tests/testthat/test_120_mass.csv.file.R
In pkrog/biodb: biodb, a library and a development framework for connecting to chemical and biological databases
MASSFILEDB.URL <- system.file("extdata", "massbank_extract_full.tsv",
package="biodb", mustWork=TRUE)
MASSFILEDB.WRONG.HEADER.URL <- system.file('testref',
'mass.csv.file-wrong_header.tsv', package="biodb", mustWork=TRUE)
MASSFILEDB.WRONG.NB.COLS.URL <- system.file('testref',
'mass.csv.file-wrong_nb_cols.tsv', package="biodb", mustWork=TRUE)
test.basic.mass.csv.file <- function(db) {
# Open file
df <- read.table(db$getPropValSlot('urls', 'base.url'), sep="\t",
header=TRUE, quote='"', stringsAsFactors=FALSE,
row.names=NULL)
# Test number of entries
expect_gt(db$getNbEntries(), 1)
expect_equal(db$getNbEntries(), sum( ! duplicated(df[c('accession')])))
# Get an entry ID
id <- df[df[['ms.level']] == 1 & ! is.na(df[['chrom.col.id']]),
'accession'][[1]]
# Test number of peaks
expect_gt(db$getNbPeaks(), 1)
expect_gt(db$getNbPeaks(mode='neg'), 1)
expect_gt(db$getNbPeaks(mode='pos'), 1)
expect_equal(db$getNbPeaks(), nrow(df))
expect_gt(db$getNbPeaks(ids=id), 1)
# Test chrom cols
expect_gt(nrow(db$getChromCol()), 1)
expect_gte(nrow(db$getChromCol(ids=id)), 1)
expect_lte(nrow(db$getChromCol(ids=id)), nrow(db$getChromCol()))
expect_true(all(db$getChromCol(ids=id)[['id']] %in%
db$getChromCol()[['id']]))
# Test mz values
expect_true(is.vector(db$getMzValues()))
expect_gt(length(db$getMzValues()), 1)
expect_error(db$getMzValues('wrong.mode.value'), silent=TRUE)
expect_gt(length(db$getMzValues('neg')), 1)
expect_gt(length(db$getMzValues('pos')), 1)
}
test.mass.csv.file.data.frame <- function(biodb) {
# Define database data frame
ids <- 'ZAP'
mz <- 12
df <- data.frame(accession=ids, mz=mz, mode='+')
# New biodb instance
conn <- biodb$getFactory()$createConn('mass.csv.file')
# Set database
conn$setDb(df)
# Set fields
conn$setField('accession', 'accession')
conn$setField('ms.mode', 'mode')
conn$setField('peak.mztheo', 'mz')
# Get M/Z values
expect_identical(mz, conn$getMzValues())
expect_identical(ids, conn$getEntryIds())
}
test.mass.csv.file.old.col.names <- function(biodb) {
# Define data frame
df <- data.frame(compoundid='A10', msmode='POS', mztheo=112.07569,
peakcomp='P9Z6W410', peakattr='[(M+H)-(H2O)-(NH3)]+',
chromcol='colAA', chromcolrt=94.8,
compoundcomp='J114L6M62O2', compoundmass=146.10553,
fullnames='Blablaine')
# New connector instance
conn <- biodb$getFactory()$createConn('mass.csv.file')
# Set database
conn$setDb(df)
# Get chrom cols
cols <- conn$getChromCol()
expect_is(cols, "data.frame")
}
test.fields <- function(biodb) {
# Get fields
col.name <- conn$getFieldColName('ms.mode')
expect_is(col.name, 'character')
expect_true(nchar(col.name) > 0)
# Test if has field
testthat::expect_true(conn$hasField('accession'))
testthat::expect_false(conn$hasField('blabla'))
testthat::expect_false(conn$hasField('nt.seq'))
# Add new field
conn$addField('nt.seq', 'N')
# Set wrong fields
testthat::expect_error(conn$setField('invalid.tag.name', colname='something'),
regexp='^.*Database field "invalid.tag.name" is not valid.$')
testthat::expect_error(conn$setField('ms.mode', colname='wrong.col.name'),
regexp='^.*Column.* is/are not defined in database file.$')
# Reseting accession field should fail
testthat::expect_error(conn$setField('accession', 'compound.id'))
}
test.undefined.fields <- function(biodb) {
conn <- biodb$getFactory()$createConn('mass.csv.file',
url=MASSFILEDB.WRONG.HEADER.URL)
testthat::expect_warning(conn$hasField('accession'),
regexp='^.*Column ".*" does not match any biodb field\\.$')
testthat::expect_error(conn$getEntryIds(),
regexp='^.*Field.* accession is/are undefined in file database\\.$')
biodb$getFactory()$deleteConn(conn$getId())
}
test.wrong.nb.cols <- function(biodb) {
conn <- biodb$getFactory()$createConn('mass.csv.file',
url=MASSFILEDB.WRONG.NB.COLS.URL)
expect_error(ids <- conn$getEntryIds(),
