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2021-08-09Removed some paths that have been throwing errors in the logs constantlyzsloan
2021-08-05Generate phenotype and covariate filenames for GEMMA from a hash of values ↵zsloan
and dataset name - previously the covariate filename was static and the phenotype filename was just random
2021-08-04wqflask: views: Remove unnecessary casting for "count"BonfaceKilz
Sometimes, the "count" value can be an "x", as opposed to an int. With the cast, an un-handled error could be thrown.
2021-08-04wqflask: views: Replace hard-coded "/tmp" dirBonfaceKilz
2021-08-03Remove hard coded PATH for csvdiff binaryBonfaceKilz
2021-08-03Replace TMPDIR hard-coded val with one set from flaskBonfaceKilz
2021-08-03wqflask: views: Only show user's diffBonfaceKilz
2021-08-03Rename display_files.html -> display_files_admin.htmlBonfaceKilz
2021-08-03Reject diff data on clickBonfaceKilz
2021-08-03Display a flash message after a file(and data) approvalBonfaceKilz
squash! Display a flash message after a file(and data) approval
2021-08-03wqflask: views: After approval, rename the file at the right pointBonfaceKilz
2021-08-03wqflask: views: Rename endpoint to "/admin/data-sample/diffs/"BonfaceKilz
2021-08-03wqflask: views: use dataset_id when inserting into metadata_auditBonfaceKilz
2021-08-03wqflask: views: Add dataset_id to diff json that'll be storedBonfaceKilz
2021-08-03wqflask: views: Add author name to generated diff's filenameBonfaceKilz
2021-08-03templates: display_files: Add a a reject buttonBonfaceKilz
2021-08-03templates: edit_phenotype: Put csv "oownload" button above "Browse"BonfaceKilz
2021-08-03templates: edit_phenotype: Remove link to the approve pageBonfaceKilz
2021-08-03wqflask: views: Flash messages during editsBonfaceKilz
2021-08-03wqflask: views: Get the publishdata_id from the fileBonfaceKilz
2021-08-03wqflask: views: Filter out approved/ rejected files during displayBonfaceKilz
* wqflask/wqflask/views.py (approve_data): Only show files that have not been approved/ rejected.
2021-08-03wqflask: views: Replace `update_raw` with `update_sample_data`BonfaceKilz
2021-08-03templates: edit_phenotype: Add some margin to links for csv downloadBonfaceKilz
2021-08-03templates: edit_phenotype: Properly centre form controlsBonfaceKilz
2021-08-03templates: edit_phenotype: Use proper page header for this pageBonfaceKilz
2021-08-03templates: edit_phenotype: add some form of padding upload buttonBonfaceKilz
2021-08-03edit_phenotype: Remove duplicate htmlBonfaceKilz
2021-08-03templates: edit_phenotype: Add file upload and "approval" buttonsBonfaceKilz
2021-08-03templates: edit_phenotype: Add enctype to form cause of file uploadsBonfaceKilz
2021-08-03wqflask: views: Return the json data for viewingBonfaceKilz
* wqflask/wqflask/views.py (display_file): New function.
2021-08-03wqflask: views: Approve data when the "approve" button is clickedBonfaceKilz
* wqflask/wqflask/views.py (approve_data): New function.
2021-08-03wqflask: views: Show diff files for the adminBonfaceKilz
* wqflask/wqflask/views.py (display_diffs_admin): New function. * wqflask/wqflask/templates/display_files.html: New template to show the diffs.
2021-08-03wqflask: views: Process file_csv if provided and get the diffBonfaceKilz
* wqflask/wqflask/views.py (update_phenotype): If a file is provided in the request, get the diff and store it in a data escrow.
2021-08-03wqflask: views: Remove un-necessary comment "#" sequenceBonfaceKilz
2021-08-03wqflask: views: Edit end-point to use the phenotype-idBonfaceKilz
squash! wqflask: views: Edit end-point to use the phenotype-id
2021-08-03wqflask: views: Add endpoint for getting the csv dataBonfaceKilz
2021-07-23minor fixes for test_correlation_page table columnsAlexander Kabui
2021-07-23set compute_all for test_compute to TrueAlexander Kabui
2021-07-23handle missing tissue input dataAlexander Kabui
2021-07-13Fixed corr_coeffient to corr_coefficientzsloan
2021-07-12Encode user_id as bytestring if not already bytestring to account for some ↵zsloan
user_ids being stored as different encoding
2021-07-12fix merge conflictAlexander Kabui
2021-07-12tests: test_markdown_routes: Remove stubbed out testsBonfaceKilz
2021-07-12templates: show_trait_details: Show edit buttons conditionallyBonfaceKilz
* wqflask/wqflask/templates/show_trait_details.html: Check the data type, and load different edit buttons.
2021-07-12wqflask: views: Add route for updating the probesetBonfaceKilz
2021-07-12templates: edit_probeset: Add template for editing probeset dataBonfaceKilz
* wqflask/wqflask/templates/edit_probeset.html: New file(template).
2021-07-12wqflask: views: Add extra route showing probeset editing formBonfaceKilz
* wqflask/wqflask/views.py (edit_probeset): New function/ route.
2021-07-12wqflask: views: Rename endpoint for editing a traitBonfaceKilz
* wqflask/wqflask/views.py (edit_trait): Rename to edit_phenotype. Also rename the endpoint to "/trait/<name>/edit/inbredset-id/<inbred_set_id>" to indicate that and inbredset-id is required. This endpoint will be only used for phenotypes. Finally, render the "edit_phenotype.html" template (update_trait): Rename to update_phenotype. Also, remove hard-coded redirect, and replace it with the correct values. * wqflask/wqflask/templates/edit_trait.html: Rename to edit_phenotype.html
2021-07-09Merge branch 'testing' into feature/use_gn3_for_correlationszsloan
2021-07-09Remove commented out function do_bicorzsloan
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