tests/testthat/test-sample.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 Sample")

model.instance <- Sample$new()
ref.json <- '{
      "id" : 1,
      "name" : "QEx-1273-prm-sp1",
      "custom" : [ 
        {"id": 1, "cv_label": null, "cv_accession": null, "name":"Extraction date", "value": "2011-12-21"}
      ],
      "species" : [
        {"id":null, "cv_label":"NCBITaxon", "cv_accession":"NCBITaxon:9606", "name":"Homo sapiens", "value":null},
        {"id":null, "cv_label":"NCBITaxon", "cv_accession":"NCBITaxon:39767", "name":"Human rhinovirus 11", "value":null}
      ],
      "tissue" : null,
      "cell_type" : [
        {"id":null, "cv_label":"CL", "cv_accession":"CL:0000182", "name":"hepatocyte","value":null}      
      ],
      "disease" : [
        {"id":null, "cv_label": "DOID", "cv_accession":"DOID:684", "name":"hepatocellular carcinoma", "value":null},
        {"id":null, "cv_label": "DOID", "cv_accession":"DOID:9451", "name":"alcoholic fatty liver","value": null}
      ],
      "description" : "Sphingolipids with concentration reported as picomolar per mg of protein, abundances are reported after calibration correction."
    }'

test_that("Sample$fromJSONString() works", {
  model.instance <- model.instance$fromJSONString(ref.json)
  expect_equal(model.instance$`id`, 1)
  expect_equal(model.instance$`name`, "QEx-1273-prm-sp1")
  expect_equal(length(model.instance$`custom`), 1)
  expect_equal(length(model.instance$`species`), 2)
  expect_null(model.instance$`tissue`)
  expect_equal(length(model.instance$`cell_type`), 1)
  expect_equal(length(model.instance$`disease`), 2)
  expect_equal(model.instance$`description`, "Sphingolipids with concentration reported as picomolar per mg of protein, abundances are reported after calibration correction.")
  
  model.instance$toJSONString()
})

test_that("Sample$toDataFrame() works", {
  sample <-
    Sample$new(
      id = 1,
      name = "Just a name for the sample",
      custom = list(
        Parameter$new(
          cv_label = "MS",
          cv_accession = "MS:1",
          name = "made up, also for testing"
        )
      ),
      tissue = list(
        Parameter$new(
          cv_label = "MS",
          cv_accession = "MS:2",
          name = "made up, also for testing"
        ),
        Parameter$new(
          name = "Human Platelet"
        )
      ),
      description = "A random description",
    )
  
  df <- sample$toDataFrame()
  expect_equal(nrow(df), 5)
  expect_equal(df[1, "PREFIX"], "MTD")
  expect_equal(df[1, "KEY"], "sample[1]")
  expect_equal(df[1, "VALUE"], "Just a name for the sample")
  expect_equal(df[2, "KEY"], "sample[1]-custom[1]")
  expect_equal(df[2, "VALUE"], "[MS, MS:1, \"made up, also for testing\", ]")
  expect_equal(df[3, "KEY"], "sample[1]-tissue[1]")
  expect_equal(df[3, "VALUE"], "[MS, MS:2, \"made up, also for testing\", ]")
  expect_equal(df[4, "KEY"], "sample[1]-tissue[2]")
  expect_equal(df[4, "VALUE"], "[, , Human Platelet, ]")  
  expect_equal(df[5, "KEY"], "sample[1]-description")
  expect_equal(df[5, "VALUE"], "A random description")
})

test_that("Sample$fromDataFrame() works", {
  sampleMtd <- 
'MTD\tsample[1]\tName of sample 1
MTD\tsample[1]-custom[1]\t[MS, MS:1, "made up, also for testing", ]
MTD\tsample[1]-cell_type[1]\t[CL, CL:0000182, "hepatocyte", ]
MTD\tsample[1]-description\tThis is a description
'
  mzTabTable <- readMzTabString(sampleMtd)
  metadataTable <- extractMetadata(mzTabTable)
  idElements <- extractIdElements(metadataTable, "sample", "name")
  model.instance <- Sample$new()
  model.instance$fromDataFrame(idElements[[1]])
  
  expect_equal(model.instance$`id`, 1)
  expect_equal(model.instance$`name`, 'Name of sample 1')
  expect_equal(length(model.instance$`custom`), 1)
  expect_equal(model.instance$`custom`[[1]]$cv_accession, "MS:1")
  expect_equal(length(model.instance$`cell_type`), 1)
  expect_equal(model.instance$`cell_type`[[1]]$cv_accession, "CL:0000182")
  expect_equal(model.instance$`description`, "This is a description")
}
)