regexp='^.* 1 .* 12 .*$')
# Error message in English: line 1 did not have 12 elements
biodb$getFactory()$deleteConn(conn$getId())
}
test.field.card.one <- function(biodb) {
# Define database data frame
ids <- c('ZAP', 'ZAP')
mzs <- c(12, 14)
modes <- c('+', '-')
df <- data.frame(ids=ids, mz=mzs, mode=modes)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(df)
# Set fields
conn$setField('accession', 'ids')
conn$setField('ms.mode', 'mode')
conn$setField('peak.mztheo', 'mz')
expect_error(conn$checkDb(),
regexp=paste0('^.*Cannot set more that one value .* into',
' single value field .*\\.$'))
}
test.getMzValues.without.peak.attr <- function(biodb) {
df <- rbind(data.frame(),
list(accession='BML80005', ms.mode='pos', ms.level=1, peak.mztheo=219.1127765, peak.intensity=373076, peak.relative.intensity=999),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(df)
# Get M/Z values
mzs <- conn$getMzValues(max.results=10)
expect_is(mzs, 'numeric')
expect_length(mzs, 1)
# Get M/Z values filtering on precursor
mzs <- conn$getMzValues(max.results=10, precursor=TRUE, ms.mode='pos')
expect_is(mzs, 'numeric')
expect_length(mzs, 0)
}
test.mass.csv.file.entry.peaks.table.col.names <- function(biodb) {
# Define db data frame
id <- 'BML80005'
df <- rbind(data.frame(), list(accession=id, mode='pos', mztheo=219.1127765,
peakcomp='CHON',
peakattr='[(M+H)-(H2O)-(NH3)]+', int=373076,
relint=999), stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(df)
conn$setField('ms.mode', 'mode')
conn$setField('peak.mztheo', 'mztheo')
conn$setField('peak.attr', 'peakattr')
conn$setField('peak.comp', 'peakcomp')
conn$setField('peak.intensity', 'int')
conn$setField('peak.relative.intensity', 'relint')
# Get entry and peaks
entry <- biodb$getFactory()$getEntry(conn$getId(), id)
expect_is(entry, 'MassCsvFileEntry')
peaks <- entry$getFieldValue('peaks')
expect_is(peaks, 'data.frame')
expect_equal(nrow(peaks), 1)
expect_gte(ncol(peaks), 1)
# Check that colnames of peaks table are all valid field names or aliases
expect_true(all(vapply(names(peaks), function(field) biodb$getEntryFields()$isDefined(field), FUN.VALUE = FALSE)))
# Check that colnames of peaks table are all official field names (not aliases)
expect_true(all(vapply(names(peaks), function(field) biodb$getEntryFields()$get(field)$getName() == field, FUN.VALUE = FALSE)))
}
test.mass.csv.file.searchMsPeaks.column.sorting <- function(biodb) {
# Define db data frame
db.df <- rbind(data.frame(accession='C1', ms.mode='POS', peak.mztheo=112.07569, peak.comp='P9Z6W410 O', peak.attr='[(M+H)-(H2O)-(NH3)]+', formula="J114L6M62O2", molecular.mass=146.10553, name='Blablaine', inchi='InChI=1S/C7H8N4O3/c1-10-4-3(8-6(10)13)5(12)11(2)7(14)9-4/h1-2H3,(H,8,13)(H,9,14)', inchikey='NA'),
data.frame(accession='C2', ms.mode='POS', peak.mztheo=208.8274, peak.comp='Y2Z6W410 O', peak.attr='[(M+H)-(H2O)]+', formula="T114L6M62O2", molecular.mass=146.10553, name='Sloopaine', inchi='InChI=1S/C7H8N4O3/c1-10-4-3(8-6(10)13)5(12)11(2)7(14)9-4/h1-2H3,(H,8,13)(H,9,14)', inchikey='FRYVQXCDSBCDAU-AKDOOQIZSA-N'),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db.df)
# Search
results <- conn$searchMsPeaks(db.df[['peak.mztheo']], mz.tol = 10, insert.input.values = FALSE)
expect_is(results, 'data.frame')
expected.cols <- sort(c(colnames(db.df), 'peak.mz', 'mass.csv.file.id'))
expect_identical(expected.cols, colnames(results))
}
test.mass.csv.file.mz.matching.limits <- function(biodb) {
# Define db data frame
db.df <- rbind(data.frame(), list(accession='C1', ms.mode='POS',
peak.mztheo=112.07569,
peak.comp='P9Z6W410 O',
peak.attr='[(M+H)-(H2O)-(NH3)]+',
formula="J114L6M62O2",
molecular.mass=146.10553,
name='Blablaine'),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db.df)
mz.tol <- 5
# Compute mz.min and mz.max
mz.tol.unit <- 'ppm'
mz <- db.df[['peak.mztheo']]
mz.sup <- mz / ( 1 + ( - mz.tol) * 1e-6)
mz.sup <- mz.sup - 1e-8 # Adjustment needed, due to computing differences.
