test_that("atlas_occurrences fails nicely if no email is provided", { galah_config(email = "", run_checks = FALSE) expect_error({ galah_call() |> filter(year == 1900) |> compute() }) galah_config(email = "ala4r@ala.org.au", run_checks = TRUE) }) test_that("atlas_occurrences doesn't allow large downloads", { galah_config(atlas = "Australia") expect_error(atlas_occurrences()) }) test_that("atlas_occurrences gives a nice error for invalid emails", { galah_config(email = "test@test.org.au") expect_error({ galah_call() |> identify("Perameles") |> compute() }) galah_config(email = "ala4r@ala.org.au") }) test_that("collapse(type = 'occurrences') creates an object", { skip_if_offline() result <- galah_call() |> identify("Perameles") |> collapse() # expect_equal(length(result), 4) expect_true(inherits(result, "query")) expect_equal(result$type, "data/occurrences") }) test_that("`compute(type = 'occurrences')` works", { skip_if_offline() base_query <- galah_call() |> identify("Vulpes vulpes") |> filter(year <= 1900, basisOfRecord == "PRESERVED_SPECIMEN") # collapse query_collapse <- collapse(base_query) expect_true(inherits(query_collapse, "query")) expect_equal(length(query_collapse), 4) expect_equal(query_collapse$type, "data/occurrences") # compute response <- compute(base_query) expect_true(inherits(response, "computed_query")) expect_true(response$type == "data/occurrences") expect_equal(names(response), c("type", "status", "total_records", "queue_size", "status_url", "cancel_url", "search_url", "fields")) }) # test all filters and type of columns in one call test_that("atlas_occurrences accepts all narrowing functions inline", { skip_if_offline() expected_cols <- c("decimalLatitude", "decimalLongitude", "eventDate", "scientificName", "taxonConceptID", "recordID", "dataResourceName", "occurrenceStatus", "stateProvince", "ZERO_COORDINATE") poly <- "POLYGON((146.7 -34.6,147.9 -34.6,147.9 -35.7,146.7 -35.7,146.7 -34.6))" base_query <- galah_call(type = "occurrences") |> identify("Polytelis swainsonii") |> filter(year == 2018) |> select(group = "basic", stateProvince, ZERO_COORDINATE) |> st_crop(poly) # w <- collapse(base_query) # collect with wait = FALSE - ensure `type` is specified x <- compute(base_query) expect_equal(names(x), c("type", "status", "total_records", "queue_size", "status_url", "cancel_url", "search_url", "fields")) expect_s3_class(x, "computed_query") # collect with wait = TRUE y <- collect(x, wait = TRUE) expect_s3_class(y, c("tbl_df", "tbl", "data.frame")) expect_setequal(names(y), expected_cols) expect_equal(unique(y$stateProvince), "New South Wales") }) # repeat above using `galah_` functions test_that("atlas_occurrences accepts all narrowing functions in pipe", { skip_if_offline() expected_cols <- c("decimalLatitude", "decimalLongitude", "eventDate", "scientificName", "taxonConceptID", "recordID", "dataResourceName", "occurrenceStatus", "stateProvince", "ZERO_COORDINATE", "COORDINATE_INVALID") poly <- "POLYGON((146.7 -34.6,147.9 -34.6,147.9 -35.7,146.7 -35.7,146.7 -34.6))" occ <- galah_call() |> galah_filter(year >= 2018) |> galah_select(group = "basic", stateProvince, ZERO_COORDINATE, COORDINATE_INVALID) |> galah_identify("Polytelis swainsonii") |> galah_geolocate(poly) |> atlas_occurrences() expect_setequal(names(occ), expected_cols) expect_equal(unique(occ$stateProvince), "New South Wales") }) test_that("atlas_occurrences() and friends accept a file name", { skip_if_offline() # set up directory for testing purposes directory <- "TEMP" unlink(directory, recursive = TRUE) dir.create(directory) galah_config(directory = directory) # set up query base_query <- galah_call() |> galah_filter(year <= 1970) |> galah_select(group = "basic") |> galah_identify("Crinia tinnula") # base_query |> count() |> collect() # n = 49 on 2023-11-15 # test `atlas_occurrences` occ1 <- base_query |> atlas_occurrences(file = "crinia_file") expect_s3_class(occ1, c("tbl_df", "tbl", "data.frame")) expect_true(any(list.files(directory) == "crinia_file.zip")) # test `collect` occ2 <- base_query |> collect(file = "crinia_collect") expect_equal(occ1, occ2) expect_true(any(list.files(directory) == "crinia_collect.zip")) # test DOIs doi <- "10.26197/ala.0c1e8744-a639-47f1-9a5f-5610017ba060" occ3 <- atlas_occurrences(doi = doi, file = "test_doi") expect_true(any(list.files(directory) == "test_doi.zip")) # doi with collect occ3 <- atlas_occurrences(doi = doi, file = "test_doi") expect_true(any(list.files(directory) == "test_doi.zip")) occ4 <- request_data() |> filter(doi == doi) |> collect(file = "test_doi2") expect_equal(occ3, occ4) expect_true(any(list.files(directory) == "test_doi2.zip")) # clean up unlink("TEMP", recursive = TRUE) cache_dir <- tempfile() dir.create(cache_dir) galah_config(directory = cache_dir) rm(cache_dir) }) test_that("atlas_occurrences() errors with an invalid DOI", { expect_error(atlas_occurrences(doi = "random_doi")) }) test_that("atlas_occurrences downloads data from a DOI", { skip_if_offline() doi <- "10.26197/ala.0c1e8744-a639-47f1-9a5f-5610017ba060" result1 <- atlas_occurrences(doi = doi) expect_s3_class(result1, c("tbl_df", "tbl", "data.frame" )) expect_equal(nrow(result1), 9) expect_equal(ncol(result1), 68) # and with other syntax result2 <- request_data() |> filter(doi == doi) |> collapse() expect_equal(length(result2), 4) expect_s3_class(result2, "query") expect_equal(result2$type, "data/occurrences-doi") result3 <- collect(result2) expect_equal(result1, result3) # TODO add file name tests }) test_that("`atlas_occurrences()` places DOI in `attr()` correctly", { skip_if_offline() directory <- "TEMP" unlink(directory, recursive = TRUE) dir.create(directory) galah_config(directory = directory) x <- galah_call() |> identify("Vulpes vulpes") |> filter(year <= 1900, basisOfRecord == "PRESERVED_SPECIMEN") |> collect(mint_doi = TRUE) y <- attr(x, "doi") expect_false(is.null(y)) expect_true(grepl("^https://doi.org/", y)) citation <- atlas_citation(x) expect_true(grepl("^Atlas of Living Australia", citation)) rm(x, y) # ditto for atlas_occurrences x <- galah_call() |> identify("Vulpes vulpes") |> filter(year <= 1900, basisOfRecord == "PRESERVED_SPECIMEN") |> atlas_occurrences(mint_doi = TRUE) y <- attr(x, "doi") expect_false(is.null(y)) expect_true(grepl("^https://doi.org/", y)) unlink(directory, recursive = TRUE) cache_dir <- tempfile() dir.create(cache_dir) galah_config(directory = cache_dir) rm(cache_dir) }) test_that("atlas_occurrences() doesn't return secret information", { skip_if_offline() RUN <- FALSE skip_if((!file.exists("testdata/SECRETS.txt") | !RUN), message = "Secret information not provided") data_request <- galah_call() |> identify("Acacia aneura") |> apply_profile(ALA) |> select(geodeticDatum, eventRemarks, sensitive, dataGeneralizations, generalisationInMetres, coordinateUncertaintyInMeters, recordedBy, datePrecision, stateProvince, group = "basic") x_start <- collapse(data_request) # option to add tests here to ensure url is correctly constructed x <- collect(x_start) # import email address from SECRETS and check again # NOTE: SECRETS.txt has been added to .gitignore # It should never be placed on GitHub email <- readLines("testdata/SECRETS.txt", warn = FALSE) galah_config(email = email) y <- collect(data_request) expect_equal(nrow(x), nrow(y)) expect_equal(ncol(x), ncol(y)) expect_equal(colnames(x), colnames(y)) expect_equal(x, y) # reset galah_config(email = "ala4r@ala.org.au") })