tests/testthat/test_030_biodb.R
In pkrog/biodb: biodb, a library and a development framework for connecting to chemical and biological databases
test.convertEntryIdFieldToDbClass <- function(biodb) {
# Check all databases
for (db in biodb$getDbsInfo()$getAll())
testthat::expect_equal(biodb$convertEntryIdFieldToDbClass(db$getEntryIdField()), db$getDbClass())
# Check a wrong database name
testthat::expect_null(biodb$convertEntryIdFieldToDbClass('chebi'))
testthat::expect_null(biodb$convertEntryIdFieldToDbClass('blabla.id'))
}
test.collapseRows <- function(biodb) {
# Basic tests
testthat::expect_null(biodb$collapseRows(NULL))
testthat::expect_identical(data.frame(), biodb$collapseRows(data.frame()))
testthat::expect_identical(data.frame(a=1), biodb$collapseRows(data.frame(a=1)))
testthat::expect_identical(data.frame(a=c(1,2)), biodb$collapseRows(data.frame(a=c(1,2))))
testthat::expect_identical(data.frame(a=c(1,2)), biodb$collapseRows(data.frame(a=c(1,2,2))))
testthat::expect_identical(data.frame(a=c(1,2),b=c('5','5|7'), stringsAsFactors=FALSE), biodb$collapseRows(data.frame(a=c(1,2,2),b=c(5,5,7))))
# Test with a different separator
# Decompose test because of the following error on Bioconductor:
# Error in `name %in% base || grepl("^%.*%$", name)`: 'length(x) = 3 > 1'
# in coercion to 'logical(1)'
# Backtrace:
# █
# 1. ├─base::do.call(fct, params)
# 2. └─(function (biodb) ...
# 3. └─testthat::expect_identical(...) test_030_biodb.R:23:8
# 4. └─testthat::quasi_label(enquo(expected), expected.label, arg =
# "expected")
# 5. ├─label %||% expr_label(expr)
# 6. └─testthat:::expr_label(expr)
# 7. └─testthat:::is_call_infix(x)
x <- data.frame(a=c(1,2),b=c('5','5;7'), stringsAsFactors=FALSE)
y <- biodb$collapseRows(data.frame(a=c(1,2,2),b=c(5,5,7)), sep=';')
testthat::expect_identical(x, y)
# Test with NA values
x <- data.frame(a=c(1,NA,NA,2),b=c('5',NA,6,'5|7'), stringsAsFactors=FALSE)
y <- biodb$collapseRows(data.frame(a=c(1,NA,NA,2,2),b=c(5,NA,6,5,7)))
testthat::expect_identical(x, y)
}
test.entriesToDataframe <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A2", "A3", "A3", "A3"),
formula=c("C3H10N2", "C6H12O6", "C6H8O7", "C6H8O7", "C6H8O7"),
msprecmz=c(80, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
# Test
x <- biodb$entriesToDataframe(list())
testthat::expect_identical(data.frame(), x)
ids <- conn$getEntryIds()
testthat::expect_length(ids, 3)
entries <- conn$getEntry(ids)
testthat::expect_length(entries, 3)
x2 <- biodb$entriesToDataframe(entries, fields=character())
testthat::expect_true(identical(data.frame(), x2))
x3 <- biodb$entriesToDataframe(entries, fields=c('formula'))
y3 <- unique(db['formula'])
testthat::expect_identical(y3, x3)
x4 <- biodb$entriesToDataframe(entries, fields=c('formula'), drop=TRUE)
testthat::expect_identical(unique(db$formula), x4)
x5 <- biodb$entriesToDataframe(entries, fields=c('accession', 'formula'))
testthat::expect_identical(unique(db[c('accession', 'formula')]), x5)
# Test with limit
sep <- biodb$getConfig()$get('multival.field.sep')
x7 <- biodb$entriesToDataframe(entries, limit=2, drop=TRUE, flatten=TRUE,
only.atomic=FALSE, fields='msprecmz')
y7 <- c(80, 90, paste(c(100, 110), collapse=sep))
testthat::expect_identical(y7, x7)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.entriesToDataframe.listOfListInput <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A2", "A3", "A3", "A3"),
formula=c("C3H10N2", "C6H12O6", "C6H8O7", "C6H8O7", "C6H8O7"),
msprecmz=c(80, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
