tests/testthat/test-ebv_manipulate.R

In ebvcube: Working with netCDF for Essential Biodiversity Variables

test_that("test ebv_create, ebv_add_data and ebv_attribute", {
  #test ebv_create ----
  #basic paths
  root <- system.file(file.path("extdata/testdata"), package="ebvcube")
  json <- file.path(root, 'cSAR-iDiv.json')
  csv <- file.path(root, 'entities.csv')
  file <- tempfile(fileext='.nc')

  #spatial info
  extent <- c(-180, 180, -90, 90)
  res <- c(1, 1)
  fillvalue <- -3.40282e+38
  prec <- 'float'
  epsg <- 4326
  sep <- ','
  timesteps <- c('1900', '2015', '2050')

  #create empty file
  expect_silent(ebv_create(jsonpath = json,
             outputpath = file,
             entities = csv,
             epsg = epsg,
             extent = extent,
             timesteps = timesteps,
             fillvalue = fillvalue,
             prec = prec,
             sep = sep,
             force_4D = TRUE,
             overwrite = TRUE,
             verbose = FALSE))

  #test publisher and user url----
  gen <- ebv_properties(file, verbose=FALSE)@general
  expect_equal(gen$creator_url, "test-creator-url")
  expect_equal(gen$publisher_url, "test-publisher-url")

  #test ebv_attribute: keyword modification  ----
  domain_old <- ebv_properties(file, verbose=FALSE)@general$ebv_domain
  if(domain_old=='Marine'){
    ebv_attribute(file, 'ebv_domain', 'Terrestrial', verbose=FALSE)
    prop <- ebv_properties(file, verbose=FALSE)@general
    expect_equal(prop$ebv_domain, 'Terrestrial')
    expect_equal(prop$keywords, "ebv_class: Community composition, ebv_name: Taxonomic and phylogenetic diversity, ebv_domain: Terrestrial, ebv_geospatial_scope: Global, ebv_entity_type: Communities, ebv_scenario_classification_name: SSP-RCP")
  }else{
    ebv_attribute(file, 'ebv_domain', 'Marine', verbose = FALSE)
    prop <- ebv_properties(file, verbose=FALSE)@general
    expect_equal(prop$ebv_domain, 'Marine')
    expect_equal(prop$keywords, "ebv_class: Community composition, ebv_name: Taxonomic and phylogenetic diversity, ebv_domain: Marine, ebv_geospatial_scope: Global, ebv_entity_type: Communities, ebv_scenario_classification_name: SSP-RCP")
  }

  #test ebv_attribute: modification of metric attribute  ----
  sn_old <- ebv_properties(file, 'scenario_1/metric_1/ebv_cube', verbose=FALSE)@metric$name
  if(sn_old=="Species richness (S)"){
    ebv_attribute(file, 'standard_name', "Species richness (ST)", 'scenario_1/metric_1', verbose=FALSE)
    prop <- ebv_properties(file,'scenario_1/metric_1/ebv_cube', verbose=FALSE)
    expect_equal(prop@metric$name, "Species richness (ST)")
    hdf <- rhdf5::H5Fopen(file)
    did <- rhdf5::H5Dopen(hdf, 'scenario_2/metric_1/ebv_cube')
    ebv_cube_name <- ebv_i_read_att(did, 'long_name', verbose=FALSE)
    rhdf5::H5Dclose(did)
    rhdf5::H5Fclose(hdf)
    expect_equal(ebv_cube_name, "Species richness (ST)")
  }else{
    ebv_attribute(file, 'standard_name', "Species richness (S)", 'scenario_1/metric_1', verbose=FALSE)
    prop <- ebv_properties(file, 'scenario_1/metric_1/ebv_cube', verbose=FALSE)
    expect_equal(prop@metric$name, "Species richness (S)")
    hdf <- rhdf5::H5Fopen(file)
    did <- rhdf5::H5Dopen(hdf, 'scenario_2/metric_1/ebv_cube')
    ebv_cube_name <- ebv_i_read_att(did, 'long_name', verbose=FALSE)
    rhdf5::H5Dclose(did)
    rhdf5::H5Fclose(hdf)
    expect_equal(ebv_cube_name, "Species richness (S)")
  }

  #test ebv_attribute: modification of scenario attribute  ----
  sn_old <- ebv_properties(file, 'scenario_2/metric_1/ebv_cube', verbose=FALSE)@scenario$name
  if(sn_old=='SSP3-RCP6.0 LU'){
    ebv_attribute(file, 'standard_name', 'SSP3-RCP6.0 LULC', 'scenario_2')
    prop <- ebv_properties(file, 'scenario_2/metric_1/ebv_cube', verbose=FALSE)@scenario
    expect_equal(prop$name, 'SSP3-RCP6.0 LULC')
  }else{
    ebv_attribute(file, 'standard_name', 'SSP3-RCP6.0 LU', 'scenario_2')
    prop <- ebv_properties(file, 'scenario_2/metric_1/ebv_cube', verbose=FALSE)@scenario
    expect_equal(prop$name, 'SSP3-RCP6.0 LU')  }

  #test ebv_attribute: modification of global attribute  ----
  title_old <- ebv_properties(file, verbose=FALSE)@general$title
  if(title_old=="Local bird diversity (cSAR/BES-SIM)"){
    ebv_attribute(file, 'title', "Local birds diversity (cSAR/BES-SIM)", verbose=FALSE)
    prop <- ebv_properties(file, verbose=FALSE)@general
    expect_equal(prop$title, "Local birds diversity (cSAR/BES-SIM)")
  }else{
    ebv_attribute(file, 'title', "Local bird diversity (cSAR/BES-SIM)", verbose=FALSE)
    prop <- ebv_properties(file, verbose=FALSE)@general
    expect_equal(prop$title, "Local bird diversity (cSAR/BES-SIM)")
  }

