| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2025-06-26 | Narrow search to only uploaded traits. | Frederick Muriuki Muriithi | |
| 2025-06-24 | Use positional parameters rather than named ones. | Frederick Muriuki Muriithi | |
| Named parameters were causing problems on staging, where the names would be converted into bytestrings and then used to index into the dictionaries, leading to `KeyError` exceptions. | |||
| 2025-06-24 | Use pathlib.Path object for file paths. | Frederick Muriuki Muriithi | |
| 2025-06-17 | Allow users to provide transposed files. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Display the success page. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Pass on the publication to the next job. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Bug: Fix logging. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Provide handler for `load-new-phenotypes-data` jobs. | Frederick Muriuki Muriithi | |
| 2025-06-10 | On success, redirect to job status check page. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Display the error. | Frederick Muriuki Muriithi | |
| 2025-06-10 | 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. | |||
| 2025-05-19 | 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 | |
| 2025-05-12 | Use builtin functions to compute log level. | Frederick Muriuki Muriithi | |
| 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 | Include the publication when provided. | Frederick Muriuki Muriithi | |
| 2025-04-21 | Proceed to jobs status update page. | Frederick Muriuki Muriithi | |
| 2025-04-21 | Use module-specific logger. | Frederick Muriuki Muriithi | |
| 2025-04-21 | Add "DataId" to top-level trait details. | Frederick Muriuki Muriithi | |
| The `DataId` is unique in the `PublishXRef` table. | |||
| 2025-04-14 | Fix typo. | Frederick Muriuki Muriithi | |
| 2025-04-14 | Move common fieldnames into exportable variable. | Frederick Muriuki Muriithi | |
| 2025-04-14 | Implement difference computations. | Frederick Muriuki Muriithi | |
| 2025-04-14 | Add tests for new difference computation function. | Frederick Muriuki Muriithi | |
| 2025-04-14 | Log out job command for easier debug. | Frederick Muriuki Muriithi | |
| 2025-04-14 | Provide species, population and dataset identifiers as job metadata. | Frederick Muriuki Muriithi | |
| 2025-03-26 | Pass in system log-level to script. | Frederick Muriuki Muriithi | |
| 2025-03-26 | Provide connection URI for mariadb. | Frederick Muriuki Muriithi | |
| 2025-03-26 | Update comment text. | Frederick Muriuki Muriithi | |
| 2025-03-25 | Run job with unbuffered outputs. | Frederick Muriuki Muriithi | |
| 2025-03-25 | Update name of launcher script used. | Frederick Muriuki Muriithi | |
| 2025-03-24 | Begin processing the uploadeded bulk-edit file. | Frederick Muriuki Muriithi | |
| 2025-03-21 | Add "PubMed_ID" field | Frederick Muriuki Muriithi | |
| The "PubMed_ID" field allows the user to edit the publication that's attached to each phenotype trait. | |||
| 2025-03-21 | Bulk Edit: Initialise the bulk-edit upload | Frederick Muriuki Muriithi | |
| * Provide UI for uploading the file * Provide (partially implemented) endpoint to handle the uploaded file. | |||
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
| about summary refs log tree commit diff |