ids <- conn$getEntryIds()
entries <- conn$getEntry(ids)
e1 <- entries[[1]]
e2 <- entries[[2]]
e3 <- entries[[3]]
fsep <- biodb$getConfig()$get('multival.field.sep')
esep <- biodb$getConfig()$get('entries.sep')
# Test
x1 <- biodb$entriesToDataframe(list(list()))
testthat::expect_identical(data.frame(), x1)
x2 <- biodb$entriesToDataframe(list(list(), list()))
testthat::expect_equal(data.frame(), x2)
x3 <- biodb$entriesToDataframe(list(e3, list(e1,e2)), own.id=FALSE)
y3 <- data.frame(accession=c('A3', paste('A1', 'A2', sep=esep)),
formula=c("C6H8O7", paste("C3H10N2", "C6H12O6", sep=esep)),
msprecmz=c(paste(100, 110, 120, sep=fsep),
paste(80, 90, sep=esep)),
stringsAsFactors=FALSE)
testthat::expect_identical(y3, x3)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.entryIdsToDataframe <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A2", "A3", "A3", "A3"),
formula=c("C3H10N2", "C6H12O6", "C6H8O7", "C6H8O7", "C6H8O7"),
msprecmz=c(80, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
# Test
x <- biodb$entryIdsToDataframe(character(), db=conn$getId())
testthat::expect_identical(data.frame(), x)
ids <- conn$getEntryIds()
x2 <- biodb$entryIdsToDataframe(ids, db=conn$getId(), fields=character())
testthat::expect_true(identical(data.frame(), x2))
x5 <- biodb$entryIdsToDataframe(ids, db=conn$getId(),
fields=c('accession', 'formula'))
testthat::expect_identical(unique(db[c('accession', 'formula')]), x5)
# Test with limit
sep <- biodb$getConfig()$get('multival.field.sep')
x7 <- biodb$entryIdsToDataframe(ids, db=conn$getId(), limit=2,
fields='msprecmz')
y7 <- data.frame(msprecmz=c(80, 90, paste(c(100, 110), collapse=sep)),
stringsAsFactors=FALSE)
testthat::expect_identical(y7, x7)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.entryIdsToDataframe.listOfListInput <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A2", "A3", "A3", "A3"),
formula=c("C3H10N2", "C6H12O6", "C6H8O7", "C6H8O7", "C6H8O7"),
msprecmz=c(80, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
ids <- conn$getEntryIds()
id1 <- ids[[1]]
id2 <- ids[[2]]
id3 <- ids[[3]]
fsep <- biodb$getConfig()$get('multival.field.sep')
esep <- biodb$getConfig()$get('entries.sep')
# Test
x1 <- biodb$entryIdsToDataframe(list(character()), db=conn$getId())
testthat::expect_identical(data.frame(), x1)
x2 <- biodb$entryIdsToDataframe(list(character(), character()),
db=conn$getId())
testthat::expect_identical(data.frame(), x2)
x3 <- biodb$entryIdsToDataframe(list(id3, c(id1,id2)), own.id=FALSE,
db=conn$getId())
y3 <- data.frame(accession=c('A3', paste('A1', 'A2', sep=esep)),
formula=c("C6H8O7", paste("C3H10N2", "C6H12O6", sep=esep)),
msprecmz=c(paste(100, 110, 120, sep=fsep),
paste(80, 90, sep=esep)),
stringsAsFactors=FALSE)
testthat::expect_identical(y3, x3)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.addColsToDataframe <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A2", "A3", "A3", "A3"),
formula=c("C3H10N2", "C6H12O6", "C6H8O7", "C6H8O7", "C6H8O7"),
msprecmz=c(80, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
# Input data frame
idf <- data.frame(ids=c("A2", "A3"), col2=c(1, 2), stringsAsFactors=FALSE)
# Test
x <- biodb$addColsToDataframe(data.frame(), db=conn$getId())
testthat::expect_identical(data.frame(), x)
x2 <- biodb$addColsToDataframe(idf, id.col='ids', db=conn$getId(), fields=character())
testthat::expect_true(identical(idf, x2))
# Test with limit
sep <- biodb$getConfig()$get('multival.field.sep')
x7 <- biodb$addColsToDataframe(idf, id.col='ids', db=conn$getId(), limit=2,
