| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-01-22 | scripts: Pass in logger to get detailed updates. | Frederick Muriuki Muriithi | |
| 2024-01-22 | UI: Show progress of R/qtl2 bundle processing. | Frederick Muriuki Muriithi | |
| 2024-01-20 | Fetch sample/case names from database | Frederick Muriuki Muriithi | |
| Fetch the sample/case names from the database rather than from a static file in the repository. Issue: https://issues.genenetwork.org/issues/quality-control/read-samples-from-database-by-species | |||
| 2024-01-19 | scripts: Process R/qtl2 bundle | Frederick Muriuki Muriithi | |
| Build script to start the processing of the R/qtl2 bundle. | |||
| 2024-01-16 | Filter out items with values of `None`. | Frederick Muriuki Muriithi | |
| The ProbeSetData table does not allow `NULL` for the `value` column for good reason - if there is no value, just don't have a record for that particular sample. | |||
| 2024-01-15 | Update imports: `take` was moved to different package. | Frederick Muriuki Muriithi | |
| 2024-01-15 | Process the `pheno` files. | Frederick Muriuki Muriithi | |
| Process the data in the pheno files and insert it into the database. | |||
| 2024-01-15 | Initialise `install_phenos` script. | Frederick Muriuki Muriithi | |
| 2024-01-15 | Extract common structure into separate modules. | Frederick Muriuki Muriithi | |
| 2024-01-11 | Update pmap data in the database. | Frederick Muriuki Muriithi | |
| 2024-01-11 | Update gmap data in the database | Frederick Muriuki Muriithi | |
| Update the genetic positions (in centiMorgans) in the database. | |||
| 2024-01-11 | Cleanup linting and typing errors. | Frederick Muriuki Muriithi | |
| 2024-01-11 | CLI: Require datasetid as an argument. | Frederick Muriuki Muriithi | |
| 2024-01-10 | Provide convenience functions to avoid subtle call errors | Frederick Muriuki Muriithi | |
| 2024-01-10 | Cross-reference genotype data to the dataset. | Frederick Muriuki Muriithi | |
| 2024-01-10 | Insert genotype data. | Frederick Muriuki Muriithi | |
| 2024-01-10 | Cross-reference individuals to populations. | Frederick Muriuki Muriithi | |
| 2024-01-10 | Insert any new individuals/samples into the database. | Frederick Muriuki Muriithi | |
| 2024-01-10 | Insert any new markers | Frederick Muriuki Muriithi | |
| Insert any new markers found into the database. | |||
| 2024-01-09 | WIP: Install genotypes from R/qtl2 bundle | Frederick Muriuki Muriithi | |
| Load the genotype information from the R/qtl2 bundle and insert it into the database. | |||
| 2024-01-09 | Fix linting errors | Frederick Muriuki Muriithi | |
| 2024-01-09 | scripts: Log to redis | Frederick Muriuki Muriithi | |
| Add a logger that will log output to a redis list. This will be useful to retrieve the output(s) of the running script to help display some form of progress to the user. | |||
| 2024-01-08 | Use extracted functions and fix bugs | 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. | |||
| 2023-12-18 | Samples: Hook-up external async script to upload the samples. | Frederick Muriuki Muriithi | |
| 2023-12-14 | samples: Create external script and fix some bugs. | Frederick Muriuki Muriithi | |
| 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 | Implement data insertion | Frederick Muriuki Muriithi | |
| - Hook up external data insertion script to webserver code - Provide rudimentary status indication - Generalise some job creation details | |||
| 2022-08-04 | Handle stderr output | Frederick Muriuki Muriithi | |
| * Fix bug where stderr was not being updated on redis appropriately | |||
| 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 | |||
| 2022-07-19 | Check connections before launching | Frederick Muriuki Muriithi | |
| * qc_app/__init__.py (refactor): Check connection before launching the application * qc_app/check_connections.py (new file): Add code to check connections * qc_app/db_utils.py (refactor): enable passing the database uri as an argument to the connection creation function. * scripts/worker.py (refactor): Use new code to check for redis connection. | |||
| 2022-07-19 | Add generic worker script | Frederick Muriuki Muriithi | |
| Add a generic worker script, whose purpose is: - to launch the specific worker script - to capture both stdin and stderr streams and put them on redis In this way, we can launch redis-aware and redis-unaware workers and capture their outputs or errors for later processing. | |||
| 2022-07-19 | Rename file validation script | Frederick Muriuki Muriithi | |
| As preparation for building a new generic worker script, this commit renames the file validation script from 'worker.py' to 'validate_file.py' so as to ensure the name conforms better to what the script does. | |||
| 2022-07-07 | Replace 'magic' with builtin 'mimetypes' | Frederick Muriuki Muriithi | |
| Use the builtin mimetypes which gives better results | |||
| 2022-06-28 | Check for inconsistent columns | Frederick Muriuki Muriithi | |
| The number columns in each contents line should be equal to the nember of columns in the header line. | |||
| 2022-06-15 | Fix linting and type errors | Frederick Muriuki Muriithi | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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