tests/testthat/test_IonDb-methods.R
In rformassspectrometry/CompoundDb: Creating and Using (Chemical) Compound Annotation Databases
test_that("show,IonDb works", {
expect_output(show(ion_db))
db <- new("IonDb")
expect_output(show(ion_db))
})
test_that("IonDb works", {
## empty.
res <- IonDb()
expect_true(is(res, "IonDb"))
## from existing CompDb using character
dbf <- tempfile()
res <- IonDb(dbf, cmp_db)
expect_true(is(res, "IonDb"))
expect_true(nrow(ions(res)) == 0)
expect_equal(compounds(cmp_db), compounds(res))
rm(dbf)
## with ions
ins <- data.frame(compound_id = "HMDB0000002", ion_adduct = "some",
ion_mz = 13.2, ion_rt = 123)
dbf <- tempfile()
res <- IonDb(dbf, cmp_db, ions = ins)
expect_true(is(res, "IonDb"))
expect_true(nrow(ions(res)) == 1)
expect_equal(ions(res), ins)
expect_equal(compounds(cmp_db), compounds(res))
## from existing CompDb using dbconnection
rm(dbf)
dbf <- tempfile()
con <- dbConnect(dbDriver("SQLite"), dbf)
res <- IonDb(con, cmp_spctra_db)
expect_true(is(res, "IonDb"))
expect_true(nrow(ions(res)) == 0)
expect_equal(compounds(cmp_db), compounds(res))
rm(dbf)
## with ions
## from existing (ro) CompDb
expect_error(res <- IonDb(cmp_db), "readonly")
## from existing (rw) CompDb
dbf <- tempfile()
con <- dbConnect(dbDriver("SQLite"), dbf)
CompoundDb:::.copy_compdb(dbconn(cmp_db), con)
cdb_dbf <- CompDb(con)
res <- IonDb(cdb_dbf)
expect_true(is(res, "IonDb"))
expect_true(nrow(ions(res)) == 0)
expect_equal(compounds(cmp_db), compounds(res))
## load previous IonDb from character
res <- IonDb(dbf)
expect_true(is(res, "IonDb"))
expect_true(nrow(ions(res)) == 0)
expect_equal(compounds(cmp_db), compounds(res))
## load previous IonDb from dbconnection
res <- IonDb(con)
expect_true(is(res, "IonDb"))
expect_true(nrow(ions(res)) == 0)
expect_equal(compounds(cmp_db), compounds(res))
dbDisconnect(con)
rm(dbf)
})
# test_that("Spectra,IonDb works", {
#
# res <- Spectra(ion_spctra_db)
# expect_true(is(res, "Spectra"))
# expect_true(length(res) == 4)
# expect_true(all(c("instrument", "predicted") %in% spectraVariables(res)))
#
# ## columns
# res <- Spectra(ion_spctra_db, columns = "compound_id")
# expect_false(all(c("instrument", "predicted") %in% spectraVariables(res)))
#
# ## filter
# res <- Spectra(ion_spctra_db, filter = ~ compound_id == "HMDB0000001")
# expect_true(length(res) == 2)
#
# ## filter and columns
# res <- Spectra(ion_spctra_db, filter = ~ compound_id == "HMDB0000001",
# columns = c("inchi", "name"))
# expect_true(all(c("spectrum_id", "name", "inchi") %in%
# spectraVariables(res)))
# expect_true(length(res) == 2)
#
# expect_error(Spectra(ion_spctra_db, filter = "ad"), "'filter' has to")
# expect_error(Spectra(ion_spctra_db, filter = ~ gene_name == "b"),
# "not supported")
# })
#
# test_that("supportedFilters works", {
# res <- supportedFilters(ion_db)
# expect_equal(colnames(res), c("filter", "field"))
# res_2 <- supportedFilters(ion_spctra_db)
