| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | |
| 2024-02-21 | Check that samples/cases are consistent | Frederick Muriuki Muriithi | |
| Ensure that **ALL** samples/cases/individuals mentioned in any of the pheno files actually exist in at least one of the geno files. | |||
| 2024-02-21 | Pass 'filename' value to error checker function. | Frederick Muriuki Muriithi | |
| 2024-02-20 | Track filename in the errors | Frederick Muriuki Muriithi | |
| R/qtl2 bundles can contain more than one file, of the same type. When errors are encountered in any of the files, we need to be able to inform the user which file it is, in addition to the line and column number. | |||
| 2024-02-15 | Filter out NULL values | Frederick Muriuki Muriithi | |
| 2024-02-15 | Only log out information if the check is actually run. | Frederick Muriuki Muriithi | |
| 2024-02-13 | Add some parallelism to the QC Checks | Frederick Muriuki Muriithi | |
| 2024-02-13 | Provide nice UI progress indicators. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Check for errors in the 'phenose' file. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Check for errors in the 'pheno' file. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Collect and display errors on 'geno' files in the bundle. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Add scaffolding for running individual files' QC checks | Frederick Muriuki Muriithi | |
| 2024-02-12 | Extract missing files check to external function | Frederick Muriuki Muriithi | |
| 2024-02-12 | Retrive and display generic bundle errors | Frederick Muriuki Muriithi | |
| Implement the first QC check for generic errors e.g. missing files in bundle, etc. Display retrieved errors on UI. | |||
| 2024-02-12 | R/qtl2 QC: Set up scaffolding for QC UI | Frederick Muriuki Muriithi | |
| Set up the scaffolding for the flows and UI that will be used when running QC against the uploaded R/qtl2 bundle. This will be fleshed out later, and the UI is likely to change somewhat, down the line. | |||
| 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. | |||
| 2024-02-05 | Run QC on the 'geno' file in R/qtl2 bundle. | Frederick Muriuki Muriithi | |
| 2024-02-05 | Add a QC step: Check all listed files exist | Frederick Muriuki Muriithi | |
| Add a QC step to the R/qtl2 bundle processing - check that all files that are listed in the control file also exist in the bundle. | |||
| 2024-02-05 | Fix linting and type errors. | Frederick Muriuki Muriithi | |
| 2024-01-24 | Checks: Update code and tests to ensure all checks pass. | Frederick Muriuki Muriithi | |
| 2024-01-24 | redis-prefix: Update file validation code | Frederick Muriuki Muriithi | |
| Update the file validation script and routes to use the redis prefix for jobs. | |||
| 2024-01-23 | Update scripts to use redis prefix. | Frederick Muriuki Muriithi | |
| 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. | |||
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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