| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | |
| 2024-12-02 | Change from 'pending' to 'started' on entry to script. | Frederick Muriuki Muriithi | |
| Update the status of the job from 'pending' to 'started' at the entry-point of the script. | |||
| 2024-11-22 | Use gn-libs code for db connection. | Frederick Muriuki Muriithi | |
| Use the code in gn-libs to connect to the database, rather than a local module. | |||
| 2024-10-24 | Reduce number of local variables created in function. | Frederick Muriuki Muriithi | |
| Use the values in the argparse.Namespace object directly to avoid creating many local variables. | |||
| 2024-10-24 | Add `jobid` to extraction directory | Frederick Muriuki Muriithi | |
| Add the job id to help "group" files that belong to the same job. | |||
| 2024-10-24 | Check pheno, phenose, and phenonum files with logging | Frederick Muriuki Muriithi | |
| Add logging to the `qc_pheno_file` function so that we get the messages pushed to redis for every file that is being checked for errors. | |||
| 2024-10-24 | Check phenocovar files with logging | Frederick Muriuki Muriithi | |
| Build a function-scope logger using the new `scripts.redis_logger.RedisMessageListHandler` log handler to log-out the messages for each phenocovar file being processed in a more thread-safe way. | |||
| 2024-10-24 | Fix linting and typing errors. | Frederick Muriuki Muriithi | |
| 2024-10-24 | Add a `--loglevel` argument to select loglevel in scripts | Frederick Muriuki Muriithi | |
| To enable selection of log levels within scripts, this commit adds the `--loglevel` argument to the list of arguments that can be passed to scripts. | |||
| 2024-10-24 | Parse entire namespace object rather than individual values. | Frederick Muriuki Muriithi | |
| 2024-10-24 | Move logger creation to `build_main` function | Frederick Muriuki Muriithi | |
| Since the module-level loggers are built mostly the same, move the creation of the logger to the more general function to reduce repetition. | |||
| 2024-10-24 | Add handler to send log messages to specific Redis list | Frederick Muriuki Muriithi | |
| Class `RedisMessageListHandler` builds a log handler that pushes any messages logged out to the redis list specified by its `fullyqualifiedkey` argument. | |||
| 2024-10-22 | Refactor `qc_pheno_file` and reuse it for different file types. | Frederick Muriuki Muriithi | |
| The QC/QA steps taken by the `qc_pheno_file` function are very similar across the "pheno", "phenose" and "phenonum" files. This commit makes the `qc_pheno_file` function a higher-order function and we pass the file-type specific check(s) as a callable (function) to be used for the QC/QA process. | |||
| 2024-10-22 | Check for errors in `pheno` files. | Frederick Muriuki Muriithi | |
| 2024-10-21 | Check `phenocovar` files for errors. | Frederick Muriuki Muriithi | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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