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 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$keywords, "ebv_class: Community composition, ebv_name: Taxonomic/phylogenetic diversity, ebv_domain: Terrestrial, ebv_spatial_scope: Global, ebv_entity_type: Communities, ebv_scenario_classification_name: SSP-RCP") }else{ ebv_attribute(file, 'ebv_domain', 'Marine') prop <- ebv_properties(file, verbose=FALSE)@general expect_equal(prop$ebv_domain, 'Marine') expect_equal(prop$keywords, "ebv_class: Community composition, ebv_name: Taxonomic/phylogenetic diversity, ebv_domain: Marine, ebv_spatial_scope: Global, ebv_entity_type: Communities, ebv_scenario_classification_name: SSP-RCP") } #test ebv_attribute: modification of metric attribute ---- sn_old <- ebv_properties(file, 'scenario_1/metric_1/ebv_cube', verbose=FALSE)@metric$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/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 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, data=array, verbose=FALSE) data <- ebv_read(file, 'scenario_1/metric_1/ebv_cube',1,1, 'a', verbose=FALSE) 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) data <- ebv_read(file, 'scenario_3/metric_2/ebv_cube',1,1:3, 'a', verbose=FALSE) 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) })