In UW-GAC/AnvilDataModels: Utilities for AnVIL data models

knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE)
library(AnvilDataModels)
library(dplyr)

tables <- params$tables
model <- params$model
return_value <- TRUE # returned to render function to indicate T/F passing checks

Data model version: r attr(model, "data_model_version")

Required columns

chk <- check_column_names(tables, model)
res <- parse_column_name_check(chk)
if (nrow(res) > 0) {
    knitr::kable(res)
} else {
    cat("All column names match data model.")
}
if (length(unlist(lapply(chk, function(x) x$missing_required_columns))) > 0) return_value <- FALSE

chk <- check_missing_values(tables, model)
res <- parse_column_type_check(chk)
if (nrow(res) > 0) {
    return_value <- FALSE
    knitr::kable(res)
} else {
    cat("No missing values in required columns.")
}

Column types

chk <- check_column_types(tables, model)
res <- parse_column_type_check(chk)
if (nrow(res) > 0) {
    return_value <- FALSE
    knitr::kable(res)
} else {
    cat("All column types match data model.")
}