tests/testthat/test-ms_run.R

In lifs-tools/rmzTab-m: R Package Client for mzTab-M Reference Implementation and Validation API

# Automatically generated by openapi-generator (https://openapi-generator.tech)
# Please update as you see appropriate

context("Test MsRun")

model.instance <- MsRun$new()

ref.json <- '{
      "id" : 1,
      "instrument_ref" : 1,
      "location" : "file:///path/to/my/file.mzML",
      "format" : { 
        "cv_label" : "MS",
        "cv_accession" : "MS:1",
        "name" : "made up, also for testing",
        "value" : null
      },
      "id_format" : { 
        "cv_label" : "MS",
        "cv_accession" : "MS:2",
        "name" : "made up for testing",
        "value" : "some, weird, value"
      },
      "fragmentation_method": [{
        "cv_label" : "MS",
        "cv_accession" : "MS:3",
        "name" : "made up for testing",
        "value" : null
      }, {
      "cv_label" : "MS",
        "cv_accession" : "MS:3a",
        "name" : "made up for testing",
        "value" : null
      }],
      "scan_polarity" : [{
        "cv_label" : "MS", 
        "cv_accession" : "MS:4",
        "name" : "made up, for testing", 
        "value" : "some value"
      }],
      "hash" : "hlkasdhlkh2139810asjdklh",
      "hash_method" : {
        "cv_label" : "MS", 
        "cv_accession" : "MS:5",
        "name" : "made up, for testing", 
        "value" : "some value"
      }
    }'

test_that("msRun", {
  model.instance <- model.instance$fromJSONString(ref.json)
  expect_equal(model.instance$`id`, 1)
  expect_equal(model.instance$`instrument_ref`, 1)
  expect_equal(model.instance$`location`, "file:///path/to/my/file.mzML")
  expect_equal(
    model.instance$`format`,
    Parameter$new(
      cv_label = "MS",
      cv_accession = "MS:1",
      name = "made up, also for testing"
    )
  )
  expect_equal(
    model.instance$`id_format`,
    Parameter$new(
      cv_label = "MS",
      cv_accession = "MS:2",
      name = "made up for testing",
      value = "some, weird, value"
    )
  )
  expect_equal(
    model.instance$`fragmentation_method`[[1]],
    Parameter$new(
      cv_label = "MS",
      cv_accession = "MS:3",
      name = "made up for testing"
    )
  )
  expect_equal(
    model.instance$`fragmentation_method`[[2]],
    Parameter$new(
      cv_label = "MS",
      cv_accession = "MS:3a",
      name = "made up for testing"
    )
  )
  expect_equal(
    model.instance$`scan_polarity`[[1]],
    Parameter$new(
      cv_label = "MS",
      cv_accession = "MS:4",
      name = "made up, for testing",
      value = "some value"
    )
  )
  expect_equal(model.instance$`hash`, "hlkasdhlkh2139810asjdklh")
  expect_equal(
    model.instance$`hash_method`,
    Parameter$new(
      cv_label = "MS",
      cv_accession = "MS:5",
      name = "made up, for testing",
      value = "some value"
    )
  )
  model.instance$toJSONString()
})

test_that("MsRun$toDataFrame() works", {
  msRun <- MsRun$new()
  msRun$`id` <- 1
  # msRun$`name` <- "Just a name for the run"
  msRun$`instrument_ref` <- 1
  msRun$`location` <- "file:///path/to/my/file.mzML"
  msRun$`format` <- Parameter$new(cv_label = "MS", cv_accession = "MS:1", name = "made up, also for testing")
  msRun$`id_format` <- Parameter$new(cv_label = "MS", cv_accession = "MS:2", name = "made up for testing", value = "some, weird, value")
  msRun$`fragmentation_method` <- list(
    Parameter$new(cv_label = "MS", cv_accession = "MS:3", name = "made up for testing"),
    Parameter$new(cv_label = "MS", cv_accession = "MS:3a", name = "made up for testing")
  )
  msRun$`scan_polarity` <- list(
    Parameter$new(cv_label = "MS", cv_accession = "MS:4", name = "made up, for testing", value = "some value")
  )
  msRun$`hash` <- "hlkasdhlkh2139810asjdklh"
  msRun$`hash_method` <- Parameter$new(cv_label = "MS", cv_accession = "MS:5", name = "made up for testing")
  