fields=c('formula', 'msprecmz'))
y7 <- cbind(idf, data.frame(formula=c("C6H12O6", "C6H8O7"),
msprecmz=c(90, paste(c(100, 110), collapse=sep)),
stringsAsFactors=FALSE))
testthat::expect_identical(y7, x7)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.entriesToSingleFieldValues <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A2", "A3", "A3", "A3"),
formula=c("C3H10N2", "C6H8O7", "C6H8O7", "C6H8O7", "C6H8O7"),
msprecmz=c(100, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
# Get IDs & entries
ids <- conn$getEntryIds()
testthat::expect_length(ids, 3)
entries <- conn$getEntry(ids)
testthat::expect_length(entries, 3)
# Test
formulae <- biodb$entriesToSingleFieldValues(entries, field='formula')
testthat::expect_identical(db$formula[ ! duplicated(db$formula)], formulae)
formulae <- biodb$entriesToSingleFieldValues(entries, field='formula',
uniq=FALSE)
testthat::expect_identical(c("C3H10N2", "C6H8O7", "C6H8O7"), formulae)
formulae <- biodb$entriesToSingleFieldValues(entries, field='formula',
sort=TRUE)
testthat::expect_identical(sort(db$formula[ ! duplicated(db$formula)]),
formulae)
formulae <- biodb$entriesToSingleFieldValues(entries, field='msprecmz')
testthat::expect_identical(db$msprecmz[ ! duplicated(db$msprecmz)],
formulae)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.entryIdsToSingleFieldValues <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A2", "A3", "A3", "A3"),
formula=c("C3H10N2", "C6H8O7", "C6H8O7", "C6H8O7", "C6H8O7"),
msprecmz=c(100, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
# Get IDs
ids <- conn$getEntryIds()
testthat::expect_length(ids, 3)
# Test
formulae <- biodb$entryIdsToSingleFieldValues(ids, db=conn$getId(),
field='formula')
testthat::expect_identical(db$formula[ ! duplicated(db$formula)], formulae)
formulae <- biodb$entryIdsToSingleFieldValues(ids, db=conn$getId(),
field='formula', uniq=FALSE)
testthat::expect_identical(c("C3H10N2", "C6H8O7", "C6H8O7"), formulae)
formulae <- biodb$entryIdsToSingleFieldValues(ids, db=conn$getId(),
field='formula', sort=TRUE)
testthat::expect_identical(sort(db$formula[ ! duplicated(db$formula)]),
formulae)
formulae <- biodb$entryIdsToSingleFieldValues(ids, db=conn$getId(),
field='msprecmz')
testthat::expect_identical(db$msprecmz[ ! duplicated(db$msprecmz)],
formulae)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.entriesFieldToVctOrLst <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A1", "A1", "A1", "A1"),
msprecmz=c(80, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
# Get entry
entry <- conn$getEntry("A1")
testthat::expect_is(entry, "BiodbEntry")
# Test
v <- biodb$entriesFieldToVctOrLst(list(entry), field='msprecmz')
testthat::expect_true(length(v[[1]]) == length(db$msprecmz))
v <- biodb$entriesFieldToVctOrLst(list(entry), field='msprecmz', limit=3)
testthat::expect_true(length(v[[1]]) == 3)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.entriesToDataframe.noPeaksDuplication <- function(biodb) {
fileUrl <- system.file("extdata", "massbank_extract_full.tsv",
package="biodb")
conn <- biodb$getFactory()$createConn('mass.csv.file', url=fileUrl)
testthat::expect_is(conn, 'MassCsvFileConn')
entries <- conn$getEntry(c('AU200952', 'AU200953'))
x <- biodb$entriesToDataframe(entries, only.atomic=FALSE, compute=TRUE,
flatten=FALSE, limit=0)
testthat::expect_false(any(duplicated(x[, c('accession', 'peak.mztheo')])))
biodb$getFactory()$deleteConn(conn)
}
# Instantiate Biodb
biodb <- biodb::createBiodbTestInstance()
# Set context
biodb::testContext("Test BiodbMain instance.")
