| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-03-29 | Quiet linter. | Frederick Muriuki Muriithi | |
| 2024-03-22 | Notify user if identifiers are not consistent. | Frederick Muriuki Muriithi | |
| 2024-03-22 | Map names in files to names in database. | Frederick Muriuki Muriithi | |
| 2024-03-22 | Fix linting issue. | Frederick Muriuki Muriithi | |
| 2024-03-20 | Fix bug: correctly merge standard-error values in file to data in db | Frederick Muriuki Muriithi | |
| `read_datavalues(…)` function returns a dict of the form: ``` { ProbeSetName01: ({…}, …), ProbeSetName02: ({…}, …), ︙ } ``` Previously, the generator would thus try to index into the keys of the datavalues, which were strings, leading to an error. This commit changes the generator to return the values of the datavalues dict as a flattened list of values. | |||
| 2024-02-28 | Fix bug: fetch from cursor, not return from cursor.execute(…)load-raw-data-no-parsing | Frederick Muriuki Muriithi | |
| 2024-02-12 | Provide better error messaging | Frederick Muriuki Muriithi | |
| Provide a better error message that can help the user figure out what they did wrong and fix it for themselves instead of the older, cryptic and extremely unhelpful error message. | |||
| 2024-01-15 | Update imports: `take` was moved to different package. | Frederick Muriuki Muriithi | |
| 2023-12-20 | Fix ID column key | Frederick Muriuki Muriithi | |
| Fix the wrong assumption that the ID key will always be "ProbeSetID". The key for the ID column could change from study to study or dataset to dataset. | |||
| 2023-11-30 | Bug: Fix insertion error | Frederick Muriuki Muriithi | |
| Fix a bug that was causing the data insertion to fail. | |||
| 2023-11-30 | Fix errors caught by pylint and mypy. | Frederick Muriuki Muriithi | |
| 2023-11-15 | Log out DB errors even when handled | Frederick Muriuki Muriithi | |
| Log out any DB errors that occur to help with tracking and debugging failures. | |||
| 2023-11-15 | Remove debugging statement. | Frederick Muriuki Muriithi | |
| 2023-11-15 | Bug: Insert ProbeSets before average data and cross-refs | Frederick Muriuki Muriithi | |
| Insert the ProbeSets first before inserting the average data and cross-referencing it. | |||
| 2023-11-15 | mypy: Fix typing errors. | Frederick Muriuki Muriithi | |
| 2023-11-15 | Linting: Fix linting errors. | Frederick Muriuki Muriithi | |
| 2023-10-30 | Prevent overwrite. Avoid inserting same probeset multiple times. | Frederick Muriuki Muriithi | |
| * Avoid overwriting existing data by adding a random string to the name of the ProbeSet * Read ProbeSet names separately from the means for the strains, to avoid entering the same ProbeSet record over and over with varying names. | |||
| 2023-10-18 | Link to `ProbeSet.Id` in XRef Table | Frederick Muriuki Muriithi | |
| The "ProbeSetId" value in the file is actually stored in the database in the `ProbeSet.Name` field, whereas the `ProbeSetXRef` table actually uses the `ProbeSet.Id` value to define the relationships. This commit fixes that issue. | |||
| 2023-10-16 | Fix bug: Insert ProbeSets if they do not exist. | Frederick Muriuki Muriithi | |
| 2023-10-16 | Fix bug: Provide the platform_id to `insert_means` | Frederick Muriuki Muriithi | |
| 2023-10-16 | Fix bug: parsing fields from query. | Frederick Muriuki Muriithi | |
| 2022-08-05 | Update job status. Display stdout and stderr outputs | Frederick Muriuki Muriithi | |
| * Display the status of the job, as it is running * Display STDERR output if an error occurs * Display STDOUT output as job is running and on successful completion of the job | |||
| 2022-08-04 | Format queries for output. Get rid of extraneous output. | Frederick Muriuki Muriithi | |
| 2022-07-19 | Save standard error data. Fix linting and typing errors. | Frederick Muriuki Muriithi | |
| 2022-07-19 | Implement data insertion (averages/means) | Frederick Muriuki Muriithi | |
| * quality_control/file_utils.py (new file): extract common file utilities. * quality_control/parsing.py (refactor): extract common file utilities. * scripts/insert_data.py: Implement data insertion for averages/means | |||
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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