gn-uploader - gn-uploader: Data uploader for GeneNetwork

Age	Commit message (Collapse)	Author
12 hours	Build script to delete phenotypes. HEAD main	Frederick Muriuki Muriithi

15 hours	Fix typos in configuration variable name.	Frederick Muriuki Muriithi

15 hours	Handle big deletes: Delete in batches.	Frederick Muriuki Muriithi
	Do avoid locking up the database server, or leading to sluggishness when doing huge deletes, do the deletions in chunks, with a tiny delay between each delete to free up the server.a See https://mariadb.com/docs/server/ha-and-performance/optimization-and-tuning/query-optimizations/big-deletes
38 hours	Provide some utilities to fetch common config variables.	Frederick Muriuki Muriithi

38 hours	Move the UPLOAD_DIRECTORY under the SCRATCH_DIRECTORY by default.	Frederick Muriuki Muriithi
	If the UPLOAD_DIRECTORY is not specified in the configuration file(s), then, by default, have it under the SCRATCH_DIRECTORY.
38 hours	Replace TEMPORARY_DIRECTORY with SCRATCH_DIRECTORY	Frederick Muriuki Muriithi
	Avoid using the terminology "TEMPORARY_DIRECTORY" which encourages use of the shared global mutable state in /tmp, that we want to move away from. Instead, we use "SCRATCH_DIRECTORY" which is an explicit specified directory for state needed for and by the gn-uploader application.
39 hours	Outline deletion: Create scaffolding for idea.	Frederick Muriuki Muriithi

40 hours	Initialise forms to help delete phenotypes.	Frederick Muriuki Muriithi

40 hours	Remove commented out proof-of-concept code.	Frederick Muriuki Muriithi

40 hours	Bug: DataTables: Check both radio buttons and checkboxes.	Frederick Muriuki Muriithi
	Extract logic for checking/unchecking a datatable's row's checkbox or radio button as relevant, into a new function. Use new function instead of multiple copies of the logic.
4 days	Remove unnecessary console.debug() statement.	Frederick Muriuki Muriithi

4 days	Fix some minor styling (css) issues.	Frederick Muriuki Muriithi

4 days	Add initial placeholder UI to confirm deletion.	Frederick Muriuki Muriithi

4 days	DataTables: Add some custom utility functions.	Frederick Muriuki Muriithi

4 days	DataTables: Improve drawCallback	Frederick Muriuki Muriithi
	* Use references from the datatables API rather than depending on specific classes existing in the tables.
4 days	DataTables: Bug -- Improve performance - use provided indexes.	Frederick Muriuki Muriithi
	* Fix the function signatures * Use the provided indexes for selection
4 days	DataTables: Bug -- Only add the data length if necessary.	Frederick Muriuki Muriithi

4 days	DataTables: Only set the "data" and "columns" options if not empty.	Frederick Muriuki Muriithi
	To prevent the utility function from breaking the way DataTables works when you provide an already populated table, only set the data and columns options if the user actually provides values for them.
5 days	Collect all selected phenotype IDs for deletion.	Frederick Muriuki Muriithi

5 days	Use a form for deletion of phenotypes.	Frederick Muriuki Muriithi

5 days	Remove data presented elsewhere.	Frederick Muriuki Muriithi

5 days	Re-organise UI	Frederick Muriuki Muriithi
	Move action buttons between introductory text and the table of phenotypes.
5 days	Initialise UI for deletion of phenotypes.	Frederick Muriuki Muriithi

5 days	Add function to delete phenotypes completely.	Frederick Muriuki Muriithi

5 days	Add function to delete numeric data for phenotypes.	Frederick Muriuki Muriithi

5 days	Use correct classes for type-hints.	Frederick Muriuki Muriithi

5 days	Lint: Remove unused imports.	Frederick Muriuki Muriithi

13 days	Remove unused, sensitive data.	Frederick Muriuki Muriithi
	We were not using this data, stored in the session. It is sensitive data, therefore, we avoid collecting it in the first place.
2026-01-13	Remove obsoleted endpoints.	Frederick Muriuki Muriithi

2026-01-13	Migrate background job to use SQLite rather than Redis.	Frederick Muriuki Muriithi

2026-01-13	Use one default handler for both error and success conditions.	Frederick Muriuki Muriithi

2026-01-13	Redirect to "Job Summary" page by default on successful completion.	Frederick Muriuki Muriithi

2026-01-13	Make default datetime formatter for module.	Frederick Muriuki Muriithi

2026-01-12	Make "Background jobs" feature available.	Frederick Muriuki Muriithi

2026-01-09	Move styling to common css file.	Frederick Muriuki Muriithi

2026-01-08	Fix return type declaration for the function.	Frederick Muriuki Muriithi

2026-01-08	Update imports.	Frederick Muriuki Muriithi

2026-01-08	Provide UI to "re-launch" stopped jobs.	Frederick Muriuki Muriithi
	Provide a UI element for future implementation of the feature that will allow a job that has been stopped to be re-run. In reality, the job will not actuall be re-run, rather, a copy of the job will be made, and the copy run instead.
2026-01-08	Stop a background job manually.	Frederick Muriuki Muriithi

2026-01-08	Use newer template for job status updates.	Frederick Muriuki Muriithi

2026-01-08	Extract common UI elements to a macro.	Frederick Muriuki Muriithi

2026-01-08	Bugfix: Fix flash, and redirect to "Job Summary" page.	Frederick Muriuki Muriithi

2026-01-08	Handle the case where the job was manually stopped.	Frederick Muriuki Muriithi

2026-01-08	Redirect to "Job Summary" page for default error handler.	Frederick Muriuki Muriithi
	Redirect to the "Job Summary" page for any job that completed with an error.
2026-01-08	Bugfix: Provide job_id as a keyword argument.	Frederick Muriuki Muriithi

2026-01-08	Delete a job.	Frederick Muriuki Muriithi
	Activate the UI element allowing the user to delete a chosen job.
2026-01-08	Remove delete buttons from this UI.	Frederick Muriuki Muriithi

2026-01-08	Add inactive "action buttons" to UI.	Frederick Muriuki Muriithi
	Add action buttons as signifiers for possible actions. Currently the buttons are inactive.
2026-01-08	Rework summary table	Frederick Muriuki Muriithi
	Move table headers to beginning of row to acquire more space for rendering information.
2026-01-08	Use extended `render_template` function.	Frederick Muriuki Muriithi