# Run tests
biodb::testThat("convertEntryIdFieldToDbClass() works correctly.",
test.convertEntryIdFieldToDbClass, biodb=biodb)
biodb::testThat('collapseRows() works correctly.', test.collapseRows,
biodb=biodb)
biodb::testThat("entriesToDataframe() works correctly.",
test.entriesToDataframe, biodb=biodb)
biodb::testThat("entriesToDataframe() handles list of list in input.",
test.entriesToDataframe.listOfListInput, biodb=biodb)
biodb::testThat("entriesToDataframe() does not duplicate peaks.",
test.entriesToDataframe.noPeaksDuplication, biodb=biodb)
biodb::testThat("entryIdsToDataframe() works correctly.",
test.entryIdsToDataframe, biodb=biodb)
biodb::testThat("entryIdsToDataframe() handles list of list in input.",
test.entryIdsToDataframe.listOfListInput, biodb=biodb)
biodb::testThat("addColsToDataframe() works correctly.",
test.addColsToDataframe, biodb=biodb)
biodb::testThat("entriesToSingleFieldValues() works correctly.",
test.entriesToSingleFieldValues, biodb=biodb)
biodb::testThat("entryIdsToSingleFieldValues() works correctly.",
test.entryIdsToSingleFieldValues, biodb=biodb)
biodb::testThat("entriesFieldToVctOrLst() works correctly.",
test.entriesFieldToVctOrLst, biodb=biodb)
# Terminate Biodb
biodb$terminate()
pkrog/biodb documentation built on Nov. 29, 2022, 4:24 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
test.convertEntryIdFieldToDbClass <- function(biodb) {
# Check all databases
for (db in biodb$getDbsInfo()$getAll())
testthat::expect_equal(biodb$convertEntryIdFieldToDbClass(db$getEntryIdField()), db$getDbClass())
# Check a wrong database name
testthat::expect_null(biodb$convertEntryIdFieldToDbClass('chebi'))
testthat::expect_null(biodb$convertEntryIdFieldToDbClass('blabla.id'))
}
test.collapseRows <- function(biodb) {
# Basic tests
testthat::expect_null(biodb$collapseRows(NULL))
testthat::expect_identical(data.frame(), biodb$collapseRows(data.frame()))
testthat::expect_identical(data.frame(a=1), biodb$collapseRows(data.frame(a=1)))
testthat::expect_identical(data.frame(a=c(1,2)), biodb$collapseRows(data.frame(a=c(1,2))))
testthat::expect_identical(data.frame(a=c(1,2)), biodb$collapseRows(data.frame(a=c(1,2,2))))
testthat::expect_identical(data.frame(a=c(1,2),b=c('5','5|7'), stringsAsFactors=FALSE), biodb$collapseRows(data.frame(a=c(1,2,2),b=c(5,5,7))))
