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

Age	Commit message (Collapse)	Author
10 days	Enable search by the publications titles and authors. HEAD main	Frederick Muriuki Muriithi

10 days	Attach publication details to each phenotype trait.	Frederick Muriuki Muriithi

10 days	Improve error messages.	Frederick Muriuki Muriithi
	To help users better understand what the problem with their data is, the errors need to be clearer to them. This commit fixes some error messages.
10 days	Fix bug with cascade of name checks.	Frederick Muriuki Muriithi
	The `meta["data_name"]` statement was leading to an exception in any case where the "data_name" key is not provided. This defeats the purpose of allowing either "dataname" or "data_name". This commit fixes that, while handling the case where neither one of the two are provided.
10 days	Provide defaults for Year and Month.	Frederick Muriuki Muriithi
	Year is a required field, but we provide the month too.
11 days	Update to error log, because it's an error, even though we return 0.	Frederick Muriuki Muriithi

11 days	Move tracing details to INFO loglevel rather than debug.	Frederick Muriuki Muriithi
	We need to trace the auth process so as to help with debugging resource creation failures.
11 days	Pull helper function out of main().	Frederick Muriuki Muriithi

13 days	Pick loggable modules from the application configurations.	Frederick Muriuki Muriithi
	To avoid having to modify code just to activate logging in a specific module, this commit makes the list of loggable modules into a configuration variable that can be loaded at startup.
13 days	Move "Upload Genotypes" button to dataset page.	Frederick Muriuki Muriithi

13 days	Retrieve ALL markers for a species regardless of data.	Frederick Muriuki Muriithi
	Retrieve all the genetic markers that exist for a particular species regardless of whether or not a particular marker has corresponding samples allele data.
13 days	Open page in a new tab.	Frederick Muriuki Muriithi

13 days	Fetch markers from JSON endpoint.	Frederick Muriuki Muriithi

13 days	Rework `list_markers`: return list of markers and basic metadata.	Frederick Muriuki Muriithi

13 days	Add generic "with_dataset" decorator.	Frederick Muriuki Muriithi

13 days	Add module-level logging.	Frederick Muriuki Muriithi

13 days	Get possibly filtered set of markers and count of total records.	Frederick Muriuki Muriithi
	Get a possibly filtered set of markers ensuring the markers are specific to the dataset. Also return the total number of markers in the dataset, even if we do not return the entire list.
13 days	Delete obsolete template.	Frederick Muriuki Muriithi

13 days	Separate related UI elements into separate rows.	Frederick Muriuki Muriithi

13 days	Only parse content when it's present.	Frederick Muriuki Muriithi

13 days	Improve UI text and reorganise the UI.	Frederick Muriuki Muriithi

13 days	Convert from "disabled" to "readonly" to ensure value is submitted.	Frederick Muriuki Muriithi
	Convert the "dataset-name" input element to "readonly" to ensure that the auto-generated name is not editable by the user, but is submitted together with the rest of the data.
2026-04-09	Use multiple threads to speed up the computations.	Frederick Muriuki Muriithi

2026-04-09	Specify the --permu_output option to QTLReaper	Frederick Muriuki Muriithi
	Specify the --permu_output option to QTLReaper to prevent it from attempting to write to the working directory, which in the guix containers is a READONLY file system.
2026-04-09	pylint: non-assigned expressions - silence linter.	Frederick Muriuki Muriithi

2026-04-09	Add a comment note on phenotype resources.	Frederick Muriuki Muriithi

2026-04-09	Prompt user for a name for the resource object.	Frederick Muriuki Muriithi

2026-04-09	Customise CSS only for specific form.	Frederick Muriuki Muriithi

2026-03-27	Genenetwork: Initialise datatable for genetic markers.	Frederick Muriuki Muriithi

2026-03-27	genotypes: Reorganise UI.	Frederick Muriuki Muriithi

2026-03-27	genotypes: Refactor to consistently use monads.	Frederick Muriuki Muriithi

2026-03-27	genotypes: Move "GET" handling out of context manager.	Frederick Muriuki Muriithi

2026-03-27	genotypes: Setup sane defaults for creating new genotype datasets.	Frederick Muriuki Muriithi

2026-03-27	genotypes: Delete obsolete template.	Frederick Muriuki Muriithi

2026-03-27	genotypes: Add module-level logger.	Frederick Muriuki Muriithi

2026-03-25	Open link in new tab/window.	Frederick Muriuki Muriithi

2026-03-25	genotypes: Remove obsolete endpoints.	Frederick Muriuki Muriithi

2026-03-25	genotypes: Simplify UI text.	Frederick Muriuki Muriithi

2026-03-25	Add the DATASET-ID argument to command-line interfaces.	Frederick Muriuki Muriithi

2026-03-18	Move button to the right.	Frederick Muriuki Muriithi

2026-03-17	Improve alignment of table column headings.	Frederick Muriuki Muriithi

2026-03-17	Replace '#' with 'Index' in tables.	Frederick Muriuki Muriithi

2026-03-17	Species: Improve UI text, and fix minor bug.	Frederick Muriuki Muriithi

2026-03-17	Publication: Update UI Text.	Frederick Muriuki Muriithi
	Update the UI text for the Publications page to the text provided by @acenteno.
2026-03-17	Change frontpage text	Frederick Muriuki Muriithi
	Update the text to the suggestion made by @acenteno. Move the sign-in button to the right.
2026-03-17	Fix indentation: Everything is re-indented; no other changes.	Frederick Muriuki Muriithi

2026-03-17	Add a frontpage banner image.	Frederick Muriuki Muriithi

2026-03-11	Check exit code of the Rust QTLReaper script.	Frederick Muriuki Muriithi

2026-03-11	Check whether files exist before attempting to operate on them.	Frederick Muriuki Muriithi

2026-03-11	Set "RUST_BACKTRACE" envvar if loglevel is DEBUG.	Frederick Muriuki Muriithi