mz.inf <- mz / ( 1 + ( + mz.tol) * 1e-6)
# Search
results1 <- conn$searchMsPeaks(mz, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos')
expect_is(results1, 'data.frame')
results2 <- conn$searchMsPeaks((mz.inf + mz.sup)/2, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos')
expect_is(results2, 'data.frame')
results3 <- conn$searchMsPeaks(mz.inf, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos')
expect_is(results3, 'data.frame')
results4 <- conn$searchMsPeaks(mz.inf - 1e-6, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos', insert.input.values=FALSE)
expect_identical(results4, data.frame())
results4.1 <- conn$searchMsPeaks(mz.inf - 1e-6, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos', insert.input.values=TRUE)
expect_is(results4.1, 'data.frame')
expect_identical(colnames(results4.1), 'mz')
results5 <- conn$searchMsPeaks(mz.sup, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos')
expect_is(results5, 'data.frame')
results6 <- conn$searchMsPeaks(mz.sup + 1e-6, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos', insert.input.values=FALSE)
expect_identical(results6, data.frame())
results6.1 <- conn$searchMsPeaks(mz.sup + 1e-6, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos', insert.input.values=TRUE)
expect_is(results6.1, 'data.frame')
expect_identical(colnames(results6.1), 'mz')
}
test.mass.csv.file.ms.mode.values <- function(biodb) {
# Define db data frame
db.df <- rbind(data.frame(), list(accession='C1', ms.mode='ZZZ',
peak.mztheo=112.07569,
peak.comp='P9Z6W410 O',
peak.attr='[(M+H)-(H2O)-(NH3)]+',
formula="J114L6M62O2",
molecular.mass=146.10553,
name='Blablaine'),
stringsAsFactors=FALSE)
# Add new MS mode value
biodb$getEntryFields()$get('ms.mode')$addAllowedValue('pos', 'POS')
expect_error(biodb$getEntryFields()$get('ms.mode')$addAllowedValue('neg',
'POS'))
biodb$getEntryFields()$get('ms.mode')$addAllowedValue('pos', 'ZZZ')
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db.df)
# Try M/Z matching
mz.tol <- 5
mz.tol.unit <- 'ppm'
mz <- db.df[['peak.mztheo']]
results <- conn$searchMsPeaks(mz, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit,
ms.mode='pos')
expect_is(results, 'data.frame')
results <- conn$searchMsPeaks(mz, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit,
ms.mode='zzz')
expect_is(results, 'data.frame')
}
test.mass.csv.file.cache.id <- function(biodb) {
# Open a connector with no URL
conn <- biodb$getFactory()$createConn('mass.csv.file')
# Test that cache ID is NULL (in memory database)
testthat::expect_null(conn$getCacheId())
# Set URL
db.file <- file.path(biodb::getTestOutputDir(), 'test.mass.csv.file.cache.id_db.tsv')
conn$setUrl('base.url', db.file)
# Test that cache ID is not NULL
testthat::expect_is(conn$getCacheId(), 'character')
testthat::expect_true(nchar(conn$getCacheId()) > 0)
cache.id <- conn$getCacheId()
# Close the connector
biodb$getFactory()$deleteConn(conn$getId())
# Open a connector to the same URL
conn <- biodb$getFactory()$createConn('mass.csv.file', url=db.file)
# Test that we get the same cache ID
testthat::expect_equal(conn$getCacheId(), cache.id)
# Close the connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.mass.csv.file.cache.confusion <- function(biodb) {
# Create data frame for new file db A
entry.id <- 'K'
df <- rbind(data.frame(accession=entry.id, ms.mode='pos', ms.level=1,
peak.mztheo=219.1127765, peak.intensity=373076,
peak.relative.intensity=999),
stringsAsFactors=FALSE)
# Open a connector to data frame and set URL to file db A
db.A.file <- file.path(biodb::getTestOutputDir(),
'test.mass.csv.file.cache.confusion_db_A.tsv')
if (file.exists(db.A.file))
unlink(db.A.file)
conn <- biodb$getFactory()$createConn('mass.csv.file', url=db.A.file)
conn$setDb(df)
# Save database
conn$allowWriting()
conn$write()
# Get entry with ID K
entry <- conn$getEntry(entry.id)
# Close connector
biodb$getFactory()$deleteConn(conn$getId())
# Open a connector to a file db B that does not exist
db.B.file <- file.path(biodb::getTestOutputDir(), 'test.mass.csv.file.cache.confusion_db_B.tsv')
if (file.exists(db.B.file))
unlink(db.B.file)
conn <- biodb$getFactory()$createConn('mass.csv.file', url = db.B.file)
conn$allowWriting()
# Get entry with the same ID K
entry <- conn$getEntry(entry.id)
# Check that no entry is returned
testthat::expect_null(entry)
# Close connector to file db B
biodb$getFactory()$deleteConn(conn$getId())
}
test_massCsvFile_entry_instantiation <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A1", "A1", "A1", "A1"),
peak.mztheo=c(80, 90, 100, 110, 120),
msprecmz=90,
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
# Get entry
entry <- conn$getEntry("A1")
testthat::expect_is(entry, "BiodbEntry")
# Test
x <- entry$getFieldsAsDataframe(fields='accession')
expX <- data.frame(accession='A1', stringsAsFactors=FALSE)
testthat::expect_identical(x, expX)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test_msmsSearch_R4.0_non_regression <- function(biodb) {
