tests/testthat/test_MsBackendMassbankSql-functions.R

In rformassspectrometry/MsBackendMassbank: Mass Spectrometry Data Backend for MassBank record Files

test_that(".valid_dbcon works", {
    expect_true(length(.valid_dbcon(dbc)) == 0)
    expect_true(length(.valid_dbcon(4)) == 1)
})

test_that("MsBackendMassbankSql works", {
    res <- MsBackendMassbankSql()
    expect_true(validObject(res))
    expect_true(is(res, "MsBackendMassbankSql"))
})

test_that(".fetch_peaks_sql works", {
    be <- MsBackendMassbankSql()
    res <- .fetch_peaks_sql(be)
    expect_true(is.data.frame(res))
    expect_equal(colnames(res), c("spectrum_id", "mz", "intensity"))
    expect_true(nrow(res) == 0)

    ## columns
    res <- .fetch_peaks_sql(be, columns = "intensity")
    expect_true(is.data.frame(res))
    expect_equal(colnames(res), c("spectrum_id", "intensity"))
    expect_true(nrow(res) == 0)
    expect_true(is.character(res[, 1L]))
    expect_true(is.numeric(res[, 2L]))
    res <- .fetch_peaks_sql(be, columns = c("intensity", "mz", "intensity"))
    expect_true(is.data.frame(res))
    expect_equal(colnames(res), c("spectrum_id", "intensity",
                                  "mz", "intensity"))
    expect_true(nrow(res) == 0)
    expect_true(is.character(res[, 1L]))
    expect_true(is.numeric(res[, 2L]))
    expect_true(is.numeric(res[, 3L]))
    expect_true(is.numeric(res[, 4L]))

    be <- backendInitialize(MsBackendMassbankSql(), dbc)
    res <- .fetch_peaks_sql(be)
    expect_true(is.data.frame(res))
    expect_equal(colnames(res), c("spectrum_id", "mz", "intensity"))
    expect_true(nrow(res) > 0)

    ## columns
    res <- MsBackendMassbank:::.fetch_peaks_sql(be, "intensity")
    expect_true(is.data.frame(res))
    expect_equal(colnames(res), c("spectrum_id", "intensity"))
    expect_true(is.numeric(res$intensity))

    res <- MsBackendMassbank:::.fetch_peaks_sql(be, c("intensity", "mz",
                                                      "intensity"))
    expect_true(is.data.frame(res))
    expect_equal(colnames(res), c("spectrum_id", "intensity",
                                  "mz", "intensity"))
    expect_true(is.numeric(res$intensity))
    expect_equal(res[, 2], res[, 4])
})

test_that(".fetch_spectra_data_sql works", {
    be <- backendInitialize(MsBackendMassbankSql(), dbc)
    res <- .fetch_spectra_data_sql(be)
    expect_true(nrow(res) > 0)
    expect_true(colnames(res) == "spectrum_id")

    res <- .fetch_spectra_data_sql(be, columns = "msLevel")
    expect_true(all(res$msLevel %in% c(NA_integer_, 2L)))

    res <- .fetch_spectra_data_sql(be, columns = "polarity")
    expect_true(all(res$polarity %in% c(1L, 0L)))

    ## synonym and compound_name
    res <- .fetch_spectra_data_sql(
        be, columns = c("spectrum_name", "inchi",
                        "compound_name", "synonym"))
    expect_equal(colnames(res),
                 c("spectrum_name", "inchi", "compound_name", "synonym"))
    expect_true(is.list(res$synonym))
    expect_true(is.character(res$compound_name))

    res <- .fetch_spectra_data_sql(
        be, columns = c("spectrum_name",
                        "compound_name", "synonym"))
    expect_equal(colnames(res),
                 c("spectrum_name", "compound_name", "synonym"))
    expect_true(is.list(res$synonym))
    expect_true(is.character(res$compound_name))

    res <- .fetch_spectra_data_sql(
        be, columns = c("inchi",
                        "compound_name", "synonym"))
    expect_equal(colnames(res),
                 c("inchi", "compound_name", "synonym"))

    res <- .fetch_spectra_data_sql(be, columns = c("synonym"))
    expect_equal(colnames(res), "synonym")
    expect_true(is.list(res$synonym))

    res <- .fetch_spectra_data_sql(
        be, columns = c("spectrum_name", "compound_name"))
    expect_equal(colnames(res), c("spectrum_name", "compound_name"))
    expect_true(is.character(res$compound_name))
})

