tests/testthat/test-finbif_occurrence.R

In finbif: Interface for the 'Finnish Biodiversity Information Facility' API

suppressMessages(insert_cassette("finbif_occurrence"))

test_that(
  "can return valid data", {

    skip_on_cran()

    expect_s3_class(
      finbif_occurrence(
        species = "Rangifer tarandus fennicus", check_taxa = FALSE,
        select = c("municipality", "region"), sample = TRUE
      ),
      "finbif_occ"
    )

    expect_null(finbif_update_cache())

    expect_s3_class(
      finbif_occurrence(
        "Rangifer tarandus fennicus", "not a valid taxon",
        select = c("record_id", "date_start", "record_fact_name"),
        check_taxa = FALSE
      ),
      "finbif_occ"
    )

    expect_s3_class(
      finbif_occurrence(
        "Rangifer tarandus fennicus",
        select = c("record_id", "date_start", "lat_wgs84", "lon_wgs84", "epsg"),
        exclude_na = TRUE
      ),
      "finbif_occ"
    )

    capture.output(
      with_progress <- suppressMessages(
        finbif_occurrence(
          "Pteromys volans",
          filter = c(bio_province = "Uusimaa"),
          select = c("default_vars", "duration"),
          sample = TRUE, n = 5000, cache = FALSE, date_time_method = "none"
        )
      )
    )

    expect_s3_class(with_progress, "finbif_occ")

    expect_s3_class(
      finbif_occurrence(
        select = "taxon_id", sample = TRUE, n = 3001, quiet = TRUE
      ),
      "finbif_occ"
    )

    expect_s3_class(
      finbif_occurrence(select = "-date_time"),
      "finbif_occ"
    )

  }

)

test_that(
  "can get a small random sample", {

    skip_on_cran()

    x <- finbif_occurrence(
      filter = c(n_total_records_max = 2000), aggregate = "records", n = 100
    )

    x <- subset(x, n_records < 3000, scientific_name_interpreted)

    expect_s3_class(
      finbif_occurrence(x[[1, 1]], sample = TRUE, n = 1001, quiet = TRUE),
      "finbif_occ"
    )

  }

)

test_that(
  "can return a count", {

    skip_on_cran()

    expect_type(
      finbif_occurrence(
        taxa = "Rangifer tarandus fennicus", count_only = TRUE
      ),
      "integer"
    )

  }

)

test_that(
  "returns data that prints valid output", {

    skip_on_cran()

    n <- 1100L

    fungi <- finbif_occurrence(
      filter = c(informal_groups = "Fungi and lichens"),
      select = to_native(
        "occurrenceID", "informalTaxonGroups", "taxonID", "vernacularName",
        "default_vars"
      ),
      n = n,
      quiet = TRUE
    )

    expect_output(print(fungi), "Records downloaded:")

    expect_output(
      print(fungi[c("scientific_name", "common_name")]), "A data"
    )

    expect_output(
      print(fungi[c(TRUE, rep_len(FALSE, n - 1L)), ]), "Records downloaded:"
    )

    expect_output(print(fungi[integer(0L), ]), "Records downloaded:")

    expect_output(
      print(fungi[1:10, c("scientific_name", "taxon_id")]), "A data"
    )

    options(finbif_cache_path = tempdir())

    expect_output(
      print(
        finbif_occurrence(
          select = c("default_vars", to_dwc("duration")), dwc = TRUE
        )
      ),
      "Records downloaded:"
    )

    expect_null(finbif_update_cache())

    expect_output(
      print(finbif_occurrence(aggregate = "species")), "Records downloaded:"
    )

    expect_output(print(finbif_occurrence()), "Records downloaded:")

  }
)

test_that(
  "warns when taxa invalid", {

    skip_on_cran()

    expect_warning(finbif_occurrence("not a valid taxa"))

  }
)

test_that(
  "returns errors appropriately", {

    skip_on_cran()

    expect_error(
      finbif_occurrence("not a valid taxa", on_check_fail = "error")
    )

    expect_error(
      finbif_occurrence(filter = list(coordinates = list(c(60, 68), c(20, 30))))
    )

    expect_error(
      finbif_occurrence("Birds", aggregate = "events")
    )

    expect_error(finbif_occurrence(n = 0))

    expect_error(finbif_occurrence(n = 1e9))

    expect_error(finbif_occurrence(aggregate = c("records", "events")))

    expect_error(finbif_occurrence(filter = c(not_a_filter = TRUE)))

