context("sample")
test_that("samples can be listed", {
samp_1 <- samples
expect_s3_class(samp_1, "Sample")
expect_s3_class(samp_1, "json_vec")
expect_gte(length(samp_1), 1L)
for (i in seq_along(samp_1)) {
expect_s3_class(samp_1[[i]], "Sample")
expect_s3_class(samp_1[[i]], "json_class")
expect_identical(get_field(samp_1[[i]], "sampleTypeCode"), "PLATE")
expect_attr(samp_1[[i]], "exp_id")
expect_s3_class(attr(samp_1[[i]], "exp_id"), "ExperimentIdentifier")
expect_s3_class(attr(samp_1[[i]], "exp_id"), "json_class")
}
check_skip()
samp_2 <- list_samples(tok, exp_ids[c(1, 2)])
expect_s3_class(samp_2, "Sample")
expect_s3_class(samp_2, "json_vec")
expect_gte(length(samp_2), 1L)
for (i in seq_along(samp_2)) {
expect_s3_class(samp_2[[i]], "Sample")
expect_s3_class(samp_2[[i]], "json_class")
expect_identical(get_field(samp_2[[i]], "sampleTypeCode"), "PLATE")
expect_attr(samp_2[[i]], "exp_id")
expect_s3_class(attr(samp_2[[i]], "exp_id"), "ExperimentIdentifier")
expect_s3_class(attr(samp_2[[i]], "exp_id"), "json_class")
}
expect_identical(samp_1, list_samples(tok, experiments[[1]]))
expect_identical(samp_2, list_samples(tok, experiments[1:2]))
samp_1 <- list_samples(tok, plates[[1]])
expect_s3_class(samp_1, "Sample")
expect_s3_class(samp_1, "json_class")
expect_identical(get_field(samp_1, "sampleTypeCode"), "PLATE")
expect_attr(samp_1, "plate_id")
expect_s3_class(attr(samp_1, "plate_id"), "PlateIdentifier")
expect_s3_class(attr(samp_1, "plate_id"), "json_class")
samp_2 <- list_samples(tok, plates[c(1, 2)])
expect_s3_class(samp_2, "Sample")
expect_s3_class(samp_2, "json_vec")
expect_length(samp_2, 2L)
for (i in seq_along(samp_2)) {
expect_s3_class(samp_2[[i]], "Sample")
expect_s3_class(samp_2[[i]], "json_class")
expect_identical(get_field(samp_2[[i]], "sampleTypeCode"), "PLATE")
expect_attr(samp_2[[i]], "plate_id")
expect_s3_class(attr(samp_2[[i]], "plate_id"), "PlateIdentifier")
expect_s3_class(attr(samp_2[[i]], "plate_id"), "json_class")
}
samp_1 <- list_samples(tok, wells[[1]])
expect_s3_class(samp_1, "Sample")
expect_s3_class(samp_1, "json_class")
expect_false(get_field(samp_1, "sampleTypeCode") == "PLATE")
expect_attr(samp_1, "well_id")
expect_s3_class(attr(samp_1, "well_id"), "WellIdentifier")
expect_s3_class(attr(samp_1, "well_id"), "json_class")
samp_2 <- list_samples(tok, wells[c(1, 2)])
expect_s3_class(samp_2, "Sample")
expect_s3_class(samp_2, "json_vec")
expect_length(samp_2, 2L)
for (i in seq_along(samp_2)) {
expect_s3_class(samp_2[[i]], "Sample")
expect_s3_class(samp_2[[i]], "json_class")
expect_false(get_field(samp_2[[i]], "sampleTypeCode") == "PLATE")
expect_attr(samp_2[[i]], "well_id")
expect_s3_class(attr(samp_2[[i]], "well_id"), "WellIdentifier")
expect_s3_class(attr(samp_2[[i]], "well_id"), "json_class")
}
})
test_that("sample types can be listed", {
check_skip()
samp_types <- list_sample_types(tok)
expect_s3_class(samp_types, "SampleType")
expect_s3_class(samp_types, "json_vec")
expect_gte(length(samp_types), 1L)
for (i in seq_along(samp_types)) {
expect_s3_class(samp_types[[i]], "SampleType")
expect_s3_class(samp_types[[i]], "json_class")
}
})
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