test_that(".spectra_data_massbank_sql works", {
    be <- MsBackendMassbankSql()
    res <- .spectra_data_massbank_sql(be)
    expect_true(is(res, "DataFrame"))
    expect_true(nrow(res) == 0L)
    expect_equal(colnames(res), names(Spectra:::.SPECTRA_DATA_COLUMNS))

    be <- backendInitialize(MsBackendMassbankSql(), dbc)
    ## Full data.
    expect_error(.spectra_data_massbank_sql(be, columns = "other"), "available")
    res <- .spectra_data_massbank_sql(be)
    expect_true(is(res, "DataFrame"))
    expect_equal(colnames(res), spectraVariables(be))
    expect_true(is(res$mz, "NumericList"))
    expect_true(is(res$intensity, "NumericList"))
    expect_true(all(is.na(res$rtime)))

    ## A single column
    res <- .spectra_data_massbank_sql(be, columns = "rtime")
    expect_true(is(res, "DataFrame"))
    expect_true(nrow(res) > 0)
    expect_equal(colnames(res), "rtime")
    expect_true(all(is.na(res$rtime)))

    res <- .spectra_data_massbank_sql(be, "msLevel")
    expect_true(is(res, "DataFrame"))
    expect_true(nrow(res) > 0)
    expect_equal(colnames(res), "msLevel")
    expect_true(all(res$msLevel %in% c(NA, 2L)))

    res <- .spectra_data_massbank_sql(be, "mz")
    expect_true(is(res, "DataFrame"))
    expect_true(nrow(res) > 0)
    expect_equal(colnames(res), "mz")
    expect_true(is(res$mz, "NumericList"))

    ## A combination of core and db
    res <- .spectra_data_massbank_sql(be, columns = c("rtime", "polarity"))
    expect_true(is(res, "DataFrame"))
    expect_true(nrow(res) > 0)
    expect_equal(colnames(res), c("rtime", "polarity"))
    expect_true(all(res$polarity %in% c(0L, 1L)))
    expect_true(all(is.na(res$rtime)))

    res <- .spectra_data_massbank_sql(
        be, columns = c("mz", "polarity", "intensity"))
    expect_true(is(res, "DataFrame"))
    expect_true(nrow(res) > 0)
    expect_equal(colnames(res), c("mz", "polarity", "intensity"))
    expect_true(all(res$polarity %in% c(0L, 1L)))
    expect_true(is(res$mz, "NumericList"))
    expect_true(is(res$intensity, "NumericList"))

    ## With local data.
    be@localData <- data.frame(rtime = seq_len(length(be)))
    res <- .spectra_data_massbank_sql(
        be, columns = c("mz", "rtime", "spectrum_id"))
    expect_true(is(res, "DataFrame"))
    expect_true(nrow(res) > 0)
    expect_equal(res$rtime, seq_len(length(be)))

    be@localData$authors <- rep("A", length(be))
    res <- .spectra_data_massbank_sql(be, columns = c("rtime", "authors"))
    expect_true(is(res, "DataFrame"))
    expect_true(nrow(res) > 0)
    expect_equal(res$authors, rep("A", length(be)))
})

test_that(".compounds_sql works", {
    res <- .compounds_sql(dbc, id = c(2, 4, 6))
    expect_true(all(c(2, 4, 6) %in% res$compound_id))
})

test_that(".map_spectraVariables_to_sql works", {
    res <- .map_spectraVariables_to_sql("msLevel")
    expect_equal(res, "ms_level")
    res <- .map_spectraVariables_to_sql(c("mz", "collisionEnergy", "ms_level"))
    expect_equal(res, c("mz", "collisionEnergy", "ms_level"))
})

test_that(".map_sql_to_spectraVariables works", {
    res <- .map_sql_to_spectraVariables("ms_level")
    expect_equal(res, "msLevel")
    res <- .map_sql_to_spectraVariables(c("precursor_mz_text", "intensity"))
    expect_equal(res, c("precursorMz", "intensity"))
})

test_that(".join_query works", {
    ## Without any tables.
    be <- MsBackendMassbankSql()
    res <- .join_query(be, c("compound_id", "spectrum_id", "cas", "inchi"))
    expect_equal(res, "msms_spectrum")

    be <- backendInitialize(MsBackendMassbankSql(), dbc)
    res <- .join_query(be, c("compound_id", "spectrum_id", "cas", "inchi"))
    expect_equal(res, paste0("msms_spectrum join ms_compound on (msms_spectrum",
                             ".compound_id=ms_compound.compound_id)"))

    res <- .join_query(be, c("spectrum_id", "spectrum_name"))
    expect_equal(res, "msms_spectrum")
})