  }
)

suppressMessages(eject_cassette("finbif_occurrence"))

suppressMessages(insert_cassette("finbif_occurrence_dups"))

test_that(
  "duplicate records are handled correctly", {

    skip_on_cran()

    n <- 1600

    dev <- identical(getOption("finbif_api_url"), "https://apitest.laji.fi")

    if (dev) {

      op <- options()

      options(finbif_max_page_size = 100L)

      n <- 300L

    }

    expect_s3_class(
      finbif_occurrence("Vulpes vulpes", sample = TRUE, n = n, quiet = TRUE),
      "finbif_occ"
    )

    if (dev) options(op)

  }

)

suppressMessages(eject_cassette("finbif_occurrence_dups"))

suppressMessages(insert_cassette("finbif_occurrence_low"))

test_that(
  "low-level operations work", {

    skip_on_cran()

    expect_type(
      finbif_occurrence(
        filter = list(
          collection = finbif_collections(taxonomic_coverage == "Coleoptera"),
          primary_habitat = "M",
          date_range_ymd = c(2000, 2010)
        ),
        aggregate = "records",
        count_only = TRUE,
        cache = FALSE
      ),
      "integer"
    )

    expect_type(
      finbif_occurrence(
        filter = list(primary_habitat = list(M = "V")), count_only = TRUE
      ),
      "integer"
    )

  }

)

suppressMessages(eject_cassette("finbif_occurrence_low"))

suppressMessages(insert_cassette("finbif_occurrence_has_media"))

test_that(
  "can process complex record variables", {

    skip_on_cran()

    has_media <- finbif_occurrence(
      filter = c(has_media = TRUE), select = c(media = "record_media_url"),
      sample = TRUE
    )

    url <- unlist(has_media[["media"]])[[1L]]

    expect_match(url, "^http")

  }
)

suppressMessages(eject_cassette("finbif_occurrence_has_media"))

suppressMessages(insert_cassette("finbif_occurrence_collection"))

test_that(
  "can process collection ids", {

    skip_on_cran()

    col_df <- finbif_occurrence(
      select = c("collection", "collection_id", "collection_code")
    )

    expect_s3_class(col_df, "finbif_occ")

    expect_false(identical(col_df[["collection"]], col_df[["collection_id"]]))

  }
)

suppressMessages(eject_cassette("finbif_occurrence_collection"))

test_that(
  "can make a multifilter request", {

    skip_on_cran()

    expect_s3_class(
      finbif_occurrence(filter = list(a = NULL, NULL), filter_col = "b"),
      "finbif_occ"
    )

    expect_s3_class(finbif_occurrence(filter = list(NULL, NULL)), "finbif_occ")


  }
)

suppressMessages(insert_cassette("finbif_occurrence_aggregate_events"))

test_that(
  "can aggregate by events", {

    skip_on_cran()

    expect_s3_class(
      finbif_occurrence(
        filter = c(location_id = "MNP.798"), aggregate = "events"
      ),
      "finbif_occ"
    )

  }

)

suppressMessages(eject_cassette("finbif_occurrence_aggregate_events"))

suppressMessages(insert_cassette("finbif_occurrence_aggregate_documents"))

test_that(
  "can aggregate by events", {

    skip_on_cran()

    expect_s3_class(
      finbif_occurrence(
        filter = c(location_id = "MNP.798"), aggregate = "documents"
      ),
      "finbif_occ"
    )

  }

)

suppressMessages(eject_cassette("finbif_occurrence_aggregate_documents"))

suppressMessages(insert_cassette("finbif_occurrence_date_time_ISO8601"))

test_that(
  "can create ISO8601 date strings", {

    skip_on_cran()

    expect_s3_class(
      finbif_occurrence(select = "date_time_ISO8601"),
      "finbif_occ"
    )

    expect_s3_class(
      finbif_occurrence(select = "eventDate", dwc = TRUE),
      "finbif_occ"
    )

  }

)

suppressMessages(eject_cassette("finbif_occurrence_date_time_ISO8601"))

suppressMessages(insert_cassette("finbif_occurrence_status"))

test_that(
  "can create occurrence status", {

    skip_on_cran()

    expect_s3_class(
      finbif_occurrence(select = "occurrence_status"), "finbif_occ"
    )

