| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2025-05-28 | Bug: Fix actual data value, not result set. | Frederick Muriuki Muriithi | |
| 2025-05-28 | Bug: Add missing commas. | Frederick Muriuki Muriithi | |
| 2025-05-28 | Maintain single list of tables — build logs and query from list | Frederick Muriuki Muriithi | |
| Maintain a list of tables to lock when running the script and build the logging messages, and lock query from the list for easier maintenance. | |||
| 2025-05-28 | Add missing import. | Frederick Muriuki Muriithi | |
| 2025-05-28 | Pass path to bundle extraction dir, and make paths relative to it. | Frederick Muriuki Muriithi | |
| Pass the path where the bundle was extracted to the function doing the work. Make the paths for the files being used be relative to the extraction directory thus passed. | |||
| 2025-05-19 | Extract the bundle first. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Add "Publication" table to locked tables. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Bug: Connection objects do not have execute() function. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Fix generic bugs | Frederick Muriuki Muriithi | |
| 2025-05-19 | Import missing symbols. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Cross-reference phenotypes, publications, and data. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Retrieve publication first. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Simplify handling of publications: Assume a maximum of one. | Frederick Muriuki Muriithi | |
| Adding publication details in the R/qtl2 bundle might not be an easy thing, so for now, assume all the phenotypes uploaded in a particular session are all published in one publication. | |||
| 2025-05-19 | Add placeholder stub to be implemented later. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Add some notes for later. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Save numeric/computational data for phenotypes. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Retrieve samples' details from the database. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Use correct files for basic phenotypes data. Add notes to self. | Frederick Muriuki Muriithi | |
| The basic phenotype data will be in files under the key "gn-metadata" -> "pheno". We support the possibility of having some descriptions in the "phenocovar" files, since that can happen also. | |||
| 2025-05-19 | Rework order of execution of potential steps. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Cleanup function call. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Fetch next available PublishXRef.DataId value for the phenotypes. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Save the basic phenotypes data into the database. | Frederick Muriuki Muriithi | |
| 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 | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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