tests/testthat/test-CRAN-name-value.R

In namedCapture: Named Capture Regular Expressions

library(testthat)
library(namedCapture)
context("name value")
source(system.file("test_engines.R", package="namedCapture", mustWork=TRUE), local=TRUE)

name.value.vec <- c(
  "  sampleType=monocyte   assayType=H3K27me3    cost=5",
  "sampleType=monocyte assayType=H3K27ac",
  " sampleType=Myeloidcell cost=30.5  assayType=H3K4me3")

name.value.pattern <- paste0(
  "(?P<name>[^ ]+?)",
  "=",
  "(?P<value>[^ ]+)")

test_engines("name group used for rownames", {
  computed <- str_match_all_named(name.value.vec, name.value.pattern)
  expected <- list(
    cbind(value=c(sampleType="monocyte", assayType="H3K27me3", cost="5")),
    cbind(value=c(sampleType="monocyte", assayType="H3K27ac")),
    cbind(value=c(sampleType="Myeloidcell", cost="30.5", assayType="H3K4me3"))
  )
  expect_identical(computed, expected)
})

sample.assay.pattern <- paste0(
  "sampleType=",
  "(?P<sampleType>[^ ]+)",
  ".*",
  "assayType=",
  "(?P<name>[^ ]+)")

test_engines("assayType used for rownames", {
  computed <- str_match_named(name.value.vec, sample.assay.pattern)
  expected <- cbind(
    sampleType=c(H3K27me3="monocyte",
                 H3K27ac="monocyte",
                 H3K4me3="Myeloidcell"))
  expect_identical(computed, expected)
})

named.subject <- c(
  first="  sampleType=monocyte   assayType=H3K27me3    cost=5",
  second="sampleType=monocyte assayType=H3K27ac",
  third=" sampleType=Myeloidcell cost=30.5  assayType=H3K4me3")

test_engines("subject names used for rownames", {
  computed <- str_match_named(named.subject, sample.assay.pattern)
  expected <- cbind(
    sampleType=c(first="monocyte",
                 second="monocyte",
                 third="Myeloidcell"),
    name=c("H3K27me3", "H3K27ac", "H3K4me3"))
  expect_identical(computed, expected)
})

test_engines("subject names used for list names", {
  computed <- str_match_all_named(named.subject, name.value.pattern)
  expected <- list(
    first=cbind(value=c(sampleType="monocyte", assayType="H3K27me3", cost="5")),
    second=cbind(value=c(sampleType="monocyte", assayType="H3K27ac")),
    third=cbind(value=c(sampleType="Myeloidcell", cost="30.5", assayType="H3K4me3"))
  )
  expect_identical(computed, expected)
})

test_engines("subject names and group name used", {
  computed <- str_match_all_named(named.subject, sample.assay.pattern)
  expected <- list(
    first=cbind(sampleType=c(H3K27me3="monocyte")),
    second=cbind(sampleType=c(H3K27ac="monocyte")),
    third=cbind(sampleType=c(H3K4me3="Myeloidcell")))
  expect_identical(computed, expected)
})