tests/testthat/test__multiple_coderuns.R

In rDataPipeline: Functions to Interact with the 'FAIR Data Pipeline'

context("Testing multiple coderuns")

# Write to registry -------------------------------------------------------

uid <- as.character(random_hash())
data_product1 <- file.path("output", "data", uid, "*")
coderun_description <- "Register a file in the pipeline"
dataproduct_description <- "A csv file"
namespace1 <- "username"

endpoint <- Sys.getenv("FDP_endpoint")

# User written config file
config_file <- file.path(tempdir(), "config_files", "multicoderun",
                         paste0("config_", uid, ".yaml"))
create_config(path = config_file,
              description = coderun_description,
              input_namespace = namespace1,
              output_namespace = namespace1)
add_write(path = config_file,
          data_product = data_product1,
          description = dataproduct_description,
          file_type = "csv")

# CLI functions
fair_run(path = config_file, skip = TRUE)

# Initialise code run
config <- file.path(Sys.getenv("FDP_CONFIG_DIR"), "config.yaml")
script <- file.path(Sys.getenv("FDP_CONFIG_DIR"), "script.sh")

for (i in 1:3) {
  handle <- initialise(config, script)

  # Write data
  data_product_x <- file.path(dirname(data_product1), i)
  path <- link_write(handle, data_product_x)
  uid_x <- paste0(uid, "_", i)
  df_x <- data.frame(a = uid_x, b = uid_x)
  write.csv(df_x, path)

  finalise(handle)

  test_that("data products recorded in working config", {
    testthat::expect_equal(handle$outputs$data_product, data_product_x)
    testthat::expect_equal(handle$outputs$use_version, "0.0.1")
  })

  output_component_url <- get_entity(handle$code_run)$outputs
  assertthat::assert_that(length(output_component_url) == 1)
  output_object_url <- get_entity(output_component_url[[1]])$object
  output_dp_url <- get_entity(output_object_url)$data_product
  assertthat::assert_that(length(output_dp_url) == 1)
  output_dp_name <- get_entity(output_dp_url[[1]])$name

  test_that("data products recorded in registry", {
    testthat::expect_equal(output_dp_name, data_product_x)
  })
}