tests/testthat/test-mz_tab.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 MzTab")

test_that("reading of mztab json works", {
  testfile <- system.file("testdata", c("lipidomics-example.mzTab.json"),package="rmzTabM")
  
  # create a new instance
  mzTab <- MzTab$new()
  
  # populate instance from JSON file
  mzTab$fromJSON(testfile)
  
  # check metadata
  expect_false(is.null(mzTab$metadata))
  expect_equal(mzTab$metadata$`mzTab-version`, "2.0.0-M")
  expect_equal(mzTab$metadata$`mzTab-ID`, "ISAS-2018-1234")
  expect_null(mzTab$metadata$title)
  expect_equal(mzTab$metadata$description, "Minimal proposed sample file for identification and quantification of lipids")
  expect_null(mzTab$metadata$contact)
  expect_length(mzTab$metadata$publication, 1)
  expect_null(mzTab$metadata$uri)
  expect_length(mzTab$metadata$`external_study_uri`, 1)
  expect_length(mzTab$metadata$`instrument`, 1)
  
  expect_null(mzTab$metadata$`quantification_method`$id)
  expect_equal(mzTab$metadata$`quantification_method`$`cv_label`, "MS")
  expect_equal(mzTab$metadata$`quantification_method`$`cv_accession`, "MS:1001838")
  expect_equal(mzTab$metadata$`quantification_method`$`name`, "SRM quantitation analysis")
  
  expect_length(mzTab$metadata$`sample`, 1)
  expect_length(mzTab$metadata$`sample_processing`, 1)
  expect_length(mzTab$metadata$`software`, 2)
  expect_null(mzTab$metadata$`derivatization_agent`)
  
  expect_length(mzTab$metadata$`ms_run`, 1)
  expect_length(mzTab$metadata$`assay`, 1)
  expect_length(mzTab$metadata$`study_variable`, 1)
  
  expect_null(mzTab$metadata$`custom`)
  expect_length(mzTab$metadata$`cv`, 3)
  
  expect_null(mzTab$metadata$`small_molecule-quantification_unit`$id)
  expect_equal(mzTab$metadata$`small_molecule-quantification_unit`$`cv_label`, "UO")
  expect_equal(mzTab$metadata$`small_molecule-quantification_unit`$`cv_accession`, "UO:0000072")
  expect_equal(mzTab$metadata$`small_molecule-quantification_unit`$`name`, "picomolal")
  
  expect_null(mzTab$metadata$`small_molecule_feature-quantification_unit`$id)
  expect_equal(mzTab$metadata$`small_molecule_feature-quantification_unit`$`cv_label`, "UO")
  expect_equal(mzTab$metadata$`small_molecule_feature-quantification_unit`$`cv_accession`, "UO:0000072")
  expect_equal(mzTab$metadata$`small_molecule_feature-quantification_unit`$`name`, "picomolal")
  
  expect_null(mzTab$metadata$`small_molecule-identification_reliability`$id)
  expect_equal(mzTab$metadata$`small_molecule-identification_reliability`$`cv_label`, "MS")
  expect_equal(mzTab$metadata$`small_molecule-identification_reliability`$`cv_accession`, "MS:1002896")
  expect_equal(mzTab$metadata$`small_molecule-identification_reliability`$`name`, "compound identification confidence level")
  
  expect_length(mzTab$metadata$`database`, 3)
  expect_length(mzTab$metadata$`id_confidence_measure`, 1)
  
  expect_null(mzTab$metadata$`colunit-small_molecule`)
  expect_null(mzTab$metadata$`colunit-small_molecule_feature`)
  expect_length(mzTab$metadata$`colunit-small_molecule_evidence`, 1)
  
  expect_null(mzTab$metadata$`colunit-small_molecule_evidence`[[1]]$param$id)
  expect_equal(mzTab$metadata$`colunit-small_molecule_evidence`[[1]]$`column_name`, "opt_global_mass_error")
  expect_equal(mzTab$metadata$`colunit-small_molecule_evidence`[[1]]$param$`cv_label`, "UO")
  expect_equal(mzTab$metadata$`colunit-small_molecule_evidence`[[1]]$param$`cv_accession`, "UO:0000169")
  expect_equal(mzTab$metadata$`colunit-small_molecule_evidence`[[1]]$param$`name`, "parts per million")
  expect_null(mzTab$metadata$`colunit-small_molecule_evidence`[[1]]$param$`value`)
  
  expect_false(is.null(mzTab$smallMoleculeSummary))
  expect_false(is.null(mzTab$smallMoleculeFeature))
  expect_false(is.null(mzTab$smallMoleculeEvidence))
  expect_length(mzTab$`smallMoleculeSummary`,1)
  expect_length(mzTab$`smallMoleculeFeature`,4)
  expect_length(mzTab$`smallMoleculeEvidence`,4)
  