# expect_true(nrow(res) < nrow(res_2))
# })
#
# test_that("metadata works", {
# res <- metadata(ion_db)
# expect_true(is.data.frame(res))
# expect_true(all(colnames(res) == c("name", "value")))
# })
#
# test_that("spectraVariables,IonDb works", {
# db <- new("IonDb")
# expect_equal(spectraVariables(db), character())
#
# res <- spectraVariables(ion_spctra_db)
# expect_true(is.character(res))
# expect_true(length(res) > 0)
# })
#
# test_that("compoundVariables,IonDb works", {
# db <- new("CompDb")
# expect_equal(compoundVariables(db), character())
#
# res <- compoundVariables(ion_db)
# expect_true(is.character(res))
# expect_true(length(res) > 0)
# expect_true(all(c("formula", "inchi") %in% res))
#
# expect_true(any(compoundVariables(ion_db, TRUE) == "compound_id"))
# })
#
# test_that("compounds works", {
# res <- compounds(ion_db, columns = character())
# expect_true(is.data.frame(res))
# expect_true(ncol(res) == 0)
# expect_true(nrow(res) == 0)
# cmps <- compounds(ion_db)
# expect_true(is(cmps, "data.frame"))
# cmps_tbl <- compounds(ion_db, columns = c("compound_id", "name"),
# return.type = "tibble")
# expect_true(is(cmps_tbl, "tbl"))
# expect_equal(colnames(cmps_tbl), c("compound_id", "name"))
#
# expect_error(compounds(ion_db, filter = "something"))
#
# expect_true(
# nrow(compounds(ion_db, filter = ~ compound_id == "HMDB0000005")) == 1)
# res <- compounds(cmp_spctra_db,
# columns = c("compound_id", "spectrum_id", "splash"))
# cmp_ids <- compounds(cmp_spctra_db, columns = "compound_id")$compound_id
# expect_true(all(cmp_ids %in% res$compound_id))
# expect_true(sum(is.na(res$spectrum_id)) == 6)
#
# ## compounds with filters
# res <- compounds(cdb, filter = ~ exactmass > 300)
# expect_true(all(res$exactmass > 300))
# res_2 <- compounds(cdb, filter = ~ exactmass > 300 & exactmass < 340)
# expect_true(nrow(res_2) < nrow(res))
#
# res <- compounds(cdb, filter = FormulaFilter("C17", "startsWith"))
# expect_true(nrow(res) > 0)
# })
test_that("ionVariables,ionDb works", {
db <- new("IonDb")
expect_equal(ionVariables(db), character())
res <- ionVariables(ion_db)
expect_true(is.character(res))
expect_true(length(res) > 0)
expect_true(all(c("compound_id", "ion_adduct", "ion_mz", "ion_rt")
%in% res))
expect_true(any(ionVariables(ion_db, TRUE) == "ion_id"))
})
test_that("ions,ionDb works", {
res <- ions(ion_db, columns = character())
expect_true(is.data.frame(res))
expect_true(ncol(res) == 0)
expect_true(nrow(res) == 0)
expect_true(is(ions(ion_db), "data.frame"))
ions_tbl <- ions(ion_db, columns = c("ion_id", "compound_id", "ion_adduct"),
return.type = "tibble")
expect_true(is(ions_tbl, "tbl"))
expect_equal(colnames(ions_tbl), c("ion_id", "compound_id", "ion_adduct"))
expect_error(compounds(ion_db, filter = "something"))
## ions with filters
res <- ions(ion_db, filter = ~ ion_rt < 100)
expect_true(all(res$ion_rt < 100))
res_2 <- ions(ion_db, filter = ~ ion_rt < 100 & ion_mz < 200)
