| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2025-05-19 | Pass Connection rather than Cursor: Transaction is maintained. | Frederick Muriuki Muriithi | |
| The idea is that all the data is saved to the database in a single transaction, rather than in bits that could lead to data inconsistencies. As it were, simply passing the connection object, and letting each function create its own cursor will still allow the transaction to be maintained and will not necessitate the refactor of multiple already existing functions. | |||
| 2025-05-19 | Initialise function to save publications | Frederick Muriuki Muriithi | |
| Do a rudimentary save of the publications: this is incomplete and probably very buggy. | |||
| 2025-05-12 | Wireframe saving the data into the database. | Frederick Muriuki Muriithi | |
| 2025-05-12 | Print out progress to STDOUT. | Frederick Muriuki Muriithi | |
| 2025-05-12 | Pass in the logger, rather than the name of the logger. | Frederick Muriuki Muriithi | |
| 2025-05-12 | Handle exceptions within the `with` to prevent silent failure | Frederick Muriuki Muriithi | |
| One, or both of the context managers is "swallowing" exceptions, leading to silent failures. This change manually handles the exceptions within the context manager to avoid such silent failures. | |||
| 2025-05-12 | Allow lowercase versions of the log-level choices. | Frederick Muriuki Muriithi | |
| 2025-05-05 | Init setup and script for async job to load phenotypes into database | Frederick Muriuki Muriithi | |
| 2025-04-25 | Handle exceptions explicitly | Frederick Muriuki Muriithi | |
| Handle any thrown exceptions explicitly to prevent the `with` statement from swallowing them, leading to silent failure of the script. | |||
| 2025-04-14 | Setup module-level loggers. | Frederick Muriuki Muriithi | |
| 2025-04-14 | Compute data differences in the script. | Frederick Muriuki Muriithi | |
| 2025-04-14 | Convert values to float where present. | Frederick Muriuki Muriithi | |
| 2025-04-14 | Move difference computation to `run()` function. | Frederick Muriuki Muriithi | |
| 2025-04-14 | Update existing linked publication(s) rather than creating new. | Frederick Muriuki Muriithi | |
| 2025-04-14 | Compute new PubMed IDs. | Frederick Muriuki Muriithi | |
| 2025-04-14 | Update imports. | Frederick Muriuki Muriithi | |
| 2025-04-14 | Compute differences with tested function. | Frederick Muriuki Muriithi | |
| 2025-04-14 | Move code to save new publications to database. | Frederick Muriuki Muriithi | |
| 2025-04-11 | Move code to fetch phenotype publications from DB to publications package. | Frederick Muriuki Muriithi | |
| 2025-04-11 | Move code to fetch publications from pubmed to publications module. | Frederick Muriuki Muriithi | |
| 2025-04-09 | Convert PubMed_ID value from file to int | Frederick Muriuki Muriithi | |
| 2025-04-09 | Compute publications differences. | Frederick Muriuki Muriithi | |
| 2025-04-09 | Save new publications retrieved from NCBI's PubMed database. | Frederick Muriuki Muriithi | |
| 2025-04-09 | Retrieve publication information from NCBI. | Frederick Muriuki Muriithi | |
| 2025-04-09 | Fix typo. | Frederick Muriuki Muriithi | |
| 2025-04-09 | Check whether there are new PubMed IDs before beginning the fetch. | Frederick Muriuki Muriithi | |
| 2025-03-26 | Pass PubMed IDs from the file to difference computation function. | Frederick Muriuki Muriithi | |
| 2025-03-26 | Add function to compute publication differences. | Frederick Muriuki Muriithi | |
| 2025-03-26 | Partial implementation: Fetch publications from NCBI. | Frederick Muriuki Muriithi | |
| 2025-03-26 | Fetch existing publications from the database. | Frederick Muriuki Muriithi | |
| 2025-03-26 | Compute differences in the descriptions. | Frederick Muriuki Muriithi | |
| 2025-03-26 | Replaces empty strings with None | Frederick Muriuki Muriithi | |
| 2025-03-26 | Collect IDs once at the top-level call to save on iterations. | Frederick Muriuki Muriithi | |
| 2025-03-26 | Check whether the IDs are valid. | Frederick Muriuki Muriithi | |
| 2025-03-25 | Add function to read the file and do basic data processing. | Frederick Muriuki Muriithi | |
| 2025-03-25 | Initialise background script to handle bulk edits. | Frederick Muriuki Muriithi | |
| 2025-01-28 | Remove obsoleted script. | Frederick Muriuki Muriithi | |
| This script was written before the understanding I gained after the demonstration by @acenteno of how the data upload works. | |||
| 2025-01-23 | Ensure names are lowercase for comparison purposes. | Frederick Muriuki Muriithi | |
| 2024-12-03 | Fix some linting and mypy issues. | Frederick Muriuki Muriithi | |
| 2024-12-03 | Improve error text | Frederick Muriuki Muriithi | |
| Move the list to the end of the text to make it easier to clip text in the UI. | |||
| 2024-12-03 | Update file metadata using a mapping | Frederick Muriuki Muriithi | |
| Update the metadata using a mapping rather than updating a field at a time to make it easier to ensure everything is updated in one go. | |||
| 2024-12-03 | Provide consistent way to build file-specific fully-qualified keys | Frederick Muriuki Muriithi | |
| 2024-12-03 | Save 'pheno' errors in redis as they are found. | Frederick Muriuki Muriithi | |
| 2024-12-03 | Add some phenocovar metadata. | Frederick Muriuki Muriithi | |
| 2024-12-03 | Save phenocovar errors in redis as they are found. | Frederick Muriuki Muriithi | |
| 2024-12-03 | Pass the redis connection and fully qualified job id | Frederick Muriuki Muriithi | |
| Pass the redis connection on to the function used to build main since it might need to use a connection to redis. Also pass the computed fully qualified job id rather than recomputing it every time. Update dependent functions to take the new arguments. | |||
| 2024-12-03 | Wrap everything in try-catch to handle errors gracefully. | Frederick Muriuki Muriithi | |
| Put everything in the build_main function within a try-catch block to ensure we capture all exceptions that might occur in different scripts and log them out. This helps with debugging errors in the asynchronous scripts. | |||
| 2024-12-02 | Fix typo. | Frederick Muriuki Muriithi | |
| 2024-12-02 | Send logs to STDOUT too. | Frederick Muriuki Muriithi | |
| 2024-12-02 | Return 0 on completion of QC processing. | Frederick Muriuki Muriithi | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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