  df <- msRun$toDataFrame()
  expect_equal(nrow(df), 9)
  expect_equal(df[1, "PREFIX"], "MTD")
  # expect_equal(df[1, "KEY"], "ms_run[1]-name")
  # expect_equal(df[1, "VALUE"], "Just a name for the run")
  expect_equal(df[1, "KEY"], "ms_run[1]-location")
  expect_equal(df[1, "VALUE"], "file:///path/to/my/file.mzML")
  expect_equal(df[2, "KEY"], "ms_run[1]-instrument_ref")
  expect_equal(df[2, "VALUE"], "instrument[1]")
  expect_equal(df[3, "KEY"], "ms_run[1]-format")
  expect_equal(df[3, "VALUE"], "[MS, MS:1, \"made up, also for testing\", ]")
  expect_equal(df[4, "KEY"], "ms_run[1]-id_format")
  expect_equal(df[4, "VALUE"], "[MS, MS:2, made up for testing, \"some, weird, value\"]")
  expect_equal(df[5, "KEY"], "ms_run[1]-fragmentation_method[1]")
  expect_equal(df[5, "VALUE"], "[MS, MS:3, made up for testing, ]")
  expect_equal(df[6, "KEY"], "ms_run[1]-fragmentation_method[2]")
  expect_equal(df[6, "VALUE"], "[MS, MS:3a, made up for testing, ]")
  expect_equal(df[7, "KEY"], "ms_run[1]-scan_polarity[1]")
  expect_equal(df[7, "VALUE"], "[MS, MS:4, \"made up, for testing\", some value]")
  expect_equal(df[8, "KEY"], "ms_run[1]-hash")
  expect_equal(df[8, "VALUE"], "hlkasdhlkh2139810asjdklh")
  expect_equal(df[9, "KEY"], "ms_run[1]-hash_method")
  expect_equal(df[9, "VALUE"], "[MS, MS:5, made up for testing, ]")
})
test_that("msRun$fromDataFrame() works", {
  model.instance <- model.instance$fromJSONString(ref.json)
  expect_equal(model.instance$`id`, 1)
  expect_equal(model.instance$`instrument_ref`, 1)
  expect_equal(model.instance$`location`, "file:///path/to/my/file.mzML")
  expect_equal(
    model.instance$`format`,
    Parameter$new(
      cv_label = "MS",
      cv_accession = "MS:1",
      name = "made up, also for testing"
    )
  )
  expect_equal(
    model.instance$`id_format`,
    Parameter$new(
      cv_label = "MS",
      cv_accession = "MS:2",
      name = "made up for testing",
      value = "some, weird, value"
    )
  )
  expect_equal(
    model.instance$`fragmentation_method`[[1]],
    Parameter$new(
      cv_label = "MS",
      cv_accession = "MS:3",
      name = "made up for testing"
    )
  )
  expect_equal(
    model.instance$`fragmentation_method`[[2]],
    Parameter$new(
      cv_label = "MS",
      cv_accession = "MS:3a",
      name = "made up for testing"
    )
  )
  expect_equal(
    model.instance$`scan_polarity`[[1]],
    Parameter$new(
      cv_label = "MS",
      cv_accession = "MS:4",
      name = "made up, for testing",
      value = "some value"
    )
  )
  expect_equal(model.instance$`hash`, "hlkasdhlkh2139810asjdklh")
  expect_equal(
    model.instance$`hash_method`,
    Parameter$new(
      cv_label = "MS",
      cv_accession = "MS:5",
      name = "made up, for testing",
      value = "some value"
    )
  )
  model.instance$toJSONString()
})