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

Age	Commit message (Collapse)	Author
5 days	Allow a publication to NOT have a PubMed ID.	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

7 days	Fix failing test.	Frederick Muriuki Muriithi

7 days	Fix issues caught by linter.	Frederick Muriuki Muriithi

7 days	Display the success page.	Frederick Muriuki Muriithi

7 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.
7 days	Pass on the publication to the next job.	Frederick Muriuki Muriithi

7 days	Bug: Fix logging.	Frederick Muriuki Muriithi

7 days	Cleanup UI detritus.	Frederick Muriuki Muriithi

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

7 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

7 days	Change message level.	Frederick Muriuki Muriithi

8 days	Fix minor bug.	Frederick Muriuki Muriithi

8 days	Run the authorisation update requests.	Frederick Muriuki Muriithi

8 days	Compute the data_link_ids from the request results.	Frederick Muriuki Muriithi

8 days	Fix bug in data for creating a new resource.	Frederick Muriuki Muriithi

8 days	Compute request data for …/data/link/phenotypes endpoint.	Frederick Muriuki Muriithi

8 days	Add debug logging to track process.	Frederick Muriuki Muriithi

8 days	Fix return: Don't use `RETURNING *`.	Frederick Muriuki Muriithi
	Fetching the results of the insert query with `RETURNING *` does not work as expected with MySQLdb. This commit, thus, returns the explicitly computed values instead.
12 days	Break up long lines.	Frederick Muriuki Muriithi

12 days	`update_auth()` scaffolding	Frederick Muriuki Muriithi
	Add untested scaffolding for how the `update_auth()` function will work. Include notes to help with figuring the feature out.
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.
12 days	Only update authorisation after all data is entered.	Frederick Muriuki Muriithi
	Pull the auth update function out of the database connection contextmanager to prevent any problems with an auth update from causing a rollback of all the data. We can always manually update the authorisation later, therefore, we do not want a failure in that causing the (potentially) time-consuming data entry process from being rolled back.
2025-06-03	Add more logging to track progress.	Frederick Muriuki Muriithi

2025-06-03	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.
2025-06-03	Extract building of data items into helper function.	Frederick Muriuki Muriithi

2025-06-03	Increase number of rows per query.	Frederick Muriuki Muriithi

2025-06-03	Debug the query: useful to figure out what's happening.	Frederick Muriuki Muriithi

2025-06-03	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	Compute data in files lazily.	Frederick Muriuki Muriithi

2025-06-02	Process NA-strings in the worker script.	Frederick Muriuki Muriithi

2025-06-02	Add note in documentation.	Frederick Muriuki Muriithi

2025-06-02	Revert "Convert N/A values to NoneType objects."	Frederick Muriuki Muriithi
	This reverts commit 6870c08d484f482cc2f2501d28b474636dd0810d. The "read_csv_file" should return the data in the CSV file, as is, before processing the N/A values.
2025-06-02	Update placeholder function	Frederick Muriuki Muriithi
	We'll probably provide a token to use to update the authorisation for the new data. The commit also explicitly raises a `NotImplement` exception for now.
2025-06-02	Add missing import.	Frederick Muriuki Muriithi

2025-06-02	Fix bug: Compute data correctly. Replace N/A strings with NoneType.	Frederick Muriuki Muriithi

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.
2025-06-02	Convert N/A values to NoneType objects.	Frederick Muriuki Muriithi

2025-06-02	Pass the phenotypes name-to-id map to functions.	Frederick Muriuki Muriithi

2025-06-02	Compute the map from a phenotype's name to its ID.	Frederick Muriuki Muriithi