db.tsv <- system.file("extdata", "massbank_extract_msms.tsv",
package='biodb')
conn <- biodb$getFactory()$createConn('mass.csv.file', url=db.tsv)
testthat::expect_is(conn, 'BiodbConn')
spectrum <- data.frame(mz=c(286.1456, 287.1488, 288.1514),
rel.int=c(100, 45, 18))
result <- conn$msmsSearch(spectrum, precursor.mz=286.1438, mz.tol=0.1,
mz.tol.unit='plain', ms.mode='pos')
testthat::expect_s3_class(result, 'data.frame')
}
test_matchingField <- function(biodb) {
# Database with no M/Z field
df <- data.frame(accession='1')
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(df)
testthat::expect_error(conn$getMatchingMzField())
# Database with peak.mztheo only
mz1 <- 132.12
df <- data.frame(accession='1', peak.mztheo=mz1)
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(df)
testthat::expect_equal(conn$getMatchingMzField(), 'peak.mztheo')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz1, mz.tol=0), '1')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz1+1, mz.tol=0),
character())
# Database with peak.mzexp only
df <- data.frame(accession='1', peak.mzexp=mz1)
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(df)
testthat::expect_equal(conn$getMatchingMzField(), 'peak.mzexp')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz1, mz.tol=0), '1')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz1+1, mz.tol=0),
character())
# Database with both peak.mztheo and peak.mzexp
mz2 <- 132.1210
mz3 <- 132.1243
df <- data.frame(accession='1', peak.mztheo=mz2, peak.mzexp=mz3)
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(df)
testthat::expect_warning(field <- conn$getMatchingMzField())
testthat::expect_equal(field, 'peak.mztheo')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz2, mz.tol=0), '1')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz2+1, mz.tol=0),
character())
testthat::expect_equal(conn$searchForMassSpectra(mz=mz3, mz.tol=0),
character())
conn$setMatchingMzField('peak.mzexp')
testthat::expect_equal(conn$getMatchingMzField(), 'peak.mzexp')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz2, mz.tol=0),
character())
testthat::expect_equal(conn$searchForMassSpectra(mz=mz3, mz.tol=0), '1')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz3+1, mz.tol=0),
character())
}
# Set context
biodb::testContext("MassCsvFile generic tests")
# Instantiate Biodb
biodb <- biodb::createBiodbTestInstance()
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setUrl('base.url', MASSFILEDB.URL)
# Make sure we have no residual cache entries from previous tests
biodb$getPersistentCache()$deleteAllFiles(conn$getCacheId(), fail=FALSE)
# Run generic tests
biodb::runGenericTests(conn, pkgName='biodb')
# Run specific tests
biodb::testContext("MassCsvFile specific tests")
biodb::testThat('Test fields manipulation works correctly.', test.fields,
conn=conn)
biodb::testThat("Mass CSV file entry construction works.",
test_massCsvFile_entry_instantiation, biodb=biodb)
biodb::testThat("MassCsvFileConn methods are correct",
test.basic.mass.csv.file, conn=conn)
biodb::testThat('Test that we detect undefined fields', test.undefined.fields,
biodb=biodb)
biodb::testThat('Setting database with a data frame works.',
test.mass.csv.file.data.frame, biodb=biodb)
biodb::testThat('Failure occurs when loading database file with a line containing wrong number of values.', test.wrong.nb.cols, biodb=biodb)
biodb::testThat('Failure occurs when a field with a cardinality of one has several values for the same accession number.', test.field.card.one, biodb=biodb)
biodb::testThat('We can search for precursor M/Z values without peak.attr column defined.', test.getMzValues.without.peak.attr, biodb=biodb)
biodb::testThat('Old column names are still recognized.',
test.mass.csv.file.old.col.names, biodb=biodb)
biodb::testThat('Peaks table of entry has official field names.',
test.mass.csv.file.entry.peaks.table.col.names, biodb=biodb)
biodb::testThat('M/Z matching limits (mz.min and mz.max) are respected.',
test.mass.csv.file.mz.matching.limits, biodb=biodb)
biodb::testThat('We can set additional values for MS mode.',
test.mass.csv.file.ms.mode.values, biodb=biodb)
biodb::testThat('Two different databases do not use the same cache files.',
test.mass.csv.file.cache.confusion, biodb=biodb)
biodb::testThat('Sorting of columns of result frame works well in searchMsPeaks().', test.mass.csv.file.searchMsPeaks.column.sorting, biodb=biodb)
biodb::testThat('Cache ID is set correctly.', test.mass.csv.file.cache.id,
biodb=biodb)
biodb::testThat('R 4.0 error "NA\'s are not allowed in y !" with msmsSearch()
call does not come back.', test_msmsSearch_R4.0_non_regression,
biodb=biodb)
biodb::testThat("We can defined the M/Z matching field.", test_matchingField,
biodb=biodb)
# Terminate Biodb
biodb$terminate()
pkrog/biodb documentation built on Nov. 29, 2022, 4:24 a.m.
