tests/testthat/test-sample_processing.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 SampleProcessing")

model.instance <- SampleProcessing$new()

ref.json <- '{
      "id" : 1,
      "sampleProcessing" : [ {
        "id" : null,
        "cv_label" : "MSIO",
        "cv_accession" : "MSIO:0000148",
        "name" : "high performance liquid chromatography",
        "value" : null
      },
      {
        "id" : null,
        "cv_label" : "MSIO",
        "cv_accession" : "MSIO:0000148",
        "name" : "high performance liquid chromatography",
        "value" : null
      } ]
    }'

test_that("sampleProcessing", {
  
  model.instance <- model.instance$fromJSONString(ref.json)
  expect_equal(model.instance$`id`, 1)
  expect_equal(length(model.instance$`sampleProcessing`), 2)
  expect_null(model.instance$`sampleProcessing`[[1]]$`id`)
  expect_equal(model.instance$`sampleProcessing`[[1]]$`cv_label`, "MSIO")
  expect_equal(model.instance$`sampleProcessing`[[1]]$`cv_accession`, "MSIO:0000148")
  expect_equal(model.instance$`sampleProcessing`[[1]]$`name`, "high performance liquid chromatography")
  expect_equal(model.instance$`sampleProcessing`[[1]]$`value`, NULL)
  
  restored.model.instance <- SampleProcessing$new()
  restored.model.instance$fromJSONString(model.instance$toJSONString())
  expect_equal(model.instance, restored.model.instance)
})

test_that("sampleProcessing$toDataFrame()", {
  model.instance <- model.instance$fromJSONString(ref.json)
  df <- model.instance$toDataFrame()
  expect_equal(df[1, "PREFIX"], "MTD")
  expect_equal(df[1, "KEY"], "sample_processing[1]")
  expect_equal(df[1, "VALUE"], "[MSIO, MSIO:0000148, high performance liquid chromatography, ]|[MSIO, MSIO:0000148, high performance liquid chromatography, ]")
})

test_that("sampleProcessing$fromDataFrame", {
  sampleProcessingMtd <-
    'MTD\tsample_processing[1]\t[MSIO, MSIO:0000148, high performance liquid chromatography, ]'  
  mzTabTable <- readMzTabString(sampleProcessingMtd)
  metadataTable <- extractMetadata(mzTabTable)
  idElements <- extractIdElements(metadataTable, "sample_processing", "param")
  model.instance <- SampleProcessing$new()
  model.instance$fromDataFrame(idElements[[1]])  
  expect_equal(model.instance$`id`, 1)
  expect_equal(length(model.instance$`sampleProcessing`), 1)
  expect_null(model.instance$`sampleProcessing`[[1]]$`id`)
  expect_equal(model.instance$`sampleProcessing`[[1]]$`cv_label`, "MSIO")
  expect_equal(model.instance$`sampleProcessing`[[1]]$`cv_accession`, "MSIO:0000148")
  expect_equal(model.instance$`sampleProcessing`[[1]]$`name`, "high performance liquid chromatography")
  expect_equal(model.instance$`sampleProcessing`[[1]]$`value`, NULL)
})