| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 9 days | Cleanup UI detritus. | Frederick Muriuki Muriithi | |
| 9 days | Provide handler for `load-new-phenotypes-data` jobs. | Frederick Muriuki Muriithi | |
| 9 days | Provide generalised success and error handling for the jobs. | Frederick Muriuki Muriithi | |
| 9 days | On success, redirect to job status check page. | Frederick Muriuki Muriithi | |
| 9 days | Display the error. | Frederick Muriuki Muriithi | |
| 9 days | Set loglevel for background job's launcher. | Frederick Muriuki Muriithi | |
| 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. | |||
| 2025-06-03 | 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 | 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 | Add some debugging statements. | Frederick Muriuki Muriithi | |
| 2025-06-02 | Parametrize the "DataId" column for different tables. | Frederick Muriuki Muriithi | |
| 2025-06-02 | Explicitly query for newly entered data. | Frederick Muriuki Muriithi | |
| The `cursor.executemany()` call only returned the last row that was inserted, rather than ALL the rows. This is not the correct thing to do, therefore, this commit fixes that by explicitly querying for all the newly entered data. | |||
| 2025-05-30 | Add dataset_id and bundle path to job metadata. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Fix typo: Fix table name. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Bug: Loop until the data is exhausted. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Fix typo, and bug. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Fix indentation. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Use full table names rather than aliases | Frederick Muriuki Muriithi | |
| Using aliases leads to errors when you have to use table locking to prevent data corruption. This commit updates queries to use the full table names rather than aliases, in order to prevent such troubles. | |||
| 2025-05-28 | Add javascript debugging function. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Handle case where the given publication_id does not exist. | 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 | Add function to save the numerical data for phenotypes. | Frederick Muriuki Muriithi | |
| 2025-05-19 | Setup log format for the application. | Frederick Muriuki Muriithi | |
| 2025-05-12 | Use builtin functions to compute log level. | Frederick Muriuki Muriithi | |
| 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 | 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 | 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 | |
| 2025-04-28 | Provide UI for publication creation. | Frederick Muriuki Muriithi | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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