expect_true(nrow(res_2) < nrow(res))
res <- ions(ion_db, filter = CompoundIdFilter("01", "endsWith"))
expect_true(nrow(res) > 0)
})
test_that("insertIon,ionDb works", {
dbf <- tempfile()
con <- dbConnect(dbDriver("SQLite"), dbf)
CompoundDb:::.copy_compdb(dbconn(ion_spctra_db), con)
idb <- IonDb(con)
more_ions <- data.frame(compound_id = c("HMDB0000005", "HMDB0000008"),
ion_adduct = c("C", "D"),
ion_mz = c(220, 300),
ion_rt = c(90, 140))
idb <- insertIon(idb, more_ions)
expect_true(nrow(ions(idb)) == 7)
expect_equal(ions(idb), rbind(ions(ion_spctra_db), more_ions))
## Different ordering of columns
more_ions <- more_ions[, c(3, 1, 2, 4)]
idb <- insertIon(idb, more_ions)
expect_true(nrow(ions(idb, c("ion_id"))) == 9)
res <- ions(idb, c("ion_id", "compound_id", "ion_adduct"))
expect_equal(res$ion_adduct, c("A", "B", "B", "C", "D", "C", "D", "C", "D"))
## Additional columns
more_ions$add_column <- "Z"
expect_error(insertIon(idb, more_ions), "no column")
idb <- insertIon(idb, more_ions, addColumns = TRUE)
expect_true(any(ionVariables(idb) == "add_column"))
res <- ions(idb)
expect_identical(res$add_column, c(rep(NA_character_, 7), "Z", "Z"))
expect_true(any(idb@.properties$tables$ms_ion == "add_column"))
## Errors
expect_error(insertIon(idb, more_ions[, 1:3]), "required")
more_ions$compound_id <- c("a", "b")
expect_error(insertIon(idb, more_ions), "compound_id")
dbDisconnect(con)
})
test_that("insertSpectra,IonDb works", {
spd <- DataFrame(
msLevel = c(2L, 2L, 2L),
polarity = c(1L, 1L, 1L),
collisionEnergy = c(20, 30, 30))
spd$mz <- list(
c(109.2, 124.2, 124.5, 170.16, 170.52),
c(83.1, 96.12, 97.14, 109.14, 124.08, 125.1, 170.16), c(50, 100))
spd$intensity <- list(
c(3.407, 47.494, 3.094, 100.0, 13.240),
c(6.685, 4.381, 3.022, 16.708, 100.0, 4.565, 40.643), c(50, 100))
sps <- Spectra(spd)
dbf <- tempfile()
con <- dbConnect(dbDriver("SQLite"), dbf)
CompoundDb:::.copy_compdb(dbconn(ion_spctra_db), con)
idb <- IonDb(con)
msms_sp <- dbReadTable(dbconn(idb), "msms_spectrum")
msms_sp_peak <- dbReadTable(dbconn(idb), "msms_spectrum_peak")
expect_error(insertSpectra(idb, sps), "'compound_id' needs")
sps$compound_id <- c("HMDB0000001", "HMDB0000001", "HMDB1000000")
expect_error(insertSpectra(idb, sps), paste("All values of spectra variable",
"'compound_id' must be in"))
sps <- sps[1:2]
insertSpectra(idb, sps, columns = c("msLevel", "polarity",
"collisionEnergy", "compound_id"))
msms_sp2 <- dbReadTable(dbconn(idb), "msms_spectrum")
msms_sp_peak2 <- dbReadTable(dbconn(idb), "msms_spectrum_peak")
ns <- nrow(msms_sp)
ns2 <- nrow(msms_sp2)
expect_equal(ns2, ns + length(sps))
expect_equal(msms_sp, msms_sp2[1:ns, colnames(msms_sp)])
np <- nrow(msms_sp_peak)
np2 <- nrow(msms_sp_peak2)
expect_equal(np2, np + sum(lengths(peaksData(sps))))
expect_equal(msms_sp_peak2$peak_id, 1:np2)
expect_equal(msms_sp_peak2[, c("mz", "intensity")],
rbind(msms_sp_peak[, c("mz", "intensity")],
