tests/testthat/test-study_variable.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 StudyVariable")

model.instance <- StudyVariable$new()

ref.json <- '{
      "id" : 1,
      "name" : "Sphingolipid SRM Quantitation",
      "assay_refs" : [ 1 ],
      "average_function" : {
        "id" : null,
        "cv_label" : "MS",
        "cv_accession" : "MS:1002883",
        "name" : "median",
        "value" : null
      },
      "variation_function" : {
        "id" : null,
        "cv_label" : "MS",
        "cv_accession" : "MS:1002885",
        "name" : "standard error",
        "value" : null
      },
      "description" : "sphingolipid srm quantitation",
      "factors" : null
    }'

test_that("studyVariable", {
  model.instance <- model.instance$fromJSONString(ref.json)
  expect_equal(model.instance$`id`, 1)
  expect_equal(model.instance$`name`, "Sphingolipid SRM Quantitation")
  expect_equal(length(model.instance$`assay_refs`), 1)
  expect_equal(model.instance$`assay_refs`[[1]], 1)
  expect_null(model.instance$`average_function`$id)
  expect_equal(model.instance$`average_function`$cv_label, "MS")
  expect_equal(model.instance$`average_function`$cv_accession, "MS:1002883")
  expect_equal(model.instance$`average_function`$name, "median")
  expect_null(model.instance$`average_function`$value)
  expect_null(model.instance$`variation_function`$id)
  expect_equal(model.instance$`variation_function`$cv_label, "MS")
  expect_equal(model.instance$`variation_function`$cv_accession, "MS:1002885")
  expect_equal(model.instance$`variation_function`$name, "standard error")
  expect_null(model.instance$`variation_function`$value)
  expect_equal(model.instance$`description`, "sphingolipid srm quantitation")
  expect_null(model.instance$`factors`)
})

test_that("studyVariable$toDataFrame works", {
  model.instance <- model.instance$fromJSONString(ref.json)
  model.instance$`assay_refs` <- list(1,3)
  df <- model.instance$toDataFrame()
  expect_equal(df[1,"PREFIX"], "MTD")
  expect_equal(df[1,"KEY"], "study_variable[1]")
  expect_equal(df[1,"VALUE"], "Sphingolipid SRM Quantitation")
  expect_equal(df[2,"KEY"], "study_variable[1]-assay_refs")
  expect_equal(df[2,"VALUE"], "assay[1]|assay[3]")
  expect_equal(df[3,"KEY"], "study_variable[1]-average_function")
  expect_equal(df[3,"VALUE"], "[MS, MS:1002883, median, ]")
  expect_equal(df[4,"KEY"], "study_variable[1]-variation_function")
  expect_equal(df[4,"VALUE"], "[MS, MS:1002885, standard error, ]")
  expect_equal(df[5,"KEY"], "study_variable[1]-description")
  expect_equal(df[5,"VALUE"], "sphingolipid srm quantitation")
})

test_that("studyVariable$fromDataFrame works", {
  studyVariableMtd <- 
'
MTD\tstudy_variable[1]\tSphingolipid SRM Quantitation																			
MTD\tstudy_variable[1]-assay_refs\tassay[1]																			
MTD\tstudy_variable[1]-description\tsphingolipid srm quantitation																			
MTD\tstudy_variable[1]-average_function\t[MS, MS:1002883, median, ]																			
MTD\tstudy_variable[1]-variation_function\t[MS, MS:1002885, standard error, ]																			
MTD\tstudy_variable[1]-factors\t[,,rapamycin dose,0.5mg]																			
'
  mzTabTable <- readMzTabString(studyVariableMtd)
  metadataTable <- extractMetadata(mzTabTable)
  idElements <- extractIdElements(metadataTable, "study_variable", "name")
  model.instance <- StudyVariable$new()
  model.instance$fromDataFrame(idElements[[1]])
  
  expect_equal(model.instance$`id`, 1)
  expect_equal(model.instance$`name`, "Sphingolipid SRM Quantitation")
  expect_equal(length(model.instance$`assay_refs`), 1)
  expect_equal(model.instance$`assay_refs`[[1]], 1)
  expect_null(model.instance$`average_function`$id)
  expect_equal(model.instance$`average_function`$cv_label, "MS")
  expect_equal(model.instance$`average_function`$cv_accession, "MS:1002883")
  expect_equal(model.instance$`average_function`$name, "median")
  expect_null(model.instance$`average_function`$value)
  expect_null(model.instance$`variation_function`$id)
  expect_equal(model.instance$`variation_function`$cv_label, "MS")
  expect_equal(model.instance$`variation_function`$cv_accession, "MS:1002885")
  expect_equal(model.instance$`variation_function`$name, "standard error")
  expect_null(model.instance$`variation_function`$value)
  expect_equal(model.instance$`description`, "sphingolipid srm quantitation")
  expect_equal(length(model.instance$`factors`), 1)
})