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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
2022-05-26Fetch the menu data from GN3Frederick Muriuki Muriithi
2022-05-26Indicate error if system in unable to fetch menuFrederick Muriuki Muriithi
2022-05-25Add 'submit' class to Submit button when selecting cofactorszsloan
This was mistakenly removed with a recent change and caused cofactors selection to stop working
2022-05-24Handle async results. Reduce poll time.Frederick Muriuki Muriithi
Handle asynchronous results for partial correlation against a select number of traits. Reduce the polling time from 10 seconds to 5 seconds
2022-05-19Change Pca to PCAzsloan
2022-05-17Make collection page tools open in new tab/windowzsloan
2022-05-17Include relevant CSS files in correlation scatterplot page to improve ↵zsloan
covariate selection appearance
2022-05-17Change collection table in get_covariates_from_collection to be the same as ↵zsloan
in get_traits_from_collection.js
2022-05-17Remove the Delete Collection option from the view collection page andzsloan
rename Delete Rows to just Remove
2022-05-16Check for queued results explicitlyFrederick Muriuki Muriithi
Rather than checking the status field, check for the queued field instead and only display the 'in progress' indicator when the computation has been queued for later.
2022-05-16Fix errors: with_target_db and target_traits issuesFrederick Muriuki Muriithi
- Ensure the 'with_target_db' value is set up correctly when sending request to GN3 API - Set up empty target traits list in case none has been provided
2022-05-10Ignore metadata when importing collection filezsloan
2022-05-10Add metadata to collection export filezsloan
2022-05-10Add user email to form so it can be included in collection export metadatazsloan
2022-05-10Add rest of JS/Python code for importing collections from fileszsloan
2022-05-10Export trait string in original formatzsloan
Previously I was splitting by colon to make it comma-delimited, but this is pointless since this file is going to be reformatted with the colons after being imported
2022-05-10Create import_collection functionzsloan
2022-05-10Add button for collection import and JS for submitting formzsloan
2022-05-10Display user email on collection list page when user_name doesn't existzsloan
2022-05-10Refactor JS code for exports somezsloan
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