do.call(rbind, Spectra:::.peaksapply(sps))))
expect_equal(msms_sp_peak2$spectrum_id,
c(msms_sp_peak$spectrum_id,
ns + rep(1:length(sps), lengths(peaksData(sps)))))
# Add additional column in spectra object to the database object
sps$newvariable <- c("value1", "value2")
dbf <- tempfile()
con <- dbConnect(dbDriver("SQLite"), dbf)
CompoundDb:::.copy_compdb(dbconn(ion_spctra_db), con)
idb <- IonDb(con)
msms_sp <- dbReadTable(dbconn(idb), "msms_spectrum")
expect_error(insertSpectra(idb, sps, columns = c("newvariable2",
"compound_id")),
"not available")
insertSpectra(idb, sps, columns = c("newvariable", "compound_id"))
msms_sp2 <- dbReadTable(dbconn(idb), "msms_spectrum")
ns <- nrow(msms_sp)
ns2 <- nrow(msms_sp2)
expect_equal(ns2, ns + length(sps))
expect_true("newvariable" %in% colnames(msms_sp2))
expect_equal(c(rep(NA, ns), sps$newvariable), msms_sp2$newvariable)
})
test_that("deleteIon,IonDb works", {
dbf <- tempfile()
con <- dbConnect(dbDriver("SQLite"), dbf)
CompoundDb:::.copy_compdb(dbconn(ion_spctra_db), con)
idb <- IonDb(con)
ids <- c(1, 2)
deleteIon(idb, ids)
tmp <- ions(ion_spctra_db, ionVariables(ion_spctra_db, includeId = TRUE))
expected_ions <- tmp[-match(ids, tmp$ion_id), ]
rownames(expected_ions) <- NULL
expect_equal(ions(idb, ionVariables(idb, includeId = TRUE)), expected_ions)
})
test_that("deleteCompound,IonDb works", {
db <- IonDb(emptyCompDb(tempfile()))
res <- deleteCompound(db, 1:4)
expect_equal(compounds(res), compounds(db))
expect_equal(ions(res), ions(db))
cmp <- data.frame(compound_id = 1:4, name = letters[1:4], synonyms = 1:4)
db <- insertCompound(db, cmp)
ins <- data.frame(compound_id = c("2", "3"), ion_adduct = "[M+H]+",
ion_mz = c(1.2, 4.3), ion_rt = c(4.3, 4.5))
db <- insertIon(db, ins)
library(RSQLite)
db <- deleteCompound(db, ids = 1)
expect_true(!any(compounds(db, "compound_id")$compound_id == 1))
expect_error(deleteCompound(db, ids = c(3, 6, 8, 10)), "compounds present")
## With Spectra data
spd <- DataFrame(
msLevel = c(2L, 2L),
polarity = c(1L, 1L),
other_column = "b")
spd$mz <- list(
c(109.2, 124.2, 124.5, 170.16, 170.52),
c(83.1, 96.12, 97.14, 109.14, 124.08, 125.1, 170.16))
spd$intensity <- list(
c(3.407, 47.494, 3.094, 100.0, 13.240),
c(6.685, 4.381, 3.022, 16.708, 100.0, 4.565, 40.643))
sps <- Spectra(spd)
sps$compound_id <- as.character(c(2, 4))
db <- insertSpectra(db, sps)
expect_error(deleteCompound(db, ids = c(1, 2)), "Ions")
expect_error(deleteCompound(db, ids = c(1, 4)), "MS2")
db <- deleteCompound(db, ids = c(1, 2), recursive = TRUE)
expect_true(!any(ions(db)$compound_id %in% c(1, 2)))
expect_equal(ions(db)$compound_id, "3")
expect_true(!any(compounds(db, "compound_id")$compound_id %in% c(1, 2)))
expect_equal(
dbGetQuery(dbconn(db), "select * from msms_spectrum")$compound_id, "4")
## errors
expect_error(deleteCompound(new("IonDb"), 2), "not initialized")
})
rformassspectrometry/CompoundDb documentation built on March 1, 2024, 11:40 p.m.