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MASSFILEDB.URL <- system.file("extdata", "massbank_extract_full.tsv",
package="biodb", mustWork=TRUE)
MASSFILEDB.WRONG.HEADER.URL <- system.file('testref',
'mass.csv.file-wrong_header.tsv', package="biodb", mustWork=TRUE)
MASSFILEDB.WRONG.NB.COLS.URL <- system.file('testref',
'mass.csv.file-wrong_nb_cols.tsv', package="biodb", mustWork=TRUE)
test.basic.mass.csv.file <- function(db) {
# Open file
df <- read.table(db$getPropValSlot('urls', 'base.url'), sep="\t",
header=TRUE, quote='"', stringsAsFactors=FALSE,
row.names=NULL)
# Test number of entries
expect_gt(db$getNbEntries(), 1)
expect_equal(db$getNbEntries(), sum( ! duplicated(df[c('accession')])))
# Get an entry ID
id <- df[df[['ms.level']] == 1 & ! is.na(df[['chrom.col.id']]),
'accession'][[1]]
# Test number of peaks
expect_gt(db$getNbPeaks(), 1)
expect_gt(db$getNbPeaks(mode='neg'), 1)
expect_gt(db$getNbPeaks(mode='pos'), 1)
expect_equal(db$getNbPeaks(), nrow(df))
expect_gt(db$getNbPeaks(ids=id), 1)
# Test chrom cols
expect_gt(nrow(db$getChromCol()), 1)
expect_gte(nrow(db$getChromCol(ids=id)), 1)
expect_lte(nrow(db$getChromCol(ids=id)), nrow(db$getChromCol()))
expect_true(all(db$getChromCol(ids=id)[['id']] %in%
db$getChromCol()[['id']]))
# Test mz values
expect_true(is.vector(db$getMzValues()))
expect_gt(length(db$getMzValues()), 1)
expect_error(db$getMzValues('wrong.mode.value'), silent=TRUE)
expect_gt(length(db$getMzValues('neg')), 1)
expect_gt(length(db$getMzValues('pos')), 1)
}
test.mass.csv.file.data.frame <- function(biodb) {
# Define database data frame
ids <- 'ZAP'
mz <- 12
df <- data.frame(accession=ids, mz=mz, mode='+')
# New biodb instance
conn <- biodb$getFactory()$createConn('mass.csv.file')
# Set database
conn$setDb(df)
# Set fields
conn$setField('accession', 'accession')
conn$setField('ms.mode', 'mode')
conn$setField('peak.mztheo', 'mz')
# Get M/Z values
expect_identical(mz, conn$getMzValues())
expect_identical(ids, conn$getEntryIds())
}
test.mass.csv.file.old.col.names <- function(biodb) {
# Define data frame
df <- data.frame(compoundid='A10', msmode='POS', mztheo=112.07569,
peakcomp='P9Z6W410', peakattr='[(M+H)-(H2O)-(NH3)]+',
chromcol='colAA', chromcolrt=94.8,
compoundcomp='J114L6M62O2', compoundmass=146.10553,
fullnames='Blablaine')
# New connector instance
conn <- biodb$getFactory()$createConn('mass.csv.file')
# Set database
conn$setDb(df)
# Get chrom cols
cols <- conn$getChromCol()
expect_is(cols, "data.frame")
}
test.fields <- function(biodb) {
# Get fields
col.name <- conn$getFieldColName('ms.mode')
expect_is(col.name, 'character')
expect_true(nchar(col.name) > 0)
# Test if has field
testthat::expect_true(conn$hasField('accession'))
testthat::expect_false(conn$hasField('blabla'))
testthat::expect_false(conn$hasField('nt.seq'))
# Add new field
conn$addField('nt.seq', 'N')
# Set wrong fields
testthat::expect_error(conn$setField('invalid.tag.name', colname='something'),
regexp='^.*Database field "invalid.tag.name" is not valid.$')
testthat::expect_error(conn$setField('ms.mode', colname='wrong.col.name'),
regexp='^.*Column.* is/are not defined in database file.$')
# Reseting accession field should fail
testthat::expect_error(conn$setField('accession', 'compound.id'))
}
test.undefined.fields <- function(biodb) {
conn <- biodb$getFactory()$createConn('mass.csv.file',
url=MASSFILEDB.WRONG.HEADER.URL)
testthat::expect_warning(conn$hasField('accession'),
regexp='^.*Column ".*" does not match any biodb field\\.$')
testthat::expect_error(conn$getEntryIds(),
regexp='^.*Field.* accession is/are undefined in file database\\.$')
biodb$getFactory()$deleteConn(conn$getId())
}
test.wrong.nb.cols <- function(biodb) {
conn <- biodb$getFactory()$createConn('mass.csv.file',
url=MASSFILEDB.WRONG.NB.COLS.URL)
expect_error(ids <- conn$getEntryIds(),
regexp='^.* 1 .* 12 .*$')
