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gn-uploader: Data uploader for GeneNetwork
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Author
2024-02-20
Track filename in the errors
Frederick Muriuki Muriithi
2024-02-20
Generalise fetching of samples/cases/individuals.
Frederick Muriuki Muriithi
2024-02-20
Read samples from geno file.
Frederick Muriuki Muriithi
2024-02-12
Build generic decimal places checker.
Frederick Muriuki Muriithi
2024-02-12
Provide the key for each file listed in the control file.
Frederick Muriuki Muriithi
2024-02-08
Use error objects rather than plain tuple values.
Frederick Muriuki Muriithi
2024-02-06
Check that pheno values are numerical and at least 3 decimal places
Frederick Muriuki Muriithi
2024-02-05
Check that data in geno file is valid
Frederick Muriuki Muriithi
2024-02-05
Fix linting and type errors.
Frederick Muriuki Muriithi
2024-02-05
Retrieve list of all files, and list of missing files
Frederick Muriuki Muriithi
2024-02-02
Ensure control file defaults are set up in code.
Frederick Muriuki Muriithi
2024-01-24
Checks: Update code and tests to ensure all checks pass.
Frederick Muriuki Muriithi
2024-01-23
Tests: Use prefixes in tests rather than starting redis server
Frederick Muriuki Muriithi
2024-01-20
Fetch sample/case names from database
Frederick Muriuki Muriithi
2024-01-15
Update imports: `take` was moved to different package.
Frederick Muriuki Muriithi
2024-01-15
Process `na.strings` even for default cases
Frederick Muriuki Muriithi
2024-01-10
Make identifier column name explicit
Frederick Muriuki Muriithi
2024-01-09
Raise exception on reading non-existing file
Frederick Muriuki Muriithi
2024-01-05
Add missing import.
Frederick Muriuki Muriithi
2024-01-05
Revert "QC: Check for only one decimal place."
Frederick Muriuki Muriithi
2024-01-04
Parse sex information from R/qtl bundle.
Frederick Muriuki Muriithi
2024-01-04
Parse cross information from R/qtl2 bundle.
Frederick Muriuki Muriithi
2024-01-04
Process sex and cross information data in "covar" files.
Frederick Muriuki Muriithi
2024-01-04
Rename test module
Frederick Muriuki Muriithi
2024-01-04
Parse multiple files with same file key.
Frederick Muriuki Muriithi
2024-01-04
Test parsing of multiple files for single key
Frederick Muriuki Muriithi
2024-01-04
Add tests for parsing cross information (covar) files.
Frederick Muriuki Muriithi
2024-01-04
Add tests for parsing 'phenocovar' files.
Frederick Muriuki Muriithi
2024-01-04
Rename test module.
Frederick Muriuki Muriithi
2024-01-03
Use generic parser. Remove obsoleted functions.
Frederick Muriuki Muriithi
2024-01-03
Parse founder_geno files. Generalise parsing files.
Frederick Muriuki Muriithi
2024-01-03
Add tests for `founder_geno` parsing.
Frederick Muriuki Muriithi
2024-01-03
Parse the phenotype data from the R/qtl2 bundle.
Frederick Muriuki Muriithi
2024-01-03
Extract processing of transposed files into reusable function.
Frederick Muriuki Muriithi
2024-01-02
Mark tests as unit tests.
Frederick Muriuki Muriithi
2023-12-28
Rework parsing of transposed geno files.
Frederick Muriuki Muriithi
2023-12-28
Handle transposed geno files.
Frederick Muriuki Muriithi
2023-12-27
Tests: Test parsing of non-transposed geno files.
Frederick Muriuki Muriithi
2023-12-27
Tests: Test parsing of pmap files. Merge testing of map files.
Frederick Muriuki Muriithi
2023-12-27
Tests: Add tests for parsing gmap files.
Frederick Muriuki Muriithi
2023-12-20
Provide instance_path at client creation.
Frederick Muriuki Muriithi
2023-12-20
Stop relying on "GUIX_ENVIRONMENT" envvar
Frederick Muriuki Muriithi
2023-11-24
QC: Check for only one decimal place.
Frederick Muriuki Muriithi
2023-11-15
Linting: Fix linting errors.
Frederick Muriuki Muriithi
2022-11-16
tests: Fix some failing tests
Frederick Muriuki Muriithi
2022-11-16
qc: Allow whole numbers or numbers where the decimals are all zeroes
Frederick Muriuki Muriithi
2022-08-31
Commit missing files.
Frederick Muriuki Muriithi
2022-08-31
Update test: use new script name.
Frederick Muriuki Muriithi
2022-07-07
Fix test
Frederick Muriuki Muriithi
2022-06-28
Check for inconsistent columns
Frederick Muriuki Muriithi
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