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test_that("show,IonDb works", {
expect_output(show(ion_db))
db <- new("IonDb")
expect_output(show(ion_db))
})
test_that("IonDb works", {
## empty.
res <- IonDb()
expect_true(is(res, "IonDb"))
## from existing CompDb using character
dbf <- tempfile()
res <- IonDb(dbf, cmp_db)
expect_true(is(res, "IonDb"))
expect_true(nrow(ions(res)) == 0)
expect_equal(compounds(cmp_db), compounds(res))
rm(dbf)
## with ions
ins <- data.frame(compound_id = "HMDB0000002", ion_adduct = "some",
ion_mz = 13.2, ion_rt = 123)
dbf <- tempfile()
res <- IonDb(dbf, cmp_db, ions = ins)
expect_true(is(res, "IonDb"))
expect_true(nrow(ions(res)) == 1)
expect_equal(ions(res), ins)
expect_equal(compounds(cmp_db), compounds(res))
## from existing CompDb using dbconnection
rm(dbf)
dbf <- tempfile()
con <- dbConnect(dbDriver("SQLite"), dbf)
res <- IonDb(con, cmp_spctra_db)
expect_true(is(res, "IonDb"))
expect_true(nrow(ions(res)) == 0)
expect_equal(compounds(cmp_db), compounds(res))
rm(dbf)
## with ions
## from existing (ro) CompDb
expect_error(res <- IonDb(cmp_db), "readonly")
## from existing (rw) CompDb
dbf <- tempfile()
con <- dbConnect(dbDriver("SQLite"), dbf)
CompoundDb:::.copy_compdb(dbconn(cmp_db), con)
cdb_dbf <- CompDb(con)
res <- IonDb(cdb_dbf)
expect_true(is(res, "IonDb"))
expect_true(nrow(ions(res)) == 0)
expect_equal(compounds(cmp_db), compounds(res))
## load previous IonDb from character
res <- IonDb(dbf)
expect_true(is(res, "IonDb"))
expect_true(nrow(ions(res)) == 0)
expect_equal(compounds(cmp_db), compounds(res))
## load previous IonDb from dbconnection
res <- IonDb(con)
expect_true(is(res, "IonDb"))
expect_true(nrow(ions(res)) == 0)
expect_equal(compounds(cmp_db), compounds(res))
dbDisconnect(con)
rm(dbf)
})
# test_that("Spectra,IonDb works", {
#
# res <- Spectra(ion_spctra_db)
# expect_true(is(res, "Spectra"))
# expect_true(length(res) == 4)
# expect_true(all(c("instrument", "predicted") %in% spectraVariables(res)))
#
# ## columns
# res <- Spectra(ion_spctra_db, columns = "compound_id")
# expect_false(all(c("instrument", "predicted") %in% spectraVariables(res)))
#
# ## filter
# res <- Spectra(ion_spctra_db, filter = ~ compound_id == "HMDB0000001")
# expect_true(length(res) == 2)
#
# ## filter and columns
# res <- Spectra(ion_spctra_db, filter = ~ compound_id == "HMDB0000001",
# columns = c("inchi", "name"))
# expect_true(all(c("spectrum_id", "name", "inchi") %in%
# spectraVariables(res)))
# expect_true(length(res) == 2)
#
# expect_error(Spectra(ion_spctra_db, filter = "ad"), "'filter' has to")
# expect_error(Spectra(ion_spctra_db, filter = ~ gene_name == "b"),
# "not supported")
# })
#
# test_that("supportedFilters works", {
# res <- supportedFilters(ion_db)
# expect_equal(colnames(res), c("filter", "field"))
# res_2 <- supportedFilters(ion_spctra_db)
# expect_true(nrow(res) < nrow(res_2))
# })
#