# Error message in English: line 1 did not have 12 elements
biodb$getFactory()$deleteConn(conn$getId())
}
test.field.card.one <- function(biodb) {
# Define database data frame
ids <- c('ZAP', 'ZAP')
mzs <- c(12, 14)
modes <- c('+', '-')
df <- data.frame(ids=ids, mz=mzs, mode=modes)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(df)
# Set fields
conn$setField('accession', 'ids')
conn$setField('ms.mode', 'mode')
conn$setField('peak.mztheo', 'mz')
expect_error(conn$checkDb(),
regexp=paste0('^.*Cannot set more that one value .* into',
' single value field .*\\.$'))
}
test.getMzValues.without.peak.attr <- function(biodb) {
df <- rbind(data.frame(),
list(accession='BML80005', ms.mode='pos', ms.level=1, peak.mztheo=219.1127765, peak.intensity=373076, peak.relative.intensity=999),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(df)
# Get M/Z values
mzs <- conn$getMzValues(max.results=10)
expect_is(mzs, 'numeric')
expect_length(mzs, 1)
# Get M/Z values filtering on precursor
mzs <- conn$getMzValues(max.results=10, precursor=TRUE, ms.mode='pos')
expect_is(mzs, 'numeric')
expect_length(mzs, 0)
}
test.mass.csv.file.entry.peaks.table.col.names <- function(biodb) {
# Define db data frame
id <- 'BML80005'
df <- rbind(data.frame(), list(accession=id, mode='pos', mztheo=219.1127765,
peakcomp='CHON',
peakattr='[(M+H)-(H2O)-(NH3)]+', int=373076,
relint=999), stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(df)
conn$setField('ms.mode', 'mode')
conn$setField('peak.mztheo', 'mztheo')
conn$setField('peak.attr', 'peakattr')
conn$setField('peak.comp', 'peakcomp')
conn$setField('peak.intensity', 'int')
conn$setField('peak.relative.intensity', 'relint')
# Get entry and peaks
entry <- biodb$getFactory()$getEntry(conn$getId(), id)
expect_is(entry, 'MassCsvFileEntry')
peaks <- entry$getFieldValue('peaks')
expect_is(peaks, 'data.frame')
expect_equal(nrow(peaks), 1)
expect_gte(ncol(peaks), 1)
# Check that colnames of peaks table are all valid field names or aliases
expect_true(all(vapply(names(peaks), function(field) biodb$getEntryFields()$isDefined(field), FUN.VALUE = FALSE)))
# Check that colnames of peaks table are all official field names (not aliases)
expect_true(all(vapply(names(peaks), function(field) biodb$getEntryFields()$get(field)$getName() == field, FUN.VALUE = FALSE)))
}
test.mass.csv.file.searchMsPeaks.column.sorting <- function(biodb) {
# Define db data frame
db.df <- rbind(data.frame(accession='C1', ms.mode='POS', peak.mztheo=112.07569, peak.comp='P9Z6W410 O', peak.attr='[(M+H)-(H2O)-(NH3)]+', formula="J114L6M62O2", molecular.mass=146.10553, name='Blablaine', inchi='InChI=1S/C7H8N4O3/c1-10-4-3(8-6(10)13)5(12)11(2)7(14)9-4/h1-2H3,(H,8,13)(H,9,14)', inchikey='NA'),
data.frame(accession='C2', ms.mode='POS', peak.mztheo=208.8274, peak.comp='Y2Z6W410 O', peak.attr='[(M+H)-(H2O)]+', formula="T114L6M62O2", molecular.mass=146.10553, name='Sloopaine', inchi='InChI=1S/C7H8N4O3/c1-10-4-3(8-6(10)13)5(12)11(2)7(14)9-4/h1-2H3,(H,8,13)(H,9,14)', inchikey='FRYVQXCDSBCDAU-AKDOOQIZSA-N'),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db.df)
# Search
results <- conn$searchMsPeaks(db.df[['peak.mztheo']], mz.tol = 10, insert.input.values = FALSE)
expect_is(results, 'data.frame')
expected.cols <- sort(c(colnames(db.df), 'peak.mz', 'mass.csv.file.id'))
expect_identical(expected.cols, colnames(results))
}
test.mass.csv.file.mz.matching.limits <- function(biodb) {
# Define db data frame
db.df <- rbind(data.frame(), list(accession='C1', ms.mode='POS',
peak.mztheo=112.07569,
peak.comp='P9Z6W410 O',
peak.attr='[(M+H)-(H2O)-(NH3)]+',
formula="J114L6M62O2",
molecular.mass=146.10553,
name='Blablaine'),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db.df)
mz.tol <- 5
# Compute mz.min and mz.max
mz.tol.unit <- 'ppm'
mz <- db.df[['peak.mztheo']]
mz.sup <- mz / ( 1 + ( - mz.tol) * 1e-6)
mz.sup <- mz.sup - 1e-8 # Adjustment needed, due to computing differences.
