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add test for import spectra target factory
inspired by examples in ropensci/jagstargets
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,65 @@ | ||
| # WARNING - Generated by {fusen} from dev/maldipickr-workflow-with-targets.Rmd: do not edit by hand | ||
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| # Tests for targets factory borrowed from | ||
| # src: https://github.com/ropensci/jagstargets/blob/2bad8b2958d0252a5993d341d38f8d9d02aeb41a/tests/testthat/test-tar_jags_rep_dic.R | ||
| test_that("tar_import_and_process_spectra works", { | ||
| expect_true(inherits(tar_import_and_process_spectra, "function")) | ||
| skip_if_not_installed("targets") | ||
| skip_if_not_installed("tarchetypes") | ||
| skip_on_cran() | ||
| targets::tar_dir({ # tar_dir() runs code from a temporary directory. | ||
| targets::tar_script({ | ||
| library(maldipickr) | ||
| list( | ||
| tar_import_and_process_spectra( | ||
| name = "anaerobe", | ||
| raw_spectra_directories = system.file( | ||
| "toy-species-spectra", | ||
| package = "maldipickr"), | ||
| tolerance = 1 | ||
| ) | ||
| )},ask = FALSE) | ||
| # Enough targets are created. | ||
| out <- targets::tar_manifest(callr_function = NULL) | ||
| expect_equal(nrow(out), 7L) | ||
| # Nodes in the graph are connected properly. | ||
| out <- targets::tar_network(callr_function = NULL, targets_only = TRUE)$edges | ||
| out <- dplyr::arrange(out, from, to) | ||
| rownames(out) <- NULL | ||
| exp <- tibble::tribble( | ||
| ~from, ~to, | ||
| "anaerobe_checks", "anaerobe_spectra_stats", | ||
| "anaerobe_checks", "anaerobe_valid_spectra", | ||
| "anaerobe_plates", "anaerobe_spectra_raw", | ||
| "anaerobe_plates", "anaerobe_spectra_stats", | ||
| "anaerobe_plates_files", "anaerobe_plates", | ||
| "anaerobe_spectra_raw", "anaerobe_checks", | ||
| "anaerobe_spectra_raw", "anaerobe_valid_spectra", | ||
| "anaerobe_valid_spectra", "anaerobe_processed" | ||
| ) | ||
| exp <- dplyr::arrange(exp, from, to) | ||
| rownames(exp) <- NULL | ||
| expect_equal(out, exp) | ||
| # The pipeline produces correctly formatted output. | ||
| capture.output(suppressWarnings(targets::tar_make(callr_function = NULL))) | ||
| expect_equal( nrow( | ||
| targets::tar_read(anaerobe_processed)[[1]][["metadata"]] | ||
| ), 6L ) | ||
| }) | ||
| }) | ||
| test_that("tar_import_and_process_spectra fails on wrong input", { | ||
| skip_if_not_installed("targets") | ||
| skip_if_not_installed("tarchetypes") | ||
| skip_on_cran() | ||
| targets::tar_dir({ # tar_dir() runs code from a temporary directory. | ||
| targets::tar_script({ | ||
| library(maldipickr) | ||
| list( | ||
| tar_import_and_process_spectra( | ||
| name = "anaerobe", | ||
| raw_spectra_directories = "data_directory_that_should_not_exist", | ||
| tolerance = 1 | ||
| ) | ||
| )},ask = FALSE) | ||
| expect_error(tar_make(), class = "tar_condition_validate") | ||
| }) | ||
| }) |