# test_that("metadata works", {
# res <- metadata(ion_db)
# expect_true(is.data.frame(res))
# expect_true(all(colnames(res) == c("name", "value")))
# })
#
# test_that("spectraVariables,IonDb works", {
# db <- new("IonDb")
# expect_equal(spectraVariables(db), character())
#
# res <- spectraVariables(ion_spctra_db)
# expect_true(is.character(res))
# expect_true(length(res) > 0)
# })
#
# test_that("compoundVariables,IonDb works", {
# db <- new("CompDb")
# expect_equal(compoundVariables(db), character())
#
# res <- compoundVariables(ion_db)
# expect_true(is.character(res))
# expect_true(length(res) > 0)
# expect_true(all(c("formula", "inchi") %in% res))
#
# expect_true(any(compoundVariables(ion_db, TRUE) == "compound_id"))
# })
#
# test_that("compounds works", {
# res <- compounds(ion_db, columns = character())
# expect_true(is.data.frame(res))
# expect_true(ncol(res) == 0)
# expect_true(nrow(res) == 0)
# cmps <- compounds(ion_db)
# expect_true(is(cmps, "data.frame"))
# cmps_tbl <- compounds(ion_db, columns = c("compound_id", "name"),
# return.type = "tibble")
# expect_true(is(cmps_tbl, "tbl"))
# expect_equal(colnames(cmps_tbl), c("compound_id", "name"))
#
# expect_error(compounds(ion_db, filter = "something"))
#
# expect_true(
# nrow(compounds(ion_db, filter = ~ compound_id == "HMDB0000005")) == 1)
# res <- compounds(cmp_spctra_db,
# columns = c("compound_id", "spectrum_id", "splash"))
# cmp_ids <- compounds(cmp_spctra_db, columns = "compound_id")$compound_id
# expect_true(all(cmp_ids %in% res$compound_id))
# expect_true(sum(is.na(res$spectrum_id)) == 6)
#
# ## compounds with filters
# res <- compounds(cdb, filter = ~ exactmass > 300)
# expect_true(all(res$exactmass > 300))
# res_2 <- compounds(cdb, filter = ~ exactmass > 300 & exactmass < 340)
# expect_true(nrow(res_2) < nrow(res))
#
# res <- compounds(cdb, filter = FormulaFilter("C17", "startsWith"))
# expect_true(nrow(res) > 0)
# })
test_that("ionVariables,ionDb works", {
db <- new("IonDb")
expect_equal(ionVariables(db), character())
res <- ionVariables(ion_db)
expect_true(is.character(res))
expect_true(length(res) > 0)
expect_true(all(c("compound_id", "ion_adduct", "ion_mz", "ion_rt")
%in% res))
expect_true(any(ionVariables(ion_db, TRUE) == "ion_id"))
})
test_that("ions,ionDb works", {
res <- ions(ion_db, columns = character())
expect_true(is.data.frame(res))
expect_true(ncol(res) == 0)
expect_true(nrow(res) == 0)
expect_true(is(ions(ion_db), "data.frame"))
ions_tbl <- ions(ion_db, columns = c("ion_id", "compound_id", "ion_adduct"),
return.type = "tibble")
expect_true(is(ions_tbl, "tbl"))
expect_equal(colnames(ions_tbl), c("ion_id", "compound_id", "ion_adduct"))
expect_error(compounds(ion_db, filter = "something"))
## ions with filters
res <- ions(ion_db, filter = ~ ion_rt < 100)
expect_true(all(res$ion_rt < 100))
res_2 <- ions(ion_db, filter = ~ ion_rt < 100 & ion_mz < 200)
expect_true(nrow(res_2) < nrow(res))