mz.inf <- mz / ( 1 + ( + mz.tol) * 1e-6)
# Search
results1 <- conn$searchMsPeaks(mz, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos')
expect_is(results1, 'data.frame')
results2 <- conn$searchMsPeaks((mz.inf + mz.sup)/2, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos')
expect_is(results2, 'data.frame')
results3 <- conn$searchMsPeaks(mz.inf, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos')
expect_is(results3, 'data.frame')
results4 <- conn$searchMsPeaks(mz.inf - 1e-6, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos', insert.input.values=FALSE)
expect_identical(results4, data.frame())
results4.1 <- conn$searchMsPeaks(mz.inf - 1e-6, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos', insert.input.values=TRUE)
expect_is(results4.1, 'data.frame')
expect_identical(colnames(results4.1), 'mz')
results5 <- conn$searchMsPeaks(mz.sup, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos')
expect_is(results5, 'data.frame')
results6 <- conn$searchMsPeaks(mz.sup + 1e-6, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos', insert.input.values=FALSE)
expect_identical(results6, data.frame())
results6.1 <- conn$searchMsPeaks(mz.sup + 1e-6, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit, ms.mode='pos', insert.input.values=TRUE)
expect_is(results6.1, 'data.frame')
expect_identical(colnames(results6.1), 'mz')
}
test.mass.csv.file.ms.mode.values <- function(biodb) {
# Define db data frame
db.df <- rbind(data.frame(), list(accession='C1', ms.mode='ZZZ',
peak.mztheo=112.07569,
peak.comp='P9Z6W410 O',
peak.attr='[(M+H)-(H2O)-(NH3)]+',
formula="J114L6M62O2",
molecular.mass=146.10553,
name='Blablaine'),
stringsAsFactors=FALSE)
# Add new MS mode value
biodb$getEntryFields()$get('ms.mode')$addAllowedValue('pos', 'POS')
expect_error(biodb$getEntryFields()$get('ms.mode')$addAllowedValue('neg',
'POS'))
biodb$getEntryFields()$get('ms.mode')$addAllowedValue('pos', 'ZZZ')
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db.df)
# Try M/Z matching
mz.tol <- 5
mz.tol.unit <- 'ppm'
mz <- db.df[['peak.mztheo']]
results <- conn$searchMsPeaks(mz, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit,
ms.mode='pos')
expect_is(results, 'data.frame')
results <- conn$searchMsPeaks(mz, mz.tol=mz.tol, mz.tol.unit=mz.tol.unit,
ms.mode='zzz')
expect_is(results, 'data.frame')
}
test.mass.csv.file.cache.id <- function(biodb) {
# Open a connector with no URL
conn <- biodb$getFactory()$createConn('mass.csv.file')
# Test that cache ID is NULL (in memory database)
testthat::expect_null(conn$getCacheId())
# Set URL
db.file <- file.path(biodb::getTestOutputDir(), 'test.mass.csv.file.cache.id_db.tsv')
conn$setUrl('base.url', db.file)
# Test that cache ID is not NULL
testthat::expect_is(conn$getCacheId(), 'character')
testthat::expect_true(nchar(conn$getCacheId()) > 0)
cache.id <- conn$getCacheId()
# Close the connector
biodb$getFactory()$deleteConn(conn$getId())
# Open a connector to the same URL
conn <- biodb$getFactory()$createConn('mass.csv.file', url=db.file)
# Test that we get the same cache ID
testthat::expect_equal(conn$getCacheId(), cache.id)
# Close the connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.mass.csv.file.cache.confusion <- function(biodb) {
# Create data frame for new file db A
entry.id <- 'K'
df <- rbind(data.frame(accession=entry.id, ms.mode='pos', ms.level=1,
peak.mztheo=219.1127765, peak.intensity=373076,
peak.relative.intensity=999),
stringsAsFactors=FALSE)
# Open a connector to data frame and set URL to file db A
db.A.file <- file.path(biodb::getTestOutputDir(),
'test.mass.csv.file.cache.confusion_db_A.tsv')
if (file.exists(db.A.file))
unlink(db.A.file)
conn <- biodb$getFactory()$createConn('mass.csv.file', url=db.A.file)
conn$setDb(df)
# Save database
conn$allowWriting()
conn$write()
# Get entry with ID K
entry <- conn$getEntry(entry.id)
# Close connector
biodb$getFactory()$deleteConn(conn$getId())
# Open a connector to a file db B that does not exist
db.B.file <- file.path(biodb::getTestOutputDir(), 'test.mass.csv.file.cache.confusion_db_B.tsv')
if (file.exists(db.B.file))
unlink(db.B.file)
conn <- biodb$getFactory()$createConn('mass.csv.file', url = db.B.file)
conn$allowWriting()
# Get entry with the same ID K
entry <- conn$getEntry(entry.id)
# Check that no entry is returned
testthat::expect_null(entry)
# Close connector to file db B
biodb$getFactory()$deleteConn(conn$getId())
}
test_massCsvFile_entry_instantiation <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A1", "A1", "A1", "A1"),
peak.mztheo=c(80, 90, 100, 110, 120),
msprecmz=90,
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
# Get entry
entry <- conn$getEntry("A1")
testthat::expect_is(entry, "BiodbEntry")
# Test
x <- entry$getFieldsAsDataframe(fields='accession')
expX <- data.frame(accession='A1', stringsAsFactors=FALSE)
testthat::expect_identical(x, expX)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test_msmsSearch_R4.0_non_regression <- function(biodb) {
