R/test_module.R

In zoon: Reproducible, Accessible & Shareable Species Distribution Modelling

#' @import roxygen2
test_module <- function(modulePath) {
  context(paste("Testing module", basename(gsub(".R$", "", modulePath))))

  time <- system.time({
    moduleName <- basename(gsub(".R$", "", modulePath))

    roxy_parse <- ZoonModuleParse(modulePath)

    ## GENERIC TESTS
    test_that(paste("Check roxy_parse", moduleName), {

      # Check roxy_parse is good
      expect_is(roxy_parse, "list",
                info = "Your function appears to the empty, or not a function")
    })

    test_that(paste("Check for generic tags", moduleName), {

      # Check for the required generic tags
      expect_true("title" %in% names(roxy_parse))
      expect_true("description" %in% names(roxy_parse))
      expect_true("name" %in% names(roxy_parse))
      expect_true("family" %in% names(roxy_parse))
      expect_true("author" %in% names(roxy_parse))
      expect_true("section" %in% names(roxy_parse))
      expect_true(any(grepl("^Version: ",
                            roxy_parse[grepl("section", names(roxy_parse))])))
      expect_true(any(grepl("^Date submitted: ",
                            roxy_parse[grepl("section", names(roxy_parse))])))
    })

    # If the family tag is present continue (this error will be reported above)
    if ("family" %in% names(roxy_parse)) {

      ## Test for module specific tags
      test_that("Check for module specific tags", {
        if (roxy_parse$family == "process" |
            roxy_parse$family == "model" |
            roxy_parse$family == "occurrence") {
          
          expect_true("section" %in% names(roxy_parse),
                      info = "Section tag missing")
          
          expect_true(
            any(grepl("^Data type: ",
                      roxy_parse[grepl("section", names(roxy_parse))])),
            info = "Data types have not been specified using the @section tag"
          )
          
          if (any(grepl("^Data type: ",
                        roxy_parse[grepl("section", names(roxy_parse))]))) {
            
            sections <- roxy_parse[grepl("section", names(roxy_parse))]
            data_types <- trimws(strsplit(
              gsub("Data type: ",
                   "",
                   sections[grepl("Data type: ", sections)]),
              split = ",")[[1]])
            data_types_tf <- data_types %in% c(
              "presence-only", "presence/background",
              "presence/absence", "abundance", "proportion"
            )
            expect_true(
              all(data_types_tf),
              info = paste("Data types",
                           paste(data_types[!data_types_tf], collapse = ", "),
                           "not supported. Data types must be one of: ",
                           "'presence-only', 'presence/background', ",
                           "'presence/absence', 'abundance', 'proportion'"
              )
            )
          }
        }
      })

      ## PARAMETER TESTS
      if (roxy_parse$family == "occurrence") {
        test_parameters(roxy_parse, modulePath = modulePath)
      }

      if (roxy_parse$family == "covariate") {
        test_parameters(roxy_parse, modulePath = modulePath)
      }

      if (roxy_parse$family == "process") {
        test_parameters(
          roxy_parse, defaultParams = ".data",
          modulePath = modulePath
        )
      }

      if (roxy_parse$family == "model") {
        test_parameters(
          roxy_parse, defaultParams = ".df",
          modulePath = modulePath
        )
      }

      if (roxy_parse$family == "output") {
        test_parameters(
          roxy_parse, defaultParams = c(".model", ".ras"),
          modulePath = modulePath
        )
      }

      ## FUNCTION OUTPUT TESTS
      test_outputs(roxy_parse, modulePath)
    }
  }) # time

  test_that(paste("Check test duration", moduleName), {
    expect_true(
      time["elapsed"] < 60,
      info = paste("Module tests should not take a long time, yours took",
                   time["elapsed"],
                   "seconds, please change your default values so that test ",
                   "workflow runs do not take too long")
    )
  })
}