# Test with a different separator
# Decompose test because of the following error on Bioconductor:
# Error in `name %in% base || grepl("^%.*%$", name)`: 'length(x) = 3 > 1'
# in coercion to 'logical(1)'
# Backtrace:
# █
# 1. ├─base::do.call(fct, params)
# 2. └─(function (biodb) ...
# 3. └─testthat::expect_identical(...) test_030_biodb.R:23:8
# 4. └─testthat::quasi_label(enquo(expected), expected.label, arg =
# "expected")
# 5. ├─label %||% expr_label(expr)
# 6. └─testthat:::expr_label(expr)
# 7. └─testthat:::is_call_infix(x)
x <- data.frame(a=c(1,2),b=c('5','5;7'), stringsAsFactors=FALSE)
y <- biodb$collapseRows(data.frame(a=c(1,2,2),b=c(5,5,7)), sep=';')
testthat::expect_identical(x, y)
# Test with NA values
x <- data.frame(a=c(1,NA,NA,2),b=c('5',NA,6,'5|7'), stringsAsFactors=FALSE)
y <- biodb$collapseRows(data.frame(a=c(1,NA,NA,2,2),b=c(5,NA,6,5,7)))
testthat::expect_identical(x, y)
}
test.entriesToDataframe <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A2", "A3", "A3", "A3"),
formula=c("C3H10N2", "C6H12O6", "C6H8O7", "C6H8O7", "C6H8O7"),
msprecmz=c(80, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
# Test
x <- biodb$entriesToDataframe(list())
testthat::expect_identical(data.frame(), x)
ids <- conn$getEntryIds()
testthat::expect_length(ids, 3)
entries <- conn$getEntry(ids)
testthat::expect_length(entries, 3)
x2 <- biodb$entriesToDataframe(entries, fields=character())
testthat::expect_true(identical(data.frame(), x2))
x3 <- biodb$entriesToDataframe(entries, fields=c('formula'))
y3 <- unique(db['formula'])
testthat::expect_identical(y3, x3)
x4 <- biodb$entriesToDataframe(entries, fields=c('formula'), drop=TRUE)
testthat::expect_identical(unique(db$formula), x4)
x5 <- biodb$entriesToDataframe(entries, fields=c('accession', 'formula'))
testthat::expect_identical(unique(db[c('accession', 'formula')]), x5)
# Test with limit
sep <- biodb$getConfig()$get('multival.field.sep')
x7 <- biodb$entriesToDataframe(entries, limit=2, drop=TRUE, flatten=TRUE,
only.atomic=FALSE, fields='msprecmz')
y7 <- c(80, 90, paste(c(100, 110), collapse=sep))
testthat::expect_identical(y7, x7)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.entriesToDataframe.listOfListInput <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A2", "A3", "A3", "A3"),
formula=c("C3H10N2", "C6H12O6", "C6H8O7", "C6H8O7", "C6H8O7"),
msprecmz=c(80, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
ids <- conn$getEntryIds()
entries <- conn$getEntry(ids)
e1 <- entries[[1]]
e2 <- entries[[2]]
e3 <- entries[[3]]
fsep <- biodb$getConfig()$get('multival.field.sep')
esep <- biodb$getConfig()$get('entries.sep')
# Test
x1 <- biodb$entriesToDataframe(list(list()))
testthat::expect_identical(data.frame(), x1)
x2 <- biodb$entriesToDataframe(list(list(), list()))
testthat::expect_equal(data.frame(), x2)
x3 <- biodb$entriesToDataframe(list(e3, list(e1,e2)), own.id=FALSE)
y3 <- data.frame(accession=c('A3', paste('A1', 'A2', sep=esep)),
formula=c("C6H8O7", paste("C3H10N2", "C6H12O6", sep=esep)),
msprecmz=c(paste(100, 110, 120, sep=fsep),
paste(80, 90, sep=esep)),
stringsAsFactors=FALSE)
testthat::expect_identical(y3, x3)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.entryIdsToDataframe <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A2", "A3", "A3", "A3"),
formula=c("C3H10N2", "C6H12O6", "C6H8O7", "C6H8O7", "C6H8O7"),
msprecmz=c(80, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
# Test
x <- biodb$entryIdsToDataframe(character(), db=conn$getId())
testthat::expect_identical(data.frame(), x)
ids <- conn$getEntryIds()
x2 <- biodb$entryIdsToDataframe(ids, db=conn$getId(), fields=character())