db.tsv <- system.file("extdata", "massbank_extract_msms.tsv",
package='biodb')
conn <- biodb$getFactory()$createConn('mass.csv.file', url=db.tsv)
testthat::expect_is(conn, 'BiodbConn')
spectrum <- data.frame(mz=c(286.1456, 287.1488, 288.1514),
rel.int=c(100, 45, 18))
result <- conn$msmsSearch(spectrum, precursor.mz=286.1438, mz.tol=0.1,
mz.tol.unit='plain', ms.mode='pos')
testthat::expect_s3_class(result, 'data.frame')
}
test_matchingField <- function(biodb) {
# Database with no M/Z field
df <- data.frame(accession='1')
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(df)
testthat::expect_error(conn$getMatchingMzField())
# Database with peak.mztheo only
mz1 <- 132.12
df <- data.frame(accession='1', peak.mztheo=mz1)
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(df)
testthat::expect_equal(conn$getMatchingMzField(), 'peak.mztheo')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz1, mz.tol=0), '1')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz1+1, mz.tol=0),
character())
# Database with peak.mzexp only
df <- data.frame(accession='1', peak.mzexp=mz1)
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(df)
testthat::expect_equal(conn$getMatchingMzField(), 'peak.mzexp')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz1, mz.tol=0), '1')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz1+1, mz.tol=0),
character())
# Database with both peak.mztheo and peak.mzexp
mz2 <- 132.1210
mz3 <- 132.1243
df <- data.frame(accession='1', peak.mztheo=mz2, peak.mzexp=mz3)
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(df)
testthat::expect_warning(field <- conn$getMatchingMzField())
testthat::expect_equal(field, 'peak.mztheo')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz2, mz.tol=0), '1')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz2+1, mz.tol=0),
character())
testthat::expect_equal(conn$searchForMassSpectra(mz=mz3, mz.tol=0),
character())
conn$setMatchingMzField('peak.mzexp')
testthat::expect_equal(conn$getMatchingMzField(), 'peak.mzexp')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz2, mz.tol=0),
character())
testthat::expect_equal(conn$searchForMassSpectra(mz=mz3, mz.tol=0), '1')
testthat::expect_equal(conn$searchForMassSpectra(mz=mz3+1, mz.tol=0),
character())
}
# Set context
biodb::testContext("MassCsvFile generic tests")
# Instantiate Biodb
biodb <- biodb::createBiodbTestInstance()
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setUrl('base.url', MASSFILEDB.URL)
# Make sure we have no residual cache entries from previous tests
biodb$getPersistentCache()$deleteAllFiles(conn$getCacheId(), fail=FALSE)
# Run generic tests
biodb::runGenericTests(conn, pkgName='biodb')
# Run specific tests
biodb::testContext("MassCsvFile specific tests")
biodb::testThat('Test fields manipulation works correctly.', test.fields,
conn=conn)
biodb::testThat("Mass CSV file entry construction works.",
test_massCsvFile_entry_instantiation, biodb=biodb)
biodb::testThat("MassCsvFileConn methods are correct",
test.basic.mass.csv.file, conn=conn)
biodb::testThat('Test that we detect undefined fields', test.undefined.fields,
biodb=biodb)
biodb::testThat('Setting database with a data frame works.',
test.mass.csv.file.data.frame, biodb=biodb)
biodb::testThat('Failure occurs when loading database file with a line containing wrong number of values.', test.wrong.nb.cols, biodb=biodb)
biodb::testThat('Failure occurs when a field with a cardinality of one has several values for the same accession number.', test.field.card.one, biodb=biodb)
biodb::testThat('We can search for precursor M/Z values without peak.attr column defined.', test.getMzValues.without.peak.attr, biodb=biodb)
biodb::testThat('Old column names are still recognized.',
test.mass.csv.file.old.col.names, biodb=biodb)
biodb::testThat('Peaks table of entry has official field names.',
test.mass.csv.file.entry.peaks.table.col.names, biodb=biodb)
biodb::testThat('M/Z matching limits (mz.min and mz.max) are respected.',
test.mass.csv.file.mz.matching.limits, biodb=biodb)
biodb::testThat('We can set additional values for MS mode.',
test.mass.csv.file.ms.mode.values, biodb=biodb)
biodb::testThat('Two different databases do not use the same cache files.',
test.mass.csv.file.cache.confusion, biodb=biodb)
biodb::testThat('Sorting of columns of result frame works well in searchMsPeaks().', test.mass.csv.file.searchMsPeaks.column.sorting, biodb=biodb)
biodb::testThat('Cache ID is set correctly.', test.mass.csv.file.cache.id,
biodb=biodb)
biodb::testThat('R 4.0 error "NA\'s are not allowed in y !" with msmsSearch()
call does not come back.', test_msmsSearch_R4.0_non_regression,
biodb=biodb)
biodb::testThat("We can defined the M/Z matching field.", test_matchingField,
biodb=biodb)
# Terminate Biodb
biodb$terminate()
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