res <- ions(ion_db, filter = CompoundIdFilter("01", "endsWith"))
expect_true(nrow(res) > 0)
})
test_that("insertIon,ionDb works", {
dbf <- tempfile()
con <- dbConnect(dbDriver("SQLite"), dbf)
CompoundDb:::.copy_compdb(dbconn(ion_spctra_db), con)
idb <- IonDb(con)
more_ions <- data.frame(compound_id = c("HMDB0000005", "HMDB0000008"),
ion_adduct = c("C", "D"),
ion_mz = c(220, 300),
ion_rt = c(90, 140))
idb <- insertIon(idb, more_ions)
expect_true(nrow(ions(idb)) == 7)
expect_equal(ions(idb), rbind(ions(ion_spctra_db), more_ions))
## Different ordering of columns
more_ions <- more_ions[, c(3, 1, 2, 4)]
idb <- insertIon(idb, more_ions)
expect_true(nrow(ions(idb, c("ion_id"))) == 9)
res <- ions(idb, c("ion_id", "compound_id", "ion_adduct"))
expect_equal(res$ion_adduct, c("A", "B", "B", "C", "D", "C", "D", "C", "D"))
## Additional columns
more_ions$add_column <- "Z"
expect_error(insertIon(idb, more_ions), "no column")
idb <- insertIon(idb, more_ions, addColumns = TRUE)
expect_true(any(ionVariables(idb) == "add_column"))
res <- ions(idb)
expect_identical(res$add_column, c(rep(NA_character_, 7), "Z", "Z"))
expect_true(any(idb@.properties$tables$ms_ion == "add_column"))
## Errors
expect_error(insertIon(idb, more_ions[, 1:3]), "required")
more_ions$compound_id <- c("a", "b")
expect_error(insertIon(idb, more_ions), "compound_id")
dbDisconnect(con)
})
test_that("insertSpectra,IonDb works", {
spd <- DataFrame(
msLevel = c(2L, 2L, 2L),
polarity = c(1L, 1L, 1L),
collisionEnergy = c(20, 30, 30))
spd$mz <- list(
c(109.2, 124.2, 124.5, 170.16, 170.52),
c(83.1, 96.12, 97.14, 109.14, 124.08, 125.1, 170.16), c(50, 100))
spd$intensity <- list(
c(3.407, 47.494, 3.094, 100.0, 13.240),
c(6.685, 4.381, 3.022, 16.708, 100.0, 4.565, 40.643), c(50, 100))
sps <- Spectra(spd)
dbf <- tempfile()
con <- dbConnect(dbDriver("SQLite"), dbf)
CompoundDb:::.copy_compdb(dbconn(ion_spctra_db), con)
idb <- IonDb(con)
msms_sp <- dbReadTable(dbconn(idb), "msms_spectrum")
msms_sp_peak <- dbReadTable(dbconn(idb), "msms_spectrum_peak")
expect_error(insertSpectra(idb, sps), "'compound_id' needs")
sps$compound_id <- c("HMDB0000001", "HMDB0000001", "HMDB1000000")
expect_error(insertSpectra(idb, sps), paste("All values of spectra variable",
"'compound_id' must be in"))
sps <- sps[1:2]
insertSpectra(idb, sps, columns = c("msLevel", "polarity",
"collisionEnergy", "compound_id"))
msms_sp2 <- dbReadTable(dbconn(idb), "msms_spectrum")
msms_sp_peak2 <- dbReadTable(dbconn(idb), "msms_spectrum_peak")
ns <- nrow(msms_sp)
ns2 <- nrow(msms_sp2)
expect_equal(ns2, ns + length(sps))
expect_equal(msms_sp, msms_sp2[1:ns, colnames(msms_sp)])
np <- nrow(msms_sp_peak)
np2 <- nrow(msms_sp_peak2)
expect_equal(np2, np + sum(lengths(peaksData(sps))))
expect_equal(msms_sp_peak2$peak_id, 1:np2)
expect_equal(msms_sp_peak2[, c("mz", "intensity")],
rbind(msms_sp_peak[, c("mz", "intensity")],
