| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 3 days | Add cross-reference IDs to job as metadata. | Frederick Muriuki Muriithi | |
| 3 days | BugFix: Logical bug - files have already been "untransposed". | Frederick Muriuki Muriithi | |
| The `read_csv_file_headers` function can read headings from non-transposed or transposed file, depending on the value of a flag. The bug was passing the value of the `*_transposed` flag from the control file, even after any transposed files have been "untransposed". This commit passes an explicit `False` value, and adds a comment to note the fix. | |||
| 3 days | Convert to tuple to allow indexing. | Frederick Muriuki Muriithi | |
| 3 days | Replace first field header with standard "id" header. | Frederick Muriuki Muriithi | |
| 3 days | Pass in the field separator, and comment char while reading file | Frederick Muriuki Muriithi | |
| Pass in the field separator character to split the fields correctly. Also pass in the comment character to safely ignore any comment lines. | |||
| 4 days | Collapse the DataTables' viewport if there's less data. | Frederick Muriuki Muriithi | |
| 5 days | Use positional parameters rather than named ones. | Frederick Muriuki Muriithi | |
| Named parameters were causing problems on staging, where the names would be converted into bytestrings and then used to index into the dictionaries, leading to `KeyError` exceptions. | |||
| 5 days | Add notification for users that data is not saved yet. | Frederick Muriuki Muriithi | |
| 5 days | Use pathlib.Path object for file paths. | Frederick Muriuki Muriithi | |
| 12 days | Allow users to provide transposed files. | Frederick Muriuki Muriithi | |
| 12 days | Fix documentation: The rows and columns were interchanged in docs. | Frederick Muriuki Muriithi | |
| 2025-06-12 | Allow a publication to *NOT* have a PubMed ID. | Frederick Muriuki Muriithi | |
| 2025-06-12 | Create a visual separation of fields. | Frederick Muriuki Muriithi | |
| 2025-06-12 | Improve publication fetching for datatables. | Frederick Muriuki Muriithi | |
| 2025-06-12 | Improve logger setup. | Frederick Muriuki Muriithi | |
| 2025-06-11 | 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. | |||
| 2025-06-11 | Enable server-side searching. | Frederick Muriuki Muriithi | |
| 2025-06-11 | Specify searchable columns. | Frederick Muriuki Muriithi | |
| 2025-06-11 | Fix failing test. | Frederick Muriuki Muriithi | |
| 2025-06-11 | Fix issues caught by linter. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Display the success page. | Frederick Muriuki Muriithi | |
| 2025-06-10 | 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. | |||
| 2025-06-10 | Pass on the publication to the next job. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Bug: Fix logging. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Cleanup UI detritus. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Provide handler for `load-new-phenotypes-data` jobs. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Provide generalised success and error handling for the jobs. | Frederick Muriuki Muriithi | |
| 2025-06-10 | On success, redirect to job status check page. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Display the error. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Set loglevel for background job's launcher. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Change message level. | Frederick Muriuki Muriithi | |
| 2025-06-09 | Fix minor bug. | Frederick Muriuki Muriithi | |
| 2025-06-09 | Run the authorisation update requests. | Frederick Muriuki Muriithi | |
| 2025-06-09 | Compute the data_link_ids from the request results. | Frederick Muriuki Muriithi | |
| 2025-06-09 | Fix bug in data for creating a new resource. | Frederick Muriuki Muriithi | |
| 2025-06-09 | Compute request data for …/data/link/phenotypes endpoint. | Frederick Muriuki Muriithi | |
| 2025-06-09 | Add debug logging to track process. | Frederick Muriuki Muriithi | |
| 2025-06-09 | 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. | |||
| 2025-06-05 | Break up long lines. | Frederick Muriuki Muriithi | |
| 2025-06-05 | `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. | |||
| 2025-06-05 | 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. | |||
| 2025-06-05 | 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 | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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