tests/testthat/test-reaction_query_test.R

In ncats/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)

test_that("test_mixed_analyte_reaction_query", {

  analytes = c(
    'chebi:58115',
    'chebi:456215',
    'chebi:58245',
    'chebi:58450',
    'chebi:17596',
    'chebi:16335',
    'chebi:16750',
    'chebi:172878',
    'chebi:62286',
    'chebi:77897',
    'uniprot:P30566',
    'uniprot:P30520',
    'uniprot:P00568',
    'uniprot:P23109',
    'uniprot:P22102',
    'uniprot:P15531'
  )

  # rampDB has been already been instantiated in helper-setup..
  rxns = RaMP::getReactionsForAnalytes(db=rampDB, analytes=analytes, humanProtein = T)
  expect_true(nrow(rxns$met2rxn) > 150)
  expect_true(nrow(rxns$prot2rxn) > 15)
  expect_true(nrow(rxns$metProteinCommonReactions) > 3)

})


test_that("test_metabolite_reaction_query", {

    mets = c(
    'chebi:58115',
    'chebi:456215',
    'chebi:58245',
    'chebi:58450',
    'chebi:17596',
    'chebi:16335',
    'chebi:16750',
    'chebi:172878',
    'chebi:62286',
    'chebi:77897'
  )

  # rampDB has been already been instantiated in helper-setup..
  rxns = RaMP::getReactionsForAnalytes(db=rampDB, analytes=mets, humanProtein = T)
  expect_true(nrow(rxns$met2rxn) > 150)
  expect_true(is.null(nrow(rxns$protein2rxn)))

})

test_that("test_protein_reaction_query", {

  proteins = c(
    'uniprot:P30566',
    'uniprot:P30520',
    'uniprot:P00568',
    'uniprot:P23109',
    'uniprot:P22102',
    'uniprot:P15531'
  )

  # rampDB has been already been instantiated in helper-setup..
  rxns = RaMP::getReactionsForAnalytes(db=rampDB, analytes=proteins, humanProtein = T)
  expect_true(nrow(rxns$prot2rxn) > 15)

})


test_that("test_mixed_analyte_reaction_class_query", {
  analytes = c(
    'chebi:58115',
    'chebi:456215',
    'chebi:58245',
    'chebi:58450',
    'chebi:17596',
    'chebi:16335',
    'chebi:16750',
    'chebi:172878',
    'chebi:62286',
    'chebi:77897',
    'uniprot:P30566',
    'uniprot:P30520',
    'uniprot:P00568',
    'uniprot:P23109',
    'uniprot:P22102',
    'uniprot:P15531'
  )

  rxnClasses <- RaMP:::getReactionClassesForAnalytes(db=rampDB, analytes=analytes)
  expect_true(nrow(rxnClasses$class_ec_level_1) > 4)
  expect_true(nrow(rxnClasses$class_ec_level_2) > 15)
  expect_true(nrow(rxnClasses$class_ec_level_3) > 25)

})


test_that("test_metabolite_reaction_class_query", {
  mets = c(
    'chebi:58115',
    'chebi:456215',
    'chebi:58245',
    'chebi:58450',
    'chebi:17596',
    'chebi:16335',
    'chebi:16750',
    'chebi:172878',
    'chebi:62286',
    'chebi:77897'
  )

  rxnClasses <- RaMP:::getReactionClassesForAnalytes(db=rampDB, analytes=mets)
  expect_true(nrow(rxnClasses$class_ec_level_1) > 4)
  expect_true(nrow(rxnClasses$class_ec_level_2) > 15)
  expect_true(nrow(rxnClasses$class_ec_level_3) > 20)

})

test_that("test_protein_reaction_class_query", {
  proteins = c(
    'uniprot:P30566',
    'uniprot:P30520',
    'uniprot:P00568',
    'uniprot:P23109',
    'uniprot:P22102',
    'uniprot:P15531'
  )
  rxnClasses <- RaMP:::getReactionClassesForAnalytes(db=rampDB, analytes=proteins)
  expect_true(nrow(rxnClasses$class_ec_level_1) > 2)
  expect_true(nrow(rxnClasses$class_ec_level_2) > 3)
  expect_true(nrow(rxnClasses$class_ec_level_3) > 4)

})