tests/testthat/test-assay.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 Assay")

model.instance <- Assay$new()
ref.json <- '{
      "id" : 1,
      "name" : "Description of assay 1",
      "custom" : [ 
        {"id": 1, "cv_label": "MSIO", "cv_accession": "MSIO:0000148", "name":"high performance liquid chromatography", "value":null}, 
        {"id": 2, "cv_label": null, "cv_accession": null, "name": "custom user param", "value":null}
      ],
      "external_uri" : null,
      "sample_ref" : 1,
      "ms_run_ref" : [ 1 ]
    }'

test_that("Assay$fromJSONString() works", {
  model.instance <- model.instance$fromJSONString(ref.json)
  expect_equal(model.instance$`id`, 1)
  expect_equal(model.instance$`name`, "Description of assay 1")
  expect_equal(length(model.instance$`custom`), 2)
  expect_null(model.instance$`external_uri`)
  expect_equal(model.instance$`sample_ref`, 1)
  expect_equal(length(model.instance$`ms_run_ref`), 1)
  expect_equal(model.instance$`ms_run_ref`[[1]], 1)
  
  model.instance$toJSONString()
})

test_that("Assay$toDataFrame() works", {
  assay <-
    Assay$new(
      id = 1,
      name = "Just a name for the assay",
      custom = list(
        Parameter$new(
          cv_label = "MS",
          cv_accession = "MS:1",
          name = "made up, also for testing"
        )
      ),
      external_uri = "file:///path/to/my/file.mzML",
      sample_ref = 2,
      ms_run_ref = list("1", "2", "3")
    )
  
  df <- assay$toDataFrame()
  expect_equal(nrow(df), 7)
  expect_equal(df[1, "PREFIX"], "MTD")
  expect_equal(df[1, "KEY"], "assay[1]")
  expect_equal(df[1, "VALUE"], "Just a name for the assay")
  expect_equal(df[2, "KEY"], "assay[1]-custom[1]")
  expect_equal(df[2, "VALUE"], "[MS, MS:1, \"made up, also for testing\", ]")
  expect_equal(df[3, "KEY"], "assay[1]-external_uri")
  expect_equal(df[3, "VALUE"], "file:///path/to/my/file.mzML")
  expect_equal(df[4, "KEY"], "assay[1]-sample_ref")
  expect_equal(df[4, "VALUE"], "sample[2]")
  expect_equal(df[5, "KEY"], "assay[1]-ms_run_ref")
  expect_equal(df[5, "VALUE"], "ms_run[1]")
  expect_equal(df[6, "KEY"], "assay[1]-ms_run_ref")
  expect_equal(df[6, "VALUE"], "ms_run[2]")
  expect_equal(df[7, "KEY"], "assay[1]-ms_run_ref")
  expect_equal(df[7, "VALUE"], "ms_run[3]")
})

test_that("Assay$fromDataFrame() works", {
  assayMtd <- 
'
MTD	assay[1]	Description of assay 1																			
MTD	assay[1]-sample_ref	sample[1]																			
MTD	assay[1]-ms_run_ref	ms_run[1]	
MTD	assay[1]-custom[1]	[MS, MS:1, "made up, also for testing", ]	
'
  mzTabTable <- readMzTabString(assayMtd)
  metadataTable <- extractMetadata(mzTabTable)
  idElements <- extractIdElements(metadataTable, "assay", "name")
  model.instance <- Assay$new()
  model.instance$fromDataFrame(idElements[[1]])
  
  expect_equal(model.instance$`id`, 1)
  expect_equal(model.instance$`name`, 'Description of assay 1')
  expect_equal(length(model.instance$`custom`), 1)
  expect_equal(model.instance$`custom`[[1]]$cv_accession, "MS:1")
  expect_null(model.instance$`external_uri`)
  expect_equal(model.instance$`sample_ref`, 1)
  expect_equal(length(model.instance$`ms_run_ref`), 1)
  expect_equal(model.instance$`ms_run_ref`[[1]], 1)
}
)