| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 6 days | Add cross-reference IDs to job as metadata. | Frederick Muriuki Muriithi | |
| 7 days | BugFix: Logical bug - files have already been "untransposed". | Frederick Muriuki Muriithi | |
| The `read_csv_file_headers` function can read headings from non-transposed or transposed file, depending on the value of a flag. The bug was passing the value of the `*_transposed` flag from the control file, even after any transposed files have been "untransposed". This commit passes an explicit `False` value, and adds a comment to note the fix. | |||
| 7 days | Convert to tuple to allow indexing. | Frederick Muriuki Muriithi | |
| 7 days | Replace first field header with standard "id" header. | Frederick Muriuki Muriithi | |
| 7 days | Pass in the field separator, and comment char while reading file | Frederick Muriuki Muriithi | |
| Pass in the field separator character to split the fields correctly. Also pass in the comment character to safely ignore any comment lines. | |||
| 2025-06-17 | Allow users to provide transposed files. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Pass on the publication to the next job. | Frederick Muriuki Muriithi | |
| 2025-06-10 | Change message level. | Frederick Muriuki Muriithi | |
| 2025-06-09 | Fix minor bug. | Frederick Muriuki Muriithi | |
| 2025-06-09 | Run the authorisation update requests. | Frederick Muriuki Muriithi | |
| 2025-06-09 | Compute the data_link_ids from the request results. | Frederick Muriuki Muriithi | |
| 2025-06-09 | Fix bug in data for creating a new resource. | Frederick Muriuki Muriithi | |
| 2025-06-09 | Compute request data for …/data/link/phenotypes endpoint. | Frederick Muriuki Muriithi | |
| 2025-06-09 | Add debug logging to track process. | Frederick Muriuki Muriithi | |
| 2025-06-09 | Fix return: Don't use `RETURNING *`. | Frederick Muriuki Muriithi | |
| Fetching the results of the insert query with `RETURNING *` does not work as expected with MySQLdb. This commit, thus, returns the explicitly computed values instead. | |||
| 2025-06-05 | Break up long lines. | Frederick Muriuki Muriithi | |
| 2025-06-05 | `update_auth()` scaffolding | Frederick Muriuki Muriithi | |
| Add untested scaffolding for how the `update_auth()` function will work. Include notes to help with figuring the feature out. | |||
| 2025-06-05 | Only update authorisation after all data is entered. | Frederick Muriuki Muriithi | |
| Pull the auth update function out of the database connection contextmanager to prevent any problems with an auth update from causing a rollback of all the data. We can always manually update the authorisation later, therefore, we do not want a failure in that causing the (potentially) time-consuming data entry process from being rolled back. | |||
| 2025-06-03 | Add more logging to track progress. | Frederick Muriuki Muriithi | |
| 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 | Extract building of data items into helper function. | 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 | Compute data in files lazily. | Frederick Muriuki Muriithi | |
| 2025-06-02 | Process NA-strings in the worker script. | Frederick Muriuki Muriithi | |
| 2025-06-02 | Update placeholder function | Frederick Muriuki Muriithi | |
| We'll probably provide a token to use to update the authorisation for the new data. The commit also explicitly raises a `NotImplement` exception for now. | |||
| 2025-06-02 | Add missing import. | Frederick Muriuki Muriithi | |
| 2025-06-02 | Fix bug: Compute data correctly. Replace N/A strings with NoneType. | Frederick Muriuki Muriithi | |
| 2025-06-02 | Add some debugging statements. | Frederick Muriuki Muriithi | |
| 2025-06-02 | Pass the phenotypes name-to-id map to functions. | Frederick Muriuki Muriithi | |
| 2025-06-02 | Compute the map from a phenotype's name to its ID. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Refactor: Extract common pattern into separate function | Frederick Muriuki Muriithi | |
| Extract the common pattern into a separate, more generalized function and pass the new function the data it requires to perform its tasks for the different file types. | |||
| 2025-05-30 | Add typing to load_data function and invoke it. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Save standard errors and counts. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Get the species, population and dataset. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Add more tables to lock list. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Fix query: Add missing field and parameter. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Fix function names. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Fix processing of numerical data to save to the database. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Fix file paths: append the path to the extraction directory. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Refactor out common `__row_to_dataitems__` function. | Frederick Muriuki Muriithi | |
| 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 | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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