testthat::expect_true(identical(data.frame(), x2))
x5 <- biodb$entryIdsToDataframe(ids, db=conn$getId(),
fields=c('accession', 'formula'))
testthat::expect_identical(unique(db[c('accession', 'formula')]), x5)
# Test with limit
sep <- biodb$getConfig()$get('multival.field.sep')
x7 <- biodb$entryIdsToDataframe(ids, db=conn$getId(), limit=2,
fields='msprecmz')
y7 <- data.frame(msprecmz=c(80, 90, paste(c(100, 110), collapse=sep)),
stringsAsFactors=FALSE)
testthat::expect_identical(y7, x7)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.entryIdsToDataframe.listOfListInput <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A2", "A3", "A3", "A3"),
formula=c("C3H10N2", "C6H12O6", "C6H8O7", "C6H8O7", "C6H8O7"),
msprecmz=c(80, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
ids <- conn$getEntryIds()
id1 <- ids[[1]]
id2 <- ids[[2]]
id3 <- ids[[3]]
fsep <- biodb$getConfig()$get('multival.field.sep')
esep <- biodb$getConfig()$get('entries.sep')
# Test
x1 <- biodb$entryIdsToDataframe(list(character()), db=conn$getId())
testthat::expect_identical(data.frame(), x1)
x2 <- biodb$entryIdsToDataframe(list(character(), character()),
db=conn$getId())
testthat::expect_identical(data.frame(), x2)
x3 <- biodb$entryIdsToDataframe(list(id3, c(id1,id2)), own.id=FALSE,
db=conn$getId())
y3 <- data.frame(accession=c('A3', paste('A1', 'A2', sep=esep)),
formula=c("C6H8O7", paste("C3H10N2", "C6H12O6", sep=esep)),
msprecmz=c(paste(100, 110, 120, sep=fsep),
paste(80, 90, sep=esep)),
stringsAsFactors=FALSE)
testthat::expect_identical(y3, x3)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.addColsToDataframe <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A2", "A3", "A3", "A3"),
formula=c("C3H10N2", "C6H12O6", "C6H8O7", "C6H8O7", "C6H8O7"),
msprecmz=c(80, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
# Input data frame
idf <- data.frame(ids=c("A2", "A3"), col2=c(1, 2), stringsAsFactors=FALSE)
# Test
x <- biodb$addColsToDataframe(data.frame(), db=conn$getId())
testthat::expect_identical(data.frame(), x)
x2 <- biodb$addColsToDataframe(idf, id.col='ids', db=conn$getId(), fields=character())
testthat::expect_true(identical(idf, x2))
# Test with limit
sep <- biodb$getConfig()$get('multival.field.sep')
x7 <- biodb$addColsToDataframe(idf, id.col='ids', db=conn$getId(), limit=2,
fields=c('formula', 'msprecmz'))
y7 <- cbind(idf, data.frame(formula=c("C6H12O6", "C6H8O7"),
msprecmz=c(90, paste(c(100, 110), collapse=sep)),
stringsAsFactors=FALSE))
testthat::expect_identical(y7, x7)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.entriesToSingleFieldValues <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A2", "A3", "A3", "A3"),
formula=c("C3H10N2", "C6H8O7", "C6H8O7", "C6H8O7", "C6H8O7"),
msprecmz=c(100, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
# Get IDs & entries
ids <- conn$getEntryIds()
testthat::expect_length(ids, 3)
entries <- conn$getEntry(ids)
testthat::expect_length(entries, 3)
# Test
formulae <- biodb$entriesToSingleFieldValues(entries, field='formula')
testthat::expect_identical(db$formula[ ! duplicated(db$formula)], formulae)
formulae <- biodb$entriesToSingleFieldValues(entries, field='formula',
uniq=FALSE)
testthat::expect_identical(c("C3H10N2", "C6H8O7", "C6H8O7"), formulae)
formulae <- biodb$entriesToSingleFieldValues(entries, field='formula',
sort=TRUE)
testthat::expect_identical(sort(db$formula[ ! duplicated(db$formula)]),
formulae)
formulae <- biodb$entriesToSingleFieldValues(entries, field='msprecmz')
testthat::expect_identical(db$msprecmz[ ! duplicated(db$msprecmz)],
