tests/testthat/test-01_create_fish_db.R

In Delta-Stewardship-Council/deltafish: Accesses an Integrated Fish Count and Length Dataset from the San Francisco Delta

library(testthat)
library(deltafish)
library(dplyr)
cat("starting to create database\n")
local <- FALSE
if (local) {
  deltafish:::create_fish_db_f(
    data_dir = file.path("~/LTMRdata/publication", "data_objects"),
    cache_dir = "deltafish",
    edi_pid = "edi.1075.2",
    update = T
  )
} else {
  create_fish_db()
}
cat("finished creating database\n")

cat("testing the outcome of create_fish_db\n")
con <- open_database()
datetimes <- open_survey(con) %>%
  distinct(Date, Datetime) %>%
  collect_data()

surv_coltypes <- open_survey(con) %>%
  head() %>%
  collect() %>%
  sapply(typeof)
fish_coltypes <- open_fish(con) %>%
  head() %>%
  collect() %>%
  sapply(typeof)

fish_coltypes_expected <- c(
  "SampleID" = "character",
  "Taxa" = "character",
  "Length" = "double",
  "Count" = "double",
  "Notes_catch" = "character"
)
if (deltafish:::show_cached_revision() == "edi.1075.1") {
  surv_coltypes_expected <- c(
    "Source" = "character",
    "Station" = "character",
    "Latitude" = "double",
    "Longitude" = "double",
    "Date" = "character",
    "Datetime" = "character",
    "Survey" = "double",
    "Depth" = "double",
    "SampleID" = "character",
    "Method" = "character",
    "Tide" = "character",
    "Sal_surf" = "double",
    "Sal_bot" = "double",
    "Temp_surf" = "double",
    "Secchi" = "double",
    "Secchi_estimated" = "integer",
    "Tow_duration" = "double",
    "Tow_area" = "double",
    "Tow_volume" = "double",
    "Cable_length" = "double",
    "Tow_direction" = "character",
    "Notes_tow" = "character",
    "Notes_flowmeter" = "character"
  )
} else {
  surv_coltypes_expected <- c(
    "Source" = "character",
    "Station" = "character",
    "Latitude" = "double",
    "Longitude" = "double",
    "Date" = "character",
    "Datetime" = "character",
    "Survey" = "double",
    "Depth" = "double",
    "SampleID" = "character",
    "Method" = "character",
    "Tide" = "character",
    "Sal_surf" = "double",
    "Sal_bot" = "double",
    "Temp_surf" = "double",
    "TurbidityNTU" = "double",
    "TurbidityFNU" = "double",
    "Secchi" = "double",
    "Secchi_estimated" = "integer",
    "Tow_duration" = "double",
    "Tow_area" = "double",
    "Tow_volume" = "double",
    "Cable_length" = "double",
    "Tow_direction" = "character",
    "Notes_tow" = "character",
    "Notes_flowmeter" = "character"
  )
}



test_that("Date and Datetime columns are formatted correctly", {
  expect_equal(class(datetimes$Date), "Date")
  expect_setequal(class(datetimes$Datetime), c("POSIXct", "POSIXt"))
})

test_that("Timezone is correct", {
  expect_equal(attr(datetimes$Datetime, "tzone"), "America/Los_Angeles")
})

test_that("up-to-date dataset with update=TRUE produces expected message", {
  expect_message(create_fish_db(update = TRUE), "Dataset already up to date")
})

test_that("bad data directory produces expected error", {
  expect_error(
    create_fish_db_f(
      data_dir = "test-dir",
      cache_dir = "test",
      update = F,
      edi_pid = "edi.1075.1"
    ),
    regexp = NULL
  )
})

test_that("column types are correct", {
  expect_equal(surv_coltypes, surv_coltypes_expected)
  expect_equal(fish_coltypes, fish_coltypes_expected)
})

close_database(con)

cat("finished testing the outcome of create_fish_db\n")