| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2025-05-19 | Fix generic bugs | Frederick Muriuki Muriithi | |
| 2025-05-19 | Import missing symbols. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Provide extra metadata to the job. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Provide missing URI to the MariaDB database to the script. | 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 | Add function to save the numerical data for phenotypes. | 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 | Read headers from a CSV file, whether transposed or not. | 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. | |||
| 2025-05-19 | Setup log format for the application. | Frederick Muriuki Muriithi | |
| 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 | Use builtin functions to compute log level. | 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 | Break "merge file" race-condition | Frederick Muriuki Muriithi | |
| Multiple requests/threads were attempting to merge the same file, leading to race conditions, and sometimes, rarely, it would lead to actual data corruption. | |||
| 2025-05-12 | Allow lowercase versions of the log-level choices. | Frederick Muriuki Muriithi | |
| 2025-05-12 | BugFix: Don't scroll to top of page on clicking "Browse" buttons. | Frederick Muriuki Muriithi | |
| This fixes the behaviour where clicking the "Browse" buttons on any of the resumable elements, the viewport would scroll to the top of the page. | |||
| 2025-05-09 | Use more of the screen width for content on smaller screens. | Frederick Muriuki Muriithi | |
| Display only the links and main content on screens smaller than 20 CSS inches — the idea is that laptop screens and smaller will only display the links and the main content, leaving the sidebar content hidden. | |||
| 2025-05-05 | Init setup and script for async job to load phenotypes into database | Frederick Muriuki Muriithi | |
| 2025-05-05 | Save/Create new phenotypes in the database. | Frederick Muriuki Muriithi | |
| 2025-05-05 | Provide endpoint for loading data after QC is successful. | Frederick Muriuki Muriithi | |
| 2025-05-05 | Require that the publication is present. | Frederick Muriuki Muriithi | |
| 2025-05-05 | Move previews below each item rather than being in the sidebar. | Frederick Muriuki Muriithi | |
| 2025-05-05 | Include the publication when provided. | Frederick Muriuki Muriithi | |
| 2025-05-05 | Allow plain text files too. | Frederick Muriuki Muriithi | |
| 2025-05-02 | Mark directories as packages to make modules unique. | Frederick Muriuki Muriithi | |
| 2025-05-02 | PoC: Use independent module-level loggers with application | Frederick Muriuki Muriithi | |
| Using flask.current_app.logger for logging in modules leads to the modules requiring an app context, even when the module itself could be used outside of the application. This commit provides a proof-of-concept (really, me finally putting in the effort to figure out logging) for how we could allow independent loggers at the module level, that can then be hooked up to the main logging in the system in question. | |||
| 2025-05-02 | Format abstracts a little better. | Frederick Muriuki Muriithi | |
| 2025-04-28 | Provide correct redirection uri, and data. | Frederick Muriuki Muriithi | |
| 2025-04-28 | Encode data to UTF-8 to prevent persistence errors. | Frederick Muriuki Muriithi | |
| 2025-04-28 | Search for radio was slow for some reason. | Frederick Muriuki Muriithi | |
| 2025-04-28 | Allow selection from existing publications. | Frederick Muriuki Muriithi | |
| 2025-04-28 | Do not auto-update publication details on conflict | Frederick Muriuki Muriithi | |
| Auto-update of a publication's details on an "insert conflict" would lead to a bug where publications could be overwritten with the wrong information. Rather than auto-update, explicitly indicate the error, and let the user manually edit the record to avoid data inconsistency. | |||
| 2025-04-28 | Implement creating publications. | Frederick Muriuki Muriithi | |
| 2025-04-28 | Add logging. | Frederick Muriuki Muriithi | |
| Without this logging statement, the chunk merging fails with an error that it cannot find one of the chunks when attempting to delete it. That error disappears as soon as I attempt to log out the error and debug. | |||
| 2025-04-28 | Enable autofill of information from PubMed. | Frederick Muriuki Muriithi | |
| 2025-04-28 | Move functions to fetch pubmed data out into a separate js file. | Frederick Muriuki Muriithi | |
| 2025-04-28 | Move generic utility functions to the utils.js file. | Frederick Muriuki Muriithi | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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