  }

)

suppressMessages(eject_cassette("finbif_occurrence_status"))

suppressMessages(insert_cassette("finbif_citation"))

test_that(
  "can create citation", {

    skip_on_cran()

    expect_s3_class(finbif_occurrence(select = "citation"), "finbif_occ")

  }

)

suppressMessages(eject_cassette("finbif_citation"))

suppressMessages(insert_cassette("finbif_get_all"))

test_that(
  "can get all records", {

    skip_on_cran()

    expect_s3_class(
      finbif_occurrence(
        filter = c(collection = "HR.778"), select = "record_id", n = -1
      ),
      "finbif_occ"
    )

  }

)

suppressMessages(eject_cassette("finbif_get_all"))

suppressMessages(insert_cassette("finbif_unlist"))

test_that(
  "can concatenate list cols", {

    skip_on_cran()

    expect_s3_class(
      finbif_occurrence(select = "informal_groups", unlist = TRUE),
      "finbif_occ"
    )

  }

)

suppressMessages(eject_cassette("finbif_unlist"))

suppressMessages(insert_cassette("finbif_red_list"))

test_that(
  "can compute red list status", {

    skip_on_cran()

    expect_s3_class(
      finbif_occurrence(select = "red_list_status"),
      "finbif_occ"
    )

  }

)

suppressMessages(eject_cassette("finbif_red_list"))

suppressMessages(insert_cassette("finbif_primary_habitat"))

test_that(
  "can compute primary habitat type from ID", {

    skip_on_cran()

    expect_s3_class(
      finbif_occurrence(select = "primary_habitat"),
      "finbif_occ"
    )

  }

)

suppressMessages(eject_cassette("finbif_primary_habitat"))

suppressMessages(insert_cassette("finbif_extract_facts"))

test_that(
  "can extract facts", {

    skip_on_cran()

    expect_s3_class(
      finbif_occurrence(
        select = "record_id", filter = c(collection = "HR.48"),
        facts = "weightInGrams", sample = TRUE
      ),
      "finbif_occ"
    )

  }

)

suppressMessages(eject_cassette("finbif_extract_facts"))

suppressMessages(insert_cassette("finbif_localise_enums"))

test_that(
  "can localise enums", {

    skip_on_cran()

    expect_s3_class(
      finbif_occurrence(select = "abundance_unit", aggregate = "records"),
      "finbif_occ"
    )

    expect_s3_class(finbif_occurrence(select = "abundance_unit"), "finbif_occ")

    expect_s3_class(
      finbif_occurrence(
        filter = list(restriction_reason = "Pesintäaika"),
        select = "restriction_reason"
      ),
      "finbif_occ"
    )

  }

)

suppressMessages(eject_cassette("finbif_localise_enums"))

suppressMessages(insert_cassette("finbif_aggregate_list_col"))

test_that(
  "can aggregate list cols", {

    skip_on_cran()

    expect_s3_class(
      finbif_occurrence(
        select = "record_annotation_created", aggregate = "records"
      ),
      "finbif_occ"
    )

  }

)

suppressMessages(eject_cassette("finbif_aggregate_list_col"))

suppressMessages(insert_cassette("finbif_invalidate_cache"))

test_that(
  "cache invalidation works", {

    skip_on_cran()

    finbif_occurrence(cache = 1e-9)

    expect_s3_class(finbif_occurrence(cache = TRUE), "finbif_occ")

    options(finbif_cache_path = NULL)

    finbif_occurrence(cache = 1e-09)

    expect_s3_class(finbif_occurrence(cache = TRUE), "finbif_occ")

  }

)

suppressMessages(eject_cassette("finbif_invalidate_cache"))

suppressMessages(insert_cassette("finbif_compute_var_zero_rows"))

test_that(
  "can compute a var from id when there are zero records", {

    skip_on_cran()

    expect_s3_class(
      finbif_occurrence(
        filter = list(collection = "HR.121", informal_groups = "Myriapods"),
        select = "municipality"
      ),
      "finbif_occ"
    )

    expect_s3_class(finbif_occurrence(cache = TRUE), "finbif_occ")

  }

)

suppressMessages(eject_cassette("finbif_compute_var_zero_rows"))