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

Age	Commit message (Collapse)	Author
10 hours	Fix bug: convert values to strings first. HEAD main	Frederick Muriuki Muriithi

10 hours	Expose 'delete-phenotypes' feature to end users.	Frederick Muriuki Muriithi

10 hours	Fix flash message class.	Frederick Muriuki Muriithi

10 hours	Print out the correct error message.	Frederick Muriuki Muriithi

8 days	Fetch and display actual details for phenotypes being deleted.	Frederick Muriuki Muriithi

8 days	Narrow selection if cross-reference IDs are provided.	Frederick Muriuki Muriithi

8 days	Set max-width to prevent <pre> from reflowing the page.	Frederick Muriuki Muriithi

8 days	Implement UI logic to trigger phenotype deletion job.	Frederick Muriuki Muriithi

8 days	Delete temporary file after completing deletion.	Frederick Muriuki Muriithi

8 days	Add messages to script to indicate progress.	Frederick Muriuki Muriithi

8 days	Fix bug in reading file: Ensure to read all lines.	Frederick Muriuki Muriithi

9 days	Fix indentation.	Frederick Muriuki Muriithi

9 days	Improve layout on small screens.	Frederick Muriuki Muriithi

9 days	Trim whitespace in class names.	Frederick Muriuki Muriithi

9 days	SHIM: Simplify preview UI. Hard-code container width.	Frederick Muriuki Muriithi
	This hard-codes the width of the table's container element to ensure that the overflow property is respected. Without the hard-coded width, the table - generated with javascript - overrides the page width, causing all content to reflow. We do not want that. This also get's rid of the unnecessary "card" interface.
9 days	Make the "no value" indicator more explicit.	Frederick Muriuki Muriithi

9 days	Remove fieldsets: They break styling.	Frederick Muriuki Muriithi

9 days	Reapply "Channel - guix-bioinformatics: Upgrade to commit 9b0955f."	Frederick Muriuki Muriithi
	This reverts commit 3dff71cfcb5beebe5c74c05f47e39faa8e18adef.
10 days	Channels: Fix commits of upstream channels to prevent build failures	Frederick Muriuki Muriithi
	* guix-past: Fix to commit 473c942. * guix-rust-past-crates: Fix to commit b8b7ffb.
10 days	Revert "Channel - guix-bioinformatics: Upgrade to commit 9b0955f."	Frederick Muriuki Muriithi
	The guix-bioinformatics commit 9b0955f leads to a cascade of breakages. I am thus reverting this commit to restore a previous sane state. This reverts commit 7a9108af8d5ad07c1593b256dc3e1a6a7243ad70.
10 days	Channel - guix-bioinformatics: Upgrade to commit 9b0955f.	Frederick Muriuki Muriithi
	Update the commit for the guix bioinformatics channel to fit in with @mbonz update at https://git.genenetwork.org/gn-machines/commit/?id=04c2a18f615bc0a387235544433989af2e8cb62b
10 days	Build script to delete phenotypes.	Frederick Muriuki Muriithi

11 days	Fix typos in configuration variable name.	Frederick Muriuki Muriithi

11 days	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
12 days	Provide some utilities to fetch common config variables.	Frederick Muriuki Muriithi

12 days	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.
12 days	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.
12 days	Outline deletion: Create scaffolding for idea.	Frederick Muriuki Muriithi

12 days	Initialise forms to help delete phenotypes.	Frederick Muriuki Muriithi

12 days	Remove commented out proof-of-concept code.	Frederick Muriuki Muriithi

12 days	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.
2026-01-23	Remove unnecessary console.debug() statement.	Frederick Muriuki Muriithi

2026-01-23	Fix some minor styling (css) issues.	Frederick Muriuki Muriithi

2026-01-23	Add initial placeholder UI to confirm deletion.	Frederick Muriuki Muriithi

2026-01-23	DataTables: Add some custom utility functions.	Frederick Muriuki Muriithi

2026-01-23	DataTables: Improve drawCallback	Frederick Muriuki Muriithi
	* Use references from the datatables API rather than depending on specific classes existing in the tables.
2026-01-23	DataTables: Bug -- Improve performance - use provided indexes.	Frederick Muriuki Muriithi
	* Fix the function signatures * Use the provided indexes for selection
2026-01-23	DataTables: Bug -- Only add the data length if necessary.	Frederick Muriuki Muriithi

2026-01-23	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.
2026-01-23	Collect all selected phenotype IDs for deletion.	Frederick Muriuki Muriithi

2026-01-23	Use a form for deletion of phenotypes.	Frederick Muriuki Muriithi

2026-01-23	Remove data presented elsewhere.	Frederick Muriuki Muriithi

2026-01-23	Re-organise UI	Frederick Muriuki Muriithi
	Move action buttons between introductory text and the table of phenotypes.
2026-01-23	Initialise UI for deletion of phenotypes.	Frederick Muriuki Muriithi

2026-01-23	Add function to delete phenotypes completely.	Frederick Muriuki Muriithi

2026-01-23	Add function to delete numeric data for phenotypes.	Frederick Muriuki Muriithi

2026-01-23	Use correct classes for type-hints.	Frederick Muriuki Muriithi

2026-01-23	Lint: Remove unused imports.	Frederick Muriuki Muriithi

2026-01-15	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