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

Age	Commit message (Collapse)	Author
4 days	Allow a publication to NOT have a PubMed ID.HEAD main	Frederick Muriuki Muriithi

5 days	Create a visual separation of fields.	Frederick Muriuki Muriithi

5 days	Improve publication fetching for datatables.	Frederick Muriuki Muriithi

5 days	Improve logger setup.	Frederick Muriuki Muriithi

6 days	Limit returned results	Frederick Muriuki Muriithi
	Limit the number of results returned to make page more responsive. This is buggy at this point — it doesn't do exactly what I expect, e.g. when I attempt to scroll, or use pagination, it doesn't actually display all the pages as expected.
6 days	Enable server-side searching.	Frederick Muriuki Muriithi

6 days	Specify searchable columns.	Frederick Muriuki Muriithi

6 days	Fix issues caught by linter.	Frederick Muriuki Muriithi

6 days	Display the success page.	Frederick Muriuki Muriithi

6 days	Bug: The Phenotype datasets need the InbredSet.Name as a prefix	Frederick Muriuki Muriithi
	The Phenotype datasets need the InbredSet.Name, (not the InbredSet.InbredSetCode) as a prefix for the data to be found and listed in the GeneNetwork menu.
6 days	Pass on the publication to the next job.	Frederick Muriuki Muriithi

6 days	Bug: Fix logging.	Frederick Muriuki Muriithi

6 days	Cleanup UI detritus.	Frederick Muriuki Muriithi

6 days	Provide handler for `load-new-phenotypes-data` jobs.	Frederick Muriuki Muriithi

6 days	Provide generalised success and error handling for the jobs.	Frederick Muriuki Muriithi

7 days	On success, redirect to job status check page.	Frederick Muriuki Muriithi

7 days	Display the error.	Frederick Muriuki Muriithi

7 days	Set loglevel for background job's launcher.	Frederick Muriuki Muriithi

12 days	Request token for use with script to update authorisations	Frederick Muriuki Muriithi
	After the script has completed loading the data into the database, the user who uploads the data will need to access the data they've uploaded. This commit requests a new token to use with the script for updating the authorisations as appropriate, to grant the user access to their data.
14 days	Save data with `LOAD DATA INFILE …` query	Frederick Muriuki Muriithi
	To help speed up the saving of the data (for really huge files) into the database, use the `LOAD DATA INFILE …` command if available, and if not fallback to the one using raw queries.
14 days	Increase number of rows per query.	Frederick Muriuki Muriithi

14 days	Debug the query: useful to figure out what's happening.	Frederick Muriuki Muriithi

14 days	Memory saving: Don't reload saved data	Frederick Muriuki Muriithi
	We already have all the data in memory, so we do not need to reload it and keep yet another copy.
2025-06-02	Add some debugging statements.	Frederick Muriuki Muriithi

2025-06-02	Parametrize the "DataId" column for different tables.	Frederick Muriuki Muriithi

2025-06-02	Explicitly query for newly entered data.	Frederick Muriuki Muriithi
	The `cursor.executemany()` call only returned the last row that was inserted, rather than ALL the rows. This is not the correct thing to do, therefore, this commit fixes that by explicitly querying for all the newly entered data.
2025-05-30	Add dataset_id and bundle path to job metadata.	Frederick Muriuki Muriithi

2025-05-30	Fix typo: Fix table name.	Frederick Muriuki Muriithi

2025-05-30	Bug: Loop until the data is exhausted.	Frederick Muriuki Muriithi

2025-05-30	Fix typo, and bug.	Frederick Muriuki Muriithi

2025-05-30	Fix indentation.	Frederick Muriuki Muriithi

2025-05-30	Use full table names rather than aliases	Frederick Muriuki Muriithi
	Using aliases leads to errors when you have to use table locking to prevent data corruption. This commit updates queries to use the full table names rather than aliases, in order to prevent such troubles.
2025-05-28	Add javascript debugging function.	Frederick Muriuki Muriithi

2025-05-19	Handle case where the given publication_id does not exist.	Frederick Muriuki Muriithi

2025-05-19	Provide extra metadata to the job.	Frederick Muriuki Muriithi

2025-05-19	Provide missing URI to the MariaDB database to the script.	Frederick Muriuki Muriithi

2025-05-19	Add function to save the numerical data for phenotypes.	Frederick Muriuki Muriithi

2025-05-19	Setup log format for the application.	Frederick Muriuki Muriithi

2025-05-12	Use builtin functions to compute log level.	Frederick Muriuki Muriithi

2025-05-12	Break "merge file" race-condition	Frederick Muriuki Muriithi
	Multiple requests/threads were attempting to merge the same file, leading to race conditions, and sometimes, rarely, it would lead to actual data corruption.
2025-05-12	BugFix: Don't scroll to top of page on clicking "Browse" buttons.	Frederick Muriuki Muriithi
	This fixes the behaviour where clicking the "Browse" buttons on any of the resumable elements, the viewport would scroll to the top of the page.
2025-05-09	Use more of the screen width for content on smaller screens.	Frederick Muriuki Muriithi
	Display only the links and main content on screens smaller than 20 CSS inches — the idea is that laptop screens and smaller will only display the links and the main content, leaving the sidebar content hidden.
2025-05-05	Init setup and script for async job to load phenotypes into database	Frederick Muriuki Muriithi

2025-05-05	Save/Create new phenotypes in the database.	Frederick Muriuki Muriithi

2025-05-05	Provide endpoint for loading data after QC is successful.	Frederick Muriuki Muriithi

2025-05-05	Require that the publication is present.	Frederick Muriuki Muriithi

2025-05-05	Move previews below each item rather than being in the sidebar.	Frederick Muriuki Muriithi

2025-05-05	Include the publication when provided.	Frederick Muriuki Muriithi

2025-05-05	Allow plain text files too.	Frederick Muriuki Muriithi

2025-05-02	PoC: Use independent module-level loggers with application	Frederick Muriuki Muriithi
	Using flask.current_app.logger for logging in modules leads to the modules requiring an app context, even when the module itself could be used outside of the application. This commit provides a proof-of-concept (really, me finally putting in the effort to figure out logging) for how we could allow independent loggers at the module level, that can then be hooked up to the main logging in the system in question.