  #test ebv_attribute: modification of ebv_cube attribute  ----
  cct_old <- ebv_properties(file, 'scenario_1/metric_1/ebv_cube', verbose=FALSE)@ebv_cube$coverage_content_type
  if(cct_old=="modelResult"){
    ebv_attribute(file, 'coverage_content_type', "modelsResult", 'scenario_1/metric_1/ebv_cube', verbose=FALSE)
    prop <- ebv_properties(file, 'scenario_1/metric_1/ebv_cube', verbose=FALSE)@ebv_cube
    expect_equal(prop$coverage_content_type, "modelsResult")
  }else{
    ebv_attribute(file, 'coverage_content_type', "modelResult", 'scenario_1/metric_1/ebv_cube', verbose=FALSE)
    prop <- ebv_properties(file, 'scenario_1/metric_1/ebv_cube', verbose=FALSE)@ebv_cube
    expect_equal(prop$coverage_content_type, "modelResult")
  }

  #test ebv_attribute: error in modification of blocked variables  ----
  expect_error(ebv_attribute(file, 'long_name', 'crs variable', 'crs'), regexp='Changes for the CRS are blocked! Rebuild netCDF if you want a different CRS definition.')
  expect_error(ebv_attribute(file, 'long_name', 'lat variable', 'lat'), regexp='Changes for the latitude dataset are blocked! Rebuild netCDF if you want a different latitude definition.')
  expect_error(ebv_attribute(file, 'long_name', 'lon variable', 'lon'), regexp='Changes for the longitude dataset are blocked! Rebuild netCDF if you want a different longitude definition.')
  expect_error(ebv_attribute(file, 'long_name', 'entity variable', 'entity'), regexp='Changes for the entity dataset are blocked! Always built automatically.')
  expect_error(ebv_attribute(file, 'long_name', 'time variable', 'time'), regexp='Changes for the time dataset are blocked! Rebuild netCDF if you want a different time definition.')

  #test ebv_attribute: check ebv class and ebv name ----
  expect_error(ebv_attribute(file, 'ebv_class', 'wrong ebv class'), regexp = 'You are trying to change the ebv_class to a value that is not possible.')
  expect_warning(ebv_attribute(file, 'ebv_class', 'Ecosystem structure'), regexp = 'The current ebv_name Taxonomic and phylogenetic diversity does not correspond the new ebv_class Ecosystem structure. Possible ebv_name values: Live cover fraction, Ecosystem distribution, Ecosystem Vertical Profile. Change ebv_name!')
  expect_error(ebv_attribute(file, 'ebv_name', 'Community abundance'), regexp = 'ou are trying to change the ebv_name to a value that is not possible for ebv_class Ecosystem structure. If both values are to be changed, change ebv_class first.')
  expect_silent(ebv_attribute(file, 'ebv_name', 'Ecosystem distribution'))

  #test ebv_attribute: check units change ----
  expect_message(ebv_attribute(file, 'units', 'fake units', 'scenario_1/metric_2'), regexp = 'You are changing an attribute that is repeated over the different scenarios in your file. All of them will be changed.')
  hdf <- rhdf5::H5Fopen(file)
  did <- rhdf5::H5Dopen(hdf, 'scenario_2/metric_2/ebv_cube')
  expect_equal(ebv_i_read_att(did, 'units'), 'fake units')
  rhdf5::H5Dclose(did)
  gid <- rhdf5::H5Gopen(hdf, 'scenario_3/metric_2')
  expect_equal(ebv_i_read_att(gid, 'units'), 'fake units')
  rhdf5::H5Gclose(gid)
  rhdf5::H5Fclose(hdf)

  # test date_modified and date_metadata_modified ----
  gen <- ebv_properties(file, verbose = FALSE)@general
  expect_equal(gen$date_metadata_modified, '2022-03-21')
  expect_equal(gen$date_modified, '2022-03-21')

  #test ebv_add_data ----
  dims <- ebv_properties(file, 'scenario_1/metric_1/ebv_cube', verbose=FALSE)@spatial$dimensions[1:2]
  RandomNum <- as.integer(runif(64800, 1, 99))
  array <- array(RandomNum, dims)
  ebv_add_data(filepath = file, datacubepath = 'scenario_1/metric_1/ebv_cube',
               entity=1,timestep=1, ignore_RAM = TRUE,
               data=array, verbose=FALSE)
  data <- ebv_read(file, 'scenario_1/metric_1/ebv_cube',1,1, 'a', verbose=FALSE, ignore_RAM = TRUE)
  expect_equal(data[90,180,1], array[90,180])
  #write tif to add data directly from tif
  RandomNum <- as.integer(runif(194400, 1, 99))
  array <- array(RandomNum, c(dims, 3))
  rast <- terra::rast(array, crs='EPSG:4326', extent=extent)
  temprast <- tempfile(fileext = '.tif')
  terra::writeRaster(rast, temprast)
  #write tif to netCDF
  ebv_add_data(filepath = file, datacubepath = 'scenario_3/metric_2/ebv_cube',
               entity=1,timestep=1:3, band = 1:3,
               data=temprast, verbose=FALSE, ignore_RAM = TRUE)
  data <- ebv_read(file, 'scenario_3/metric_2/ebv_cube',1,1:3, 'a', verbose=FALSE, ignore_RAM = TRUE)
  expect_equal(data[90,180,3], array[90,180,3])
  expect_equal(data[90,80,2], array[90,80,2])
  expect_equal(data[9,180,1], array[9,180,1])

  #remove files
  file.remove(temprast)
  file.remove(file)

})