tests/testthat/test_adding_metadata.R

In sipss/AlpsNMR: Automated spectraL Processing System for NMR

test_that("nmr_meta_get works", {
    dataset <- new_nmr_dataset_1D(
        ppm_axis = c(0:10),
        data_1r = matrix(sample(0:43, replace = TRUE), nrow = 4),
        metadata = list(external = data.frame(NMRExperiment = c("10", "20", "30", "40")))
    )
    dataset[["metadata"]][["external"]][["NMRExperiment"]] <- as.character(dataset[["metadata"]][["external"]][["NMRExperiment"]])
    meta <- nmr_meta_get(dataset, groups = "external")
    expect_equal(meta[[1, 1]], "10")
})

test_that("nmr_meta_add_tidy_excel works", {
    dataset <- new_nmr_dataset_1D(
        ppm_axis = c(0:10),
        data_1r = matrix(sample(0:43, replace = TRUE), nrow = 4),
        metadata = list(external = data.frame(NMRExperiment = c("10", "20", "30", "40")))
    )
    dataset[["metadata"]][["external"]][["NMRExperiment"]] <- as.character(dataset[["metadata"]][["external"]][["NMRExperiment"]])

    dir_to_demo_dataset <- system.file("dataset-demo", package = "AlpsNMR")
    MeOH_plasma_extraction_xlsx <- file.path(dir_to_demo_dataset, "dummy_metadata.xlsx")

    dataset <- nmr_meta_add_tidy_excel(dataset, MeOH_plasma_extraction_xlsx)
    expect_match(dataset[["metadata"]][["external"]][["SubjectID"]][[1]], "Ana", ignore.case = TRUE)
})


test_that("nmr_meta_add works", {
    dir_to_demo_dataset <- system.file("dataset-demo", package = "AlpsNMR")
    dataset <- nmr_read_samples_dir(dir_to_demo_dataset)
    MeOH_plasma_extraction_xlsx <- file.path(dir_to_demo_dataset, "dummy_metadata.xlsx")
    exp_subj_id <- readxl::read_excel(MeOH_plasma_extraction_xlsx, sheet = 1)
    dataset <- nmr_meta_add(dataset, metadata = exp_subj_id, by = "NMRExperiment")
    meta <- nmr_meta_get(dataset, groups = "external")
    expect_match(meta[[1, 2]], "Ana", ignore.case = TRUE)
})