-attributes with their IDs in brackets.
2022-05-27Save diffed data to redis (wip)BonfaceKilz
* wqflask/wqflask/metadata_edits.py (show_case_attribute_columns): pass the diff'ed data to the template (update_case_attributes): New function. Parses data from JS and saves it redis in "case-attr-diffs:review" * wqflask/wqflask/templates/case_attributes.html: Make post request---to save the data to redis for approval.
2022-05-27Make a POST request on data editBonfaceKilz
* wqflask/wqflask/metadata_edits.py: When editing a case-attribute, make a post request to the relevant end-point.
2022-05-27Parse case attributes as a tuple, not as a dictBonfaceKilz
* wqflask/wqflask/metadata_edits.py (approve_data): Return the fetched case_attributes as is. * wqflask/wqflask/templates/case_attributes.html: Parse the case attributes as a tuple.
2022-05-27Update case-attributes page to make it editableBonfaceKilz
2022-05-27Fix the url to the GN3 serverFrederick Muriuki Muriithi
2022-05-27Display correlation computation errors correctlyFrederick Muriuki Muriithi
- Display any correlation computation errors in a form that tells the user what they did wrong.
2022-05-27Fix UI ErrorsFrederick Muriuki Muriithi
- Display index correctly - Move checkbox element to the table body - Make progress indicator prominent
2022-05-26Enumerate rows and add checkboxesFrederick Muriuki Muriithi
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