tests/testthat/test-runEnrichReactionClass.R

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

for (rampDB in test_databases) {
  test_that("reaction enrichment data returns correctly formatted output", {

    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')

    result <- runEnrichReactionClass(analytes = analytes, db = rampDB)
    expect_equal(
      (length(result) > 1),
      TRUE
    )
    expect_true(
      NROW(result) != 0
    )

    expect_true(
      !is.null(result))
  })

  test_that("reaction class enrichment data is returned correctly when selecting for specific EC level, runEnrichReactionClass", {

    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')

    reaction.classes <- getReactionClassesForAnalytes(db = rampDB, analytes = analytes)
    enrichedReactionSets <- runEnrichReactionClass(db = rampDB, analytes = analytes)
    EC_level1 <- enrichedReactionSets$EC_Level1Stats


    expect_true(
      NROW(EC_level1) != 0
    )

    expect_true(
      !is.null(EC_level1))
  })


  test_that("enrichment in chebi data returns correctly formatted output", {

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

    result <- runEnrichReactionClass(db = rampDB, analytes = chebi)
    expect_equal(
      (length(result) > 1),
      TRUE
    )
    expect_equal(
      class(result[[1]]),
      "data.frame"
    )
    expect_equal(
      (ncol(result[[1]]) > 5),
      TRUE
    )
  })


  test_that("enrichment in uniprot data returns correctly formatted output", {

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

    result <- runEnrichReactionClass(db = rampDB, analytes = uniprot)
    expect_equal(
      (length(result) > 1),
      TRUE
    )
    expect_equal(
      class(result[[1]]),
      "data.frame"
    )
    expect_equal(
      (ncol(result[[1]]) > 5),
      TRUE
    )
  })
}