Update epidist_db() to give more fine-grained control
#231
Workflow file for this run
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| name: Validate JSONs | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| jobs: | |
| validate-json: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| packages: | |
| any::jsonlite | |
| any::jsonvalidate | |
| any::yaml | |
| - name: Validate JSON | |
| run: | | |
| # read in epiparameter database | |
| data <- utils::read.csv( | |
| file = file.path("inst", "extdata", "parameters.csv"), | |
| header = TRUE | |
| ) | |
| # convert cells with arrays to numeric | |
| for (i in grep(pattern = "_ci_limits$", x = colnames(data))) { | |
| if (!all(is.na(data[[i]]))) { | |
| data[[i]] <- lapply( | |
| strsplit(x = data[[i]], split = ",", fixed = TRUE), | |
| as.numeric | |
| ) | |
| } | |
| } | |
| data_json <- jsonlite::toJSON( | |
| x = data, | |
| dataframe = "columns", | |
| na = NULL, | |
| pretty = TRUE | |
| ) | |
| # read schema | |
| schema <- yaml::read_yaml( | |
| file.path("inst", "extdata", "data_dictionary.yaml") | |
| ) | |
| schema_json <- jsonlite::toJSON( | |
| x = schema, | |
| dataframe = "column", | |
| auto_unbox = TRUE, | |
| pretty = TRUE | |
| ) | |
| jsonvalidate::json_validate( | |
| json = data_json, | |
| schema = schema_json, | |
| engine = "ajv", | |
| verbose = TRUE, | |
| greedy = TRUE, | |
| strict = TRUE, | |
| error = TRUE | |
| ) | |
| shell: Rscript {0} |