  # check Summary 1 (sml_id can be different!)
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`sml_id`, 1)
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`smf_id_refs`, list(c(1,2,3,4))) # this is a bit weird, not sure why it is represented like that
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`chemical_name`, list("Cer(d18:1/24:0)"))
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`database_identifier`, list("LM:LMSP02010012"))
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`chemical_formula`, list("C42H83NO3"))
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`smiles`, list("CCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)/C=C/CCCCCCCCCCCCC"))
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`inchi`, list("InChI=1S/C42H83NO3/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-38-42(46)43-40(39-44)41(45)37-35-33-31-29-27-25-16-14-12-10-8-6-4-2/h35,37,40-41,44-45H,3-34,36,38-39H2,1-2H3,(H,43,46)/b37-35+/t40-,41+/m0/s1"))
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`uri`, list("http://www.lipidmaps.org/data/LMSDRecord.php?LM_ID=LMSP02010012"))
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`theoretical_neutral_mass`, list(649.6373))
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`adduct_ions`, list("[M+H]+"))
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`reliability`, "2")
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`best_id_confidence_measure`$name, "qualifier ions exact mass")
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`best_id_confidence_value`, 0.958)
  
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`abundance_assay`[[1]], 4.448784E-05)
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`abundance_study_variable`[[1]], 4.448784E-05)
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$`abundance_variation_study_variable`[[1]], 0)
  
  # opt columns
  expect_length(mzTab$`smallMoleculeSummary`[[1]]$opt, 3)
  
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$opt[[1]]$`identifier`, "global_lipid_category")
  expect_null(mzTab$`smallMoleculeSummary`[[1]]$opt[[1]]$`parameter`)
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$opt[[1]]$`value`, "Sphingolipids")
  
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$opt[[2]]$`identifier`, "global_lipid_species")
  expect_null(mzTab$`smallMoleculeSummary`[[1]]$opt[[2]]$`parameter`)
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$opt[[2]]$`value`, "Cer 42:1")
  
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$opt[[3]]$`identifier`, "global_lipid_best_id_level")
  expect_null(mzTab$`smallMoleculeSummary`[[1]]$opt[[3]]$`parameter`)
  expect_equal(mzTab$`smallMoleculeSummary`[[1]]$opt[[3]]$`value`, "Cer d18:1/24:0")
  
  # check features
  expect_length(mzTab$`smallMoleculeFeature`[[1]]$opt, 1)
  expect_equal(mzTab$`smallMoleculeFeature`[[1]]$opt[[1]]$`identifier`, "global_quantifiers_SMF_ID_REFS")
  expect_null(mzTab$`smallMoleculeFeature`[[1]]$opt[[1]]$`parameter`)
  expect_equal(mzTab$`smallMoleculeFeature`[[1]]$opt[[1]]$`value`, "3")
  
  expect_length(mzTab$`smallMoleculeFeature`[[2]]$opt, 1)
  expect_equal(mzTab$`smallMoleculeFeature`[[2]]$opt[[1]]$`identifier`, "global_quantifiers_SMF_ID_REFS")
  expect_null(mzTab$`smallMoleculeFeature`[[2]]$opt[[1]]$`parameter`)
  expect_equal(mzTab$`smallMoleculeFeature`[[2]]$opt[[1]]$`value`, "null")
  
  expect_length(mzTab$`smallMoleculeFeature`[[3]]$opt, 1)
  expect_equal(mzTab$`smallMoleculeFeature`[[3]]$opt[[1]]$`identifier`, "global_quantifiers_SMF_ID_REFS")
  expect_null(mzTab$`smallMoleculeFeature`[[3]]$opt[[1]]$`parameter`)
  expect_equal(mzTab$`smallMoleculeFeature`[[3]]$opt[[1]]$`value`, "null")
  
  expect_length(mzTab$`smallMoleculeFeature`[[4]]$opt, 1)
  expect_equal(mzTab$`smallMoleculeFeature`[[4]]$opt[[1]]$`identifier`, "global_quantifiers_SMF_ID_REFS")
  expect_null(mzTab$`smallMoleculeFeature`[[4]]$opt[[1]]$`parameter`)
  expect_equal(mzTab$`smallMoleculeFeature`[[4]]$opt[[1]]$`value`, "null")
  
  # check evidence
  expect_length(mzTab$`smallMoleculeEvidence`[[1]]$opt, 2)
  expect_equal(mzTab$`smallMoleculeEvidence`[[1]]$opt[[1]]$`identifier`, "global_mass_error")
  expect_null(mzTab$`smallMoleculeEvidence`[[1]]$opt[[1]]$`parameter`)
  expect_equal(mzTab$`smallMoleculeEvidence`[[1]]$opt[[1]]$`value`, "-2.1517")
  
  expect_equal(mzTab$`smallMoleculeEvidence`[[1]]$opt[[2]]$`identifier`, "global_qualifiers_evidence_grouping_ID_REFS")
  expect_null(mzTab$`smallMoleculeEvidence`[[1]]$opt[[2]]$`parameter`)
  expect_equal(mzTab$`smallMoleculeEvidence`[[1]]$opt[[2]]$`value`, "2")
})