Nothing
## ---- include = FALSE----------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----demo-check-function, message = FALSE--------------------------------
library("dccvalidator")
library("readr")
## Load a sample manifest
manifest <- read_tsv(
system.file("extdata", "test_manifest.txt", package = "dccvalidator")
)
manifest
## Check that required columns are complete in the manifest
result <- check_cols_complete(
manifest,
required_cols = c("path", "parent", "grant")
)
result
## ----see-result-details--------------------------------------------------
result$message
result$behavior
result$data
## ----custom-function-----------------------------------------------------
dat <- data.frame(pH = c(2, 6, 3, -2, 0, 15))
check_values_ph <- function(data, ph_col = "pH",
success_msg = "All pH values are valid",
fail_msg = "Some pH values are outside the range 0-14",
behavior_msg = "pH values should be between 0-14") {
values <- data[, ph_col, drop = TRUE]
if (all(values >= 0 & values <= 14)) {
check_pass(
msg = success_msg,
behavior = behavior_msg
)
} else {
check_fail(
msg = fail_msg,
behavior = behavior_msg,
data = values[values > 14 | values < 0]
)
}
}
check_values_ph(dat)
## ----check-condition-example---------------------------------------------
check_values_ph <- function(data, ph_col = "pH",
success_msg = "All pH values are valid",
fail_msg = "Some pH values are outside the range 0-14",
behavior_msg = "pH values should be between 0-14") {
values <- na.omit(data[, ph_col, drop = TRUE])
all_valid <- all(values >= 0 & values <= 14)
check_condition(
msg = ifelse(all_valid, success_msg, fail_msg),
behavior = behavior_msg,
data = if (!all_valid) values[values > 14 | values < 0],
type = ifelse(all_valid, "check_pass", "check_fail")
)
}
## ----show-module-demo, eval = FALSE--------------------------------------
# library("shiny")
# library("shinydashboard")
#
# server <- function(input, output) {
# # Load sample data
# manifest <- read_tsv(
# system.file("extdata", "test_manifest.txt", package = "dccvalidator")
# )
# biosp <- read_csv(
# system.file("extdata", "test_biospecimen.csv", package = "dccvalidator")
# )
#
# # Add logic to run the checks you are interested in and store the results in a
# # list. Here is an example:
# res <- list(
# check_cols_complete(
# manifest,
# c("path", "parent", "grant"),
# success_msg = "All required columns present are complete in the manifest",
# fail_msg = "Some required columns are incomplete in the manifest"
# ),
# check_cols_complete(
# biosp,
# "specimenID",
# success_msg = "All required columns present are complete in the biospecimen metadata",
# fail_msg = "Some required columns are incomplete in the biospecimen metadata"
# ),
# check_specimen_ids_dup(
# biosp,
# success_msg = "Specimen IDs in the biospecimen metadata file are unique",
# fail_msg = "Duplicate specimen IDs found in the biospecimen metadata file"
# )
# )
#
# # Show results in boxes
# callModule(results_boxes_server, "Validation Results", res)
# }
#
# ui <- function(request) {
# dashboardPage(
# header = dashboardHeader(),
# sidebar = dashboardSidebar(),
# body = dashboardBody(
# includeCSS(
# system.file("app/www/custom.css", package = "dccvalidator")
# ),
# results_boxes_ui("Validation Results")
# )
# )
# }
#
# shinyApp(ui, server)
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