context("Barcode patterns")
test_that("tss pattern", {
expect_true(all(str_detect(.bc$tss$code, .pattern$tss)))
})
test_that("center pattern", {
expect_true(all(str_detect(.bc$center$code, .pattern$center)))
})
test_that("sample pattern", {
samples <- c("01", "02B")
expect_true(all(str_detect(samples, .pattern$sample)))
expect_false(str_detect("2B", .pattern$sample))
})
context("Parsed barcodes")
barcodes <- list(tss = "TCGA-02",
participant = "TCGA-02-0001",
drug = "TCGA-02-0001-C1",
exam = "TCGA-02-0001-E3124",
surgery = "TCGA-02-0001-S145",
radiation = "TCGA-02-0001-R2",
sample = "TCGA-02-0001-01",
portion = "TCGA-02-0001-01C-01",
shipped = "TCGA-CM-5341-01A-21-1933-20",
slide = "TCGA-02-0001-01C-01-TS1",
analyte = "TCGA-02-0001-01C-01D",
aliquote = "TCGA-02-0001-01C-01D-0182-01")
test_that("TSS barcode parsed correctly", {
expect <- names(.type$tss)
parsed <- parse_barcodes(barcodes$tss)
expect_identical(names(parsed), expect)
})
test_that("Participant barcode parsed correctly", {
expect <- names(.type$participant)
parsed <- parse_barcodes(barcodes$participant)
expect_identical(names(parsed), expect)
})
test_that("Drug barcode parsed correctly", {
expect <- names(.type$drug)
parsed <- parse_barcodes(barcodes$drug)
expect_identical(names(parsed), expect)
})
test_that("Examination barcode parsed correctly", {
expect <- names(.type$exam)
parsed <- parse_barcodes(barcodes$exam)
expect_identical(names(parsed), expect)
})
test_that("Surgery barcode parsed correctly", {
expect <- names(.type$surgery)
parsed <- parse_barcodes(barcodes$surgery)
expect_identical(names(parsed), expect)
})
test_that("Radiation barcode parsed correctly", {
expect <- names(.type$radiation)
parsed <- parse_barcodes(barcodes$radiation)
expect_identical(names(parsed), expect)
})
test_that("Sample barcode parsed correctly", {
expect <- names(.type$sample)
parsed <- parse_barcodes(barcodes$sample)
expect_identical(names(parsed), expect)
})
test_that("Portion barcode parsed correctly", {
expect <- names(.type$portion)
expect <- c(head(expect, -1), "vial", "portion")
parsed <- parse_barcodes(barcodes$portion)
expect_identical(names(parsed), expect)
})
test_that("Shipped portion barcode parsed correctly", {
expect <- names(.type$aliquot)
expect <- c(head(expect, -3), "vial", tail(expect, 3))
parsed <- parse_barcodes(barcodes$shipped)
expect_identical(names(parsed), expect)
})
test_that("Slide barcode parsed correctly", {
expect <- names(.type$slide)
expect <- c(head(expect, -2), "vial", tail(expect, 2))
parsed <- parse_barcodes(barcodes$slide)
expect_identical(names(parsed), expect)
})
test_that("Analyte barcode parsed correctly", {
expect <- names(.type$portion)
expect <- c(head(expect, -1), "vial", "portion", "analyte")
parsed <- parse_barcodes(barcodes$analyte)
expect_identical(names(parsed), expect)
})
test_that("Aliquot barcode parsed correctly", {
expect <- names(.type$aliquot)
expect <- c(head(expect, -3), "vial", "portion", "analyte", "plate", "center")
parsed <- parse_barcodes(barcodes$aliquote)
expect_identical(names(parsed), expect)
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.