do.call(rbind, Spectra:::.peaksapply(sps))))
expect_equal(msms_sp_peak2$spectrum_id,
c(msms_sp_peak$spectrum_id,
ns + rep(1:length(sps), lengths(peaksData(sps)))))
# Add additional column in spectra object to the database object
sps$newvariable <- c("value1", "value2")
dbf <- tempfile()
con <- dbConnect(dbDriver("SQLite"), dbf)
CompoundDb:::.copy_compdb(dbconn(ion_spctra_db), con)
idb <- IonDb(con)
msms_sp <- dbReadTable(dbconn(idb), "msms_spectrum")
expect_error(insertSpectra(idb, sps, columns = c("newvariable2",
"compound_id")),
"not available")
insertSpectra(idb, sps, columns = c("newvariable", "compound_id"))
msms_sp2 <- dbReadTable(dbconn(idb), "msms_spectrum")
ns <- nrow(msms_sp)
ns2 <- nrow(msms_sp2)
expect_equal(ns2, ns + length(sps))
expect_true("newvariable" %in% colnames(msms_sp2))
expect_equal(c(rep(NA, ns), sps$newvariable), msms_sp2$newvariable)
})
test_that("deleteIon,IonDb works", {
dbf <- tempfile()
con <- dbConnect(dbDriver("SQLite"), dbf)
CompoundDb:::.copy_compdb(dbconn(ion_spctra_db), con)
idb <- IonDb(con)
ids <- c(1, 2)
deleteIon(idb, ids)
tmp <- ions(ion_spctra_db, ionVariables(ion_spctra_db, includeId = TRUE))
expected_ions <- tmp[-match(ids, tmp$ion_id), ]
rownames(expected_ions) <- NULL
expect_equal(ions(idb, ionVariables(idb, includeId = TRUE)), expected_ions)
})
test_that("deleteCompound,IonDb works", {
db <- IonDb(emptyCompDb(tempfile()))
res <- deleteCompound(db, 1:4)
expect_equal(compounds(res), compounds(db))
expect_equal(ions(res), ions(db))
cmp <- data.frame(compound_id = 1:4, name = letters[1:4], synonyms = 1:4)
db <- insertCompound(db, cmp)
ins <- data.frame(compound_id = c("2", "3"), ion_adduct = "[M+H]+",
ion_mz = c(1.2, 4.3), ion_rt = c(4.3, 4.5))
db <- insertIon(db, ins)
library(RSQLite)
db <- deleteCompound(db, ids = 1)
expect_true(!any(compounds(db, "compound_id")$compound_id == 1))
expect_error(deleteCompound(db, ids = c(3, 6, 8, 10)), "compounds present")
## With Spectra data
spd <- DataFrame(
msLevel = c(2L, 2L),
polarity = c(1L, 1L),
other_column = "b")
spd$mz <- list(
c(109.2, 124.2, 124.5, 170.16, 170.52),
c(83.1, 96.12, 97.14, 109.14, 124.08, 125.1, 170.16))
spd$intensity <- list(
c(3.407, 47.494, 3.094, 100.0, 13.240),
c(6.685, 4.381, 3.022, 16.708, 100.0, 4.565, 40.643))
sps <- Spectra(spd)
sps$compound_id <- as.character(c(2, 4))
db <- insertSpectra(db, sps)
expect_error(deleteCompound(db, ids = c(1, 2)), "Ions")
expect_error(deleteCompound(db, ids = c(1, 4)), "MS2")
db <- deleteCompound(db, ids = c(1, 2), recursive = TRUE)
expect_true(!any(ions(db)$compound_id %in% c(1, 2)))
expect_equal(ions(db)$compound_id, "3")
expect_true(!any(compounds(db, "compound_id")$compound_id %in% c(1, 2)))
expect_equal(
dbGetQuery(dbconn(db), "select * from msms_spectrum")$compound_id, "4")
## errors
expect_error(deleteCompound(new("IonDb"), 2), "not initialized")
})
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