formulae)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.entryIdsToSingleFieldValues <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A2", "A3", "A3", "A3"),
formula=c("C3H10N2", "C6H8O7", "C6H8O7", "C6H8O7", "C6H8O7"),
msprecmz=c(100, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
# Get IDs
ids <- conn$getEntryIds()
testthat::expect_length(ids, 3)
# Test
formulae <- biodb$entryIdsToSingleFieldValues(ids, db=conn$getId(),
field='formula')
testthat::expect_identical(db$formula[ ! duplicated(db$formula)], formulae)
formulae <- biodb$entryIdsToSingleFieldValues(ids, db=conn$getId(),
field='formula', uniq=FALSE)
testthat::expect_identical(c("C3H10N2", "C6H8O7", "C6H8O7"), formulae)
formulae <- biodb$entryIdsToSingleFieldValues(ids, db=conn$getId(),
field='formula', sort=TRUE)
testthat::expect_identical(sort(db$formula[ ! duplicated(db$formula)]),
formulae)
formulae <- biodb$entryIdsToSingleFieldValues(ids, db=conn$getId(),
field='msprecmz')
testthat::expect_identical(db$msprecmz[ ! duplicated(db$msprecmz)],
formulae)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.entriesFieldToVctOrLst <- function(biodb) {
# Create database
db <- data.frame(
accession=c("A1", "A1", "A1", "A1", "A1"),
msprecmz=c(80, 90, 100, 110, 120),
stringsAsFactors=FALSE)
# Create connector
conn <- biodb$getFactory()$createConn('mass.csv.file')
conn$setDb(db)
# Get entry
entry <- conn$getEntry("A1")
testthat::expect_is(entry, "BiodbEntry")
# Test
v <- biodb$entriesFieldToVctOrLst(list(entry), field='msprecmz')
testthat::expect_true(length(v[[1]]) == length(db$msprecmz))
v <- biodb$entriesFieldToVctOrLst(list(entry), field='msprecmz', limit=3)
testthat::expect_true(length(v[[1]]) == 3)
# Delete connector
biodb$getFactory()$deleteConn(conn$getId())
}
test.entriesToDataframe.noPeaksDuplication <- function(biodb) {
fileUrl <- system.file("extdata", "massbank_extract_full.tsv",
package="biodb")
conn <- biodb$getFactory()$createConn('mass.csv.file', url=fileUrl)
testthat::expect_is(conn, 'MassCsvFileConn')
entries <- conn$getEntry(c('AU200952', 'AU200953'))
x <- biodb$entriesToDataframe(entries, only.atomic=FALSE, compute=TRUE,
flatten=FALSE, limit=0)
testthat::expect_false(any(duplicated(x[, c('accession', 'peak.mztheo')])))
biodb$getFactory()$deleteConn(conn)
}
# Instantiate Biodb
biodb <- biodb::createBiodbTestInstance()
# Set context
biodb::testContext("Test BiodbMain instance.")
# Run tests
biodb::testThat("convertEntryIdFieldToDbClass() works correctly.",
test.convertEntryIdFieldToDbClass, biodb=biodb)
biodb::testThat('collapseRows() works correctly.', test.collapseRows,
biodb=biodb)
biodb::testThat("entriesToDataframe() works correctly.",
test.entriesToDataframe, biodb=biodb)
biodb::testThat("entriesToDataframe() handles list of list in input.",
test.entriesToDataframe.listOfListInput, biodb=biodb)
biodb::testThat("entriesToDataframe() does not duplicate peaks.",
test.entriesToDataframe.noPeaksDuplication, biodb=biodb)
biodb::testThat("entryIdsToDataframe() works correctly.",
test.entryIdsToDataframe, biodb=biodb)
biodb::testThat("entryIdsToDataframe() handles list of list in input.",
test.entryIdsToDataframe.listOfListInput, biodb=biodb)
biodb::testThat("addColsToDataframe() works correctly.",
test.addColsToDataframe, biodb=biodb)
biodb::testThat("entriesToSingleFieldValues() works correctly.",
test.entriesToSingleFieldValues, biodb=biodb)
biodb::testThat("entryIdsToSingleFieldValues() works correctly.",
test.entryIdsToSingleFieldValues, biodb=biodb)
biodb::testThat("entriesFieldToVctOrLst() works correctly.",
test.entriesFieldToVctOrLst, biodb=biodb)
# Terminate Biodb
biodb$terminate()
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.