MASSFILEDB.URL <- system.file("extdata", "massbank_extract_full.tsv",
package="biodb")
COMPFILEDB.URL <- system.file("extdata", "chebi_extract.tsv", package="biodb")
# Generated files
MASS.SQLITE.URL <- file.path(system.file("extdata", package="biodb"),
'generated', "massbank_extract_full.sqlite")
COMP.SQLITE.URL <- file.path(system.file("extdata", package="biodb"),
'generated', "chebi_extract.sqlite")
test_createCompSQLiteDbFromCsvFile <- function(biodb) {
testthat::expect_false(file.exists(COMP.SQLITE.URL))
# Create folder
folder <- dirname(COMP.SQLITE.URL)
if ( ! dir.exists(folder))
dir.create(folder, recursive=TRUE)
# Create connectors
csvConn <- biodb$getFactory()$createConn('comp.csv.file',
url=COMPFILEDB.URL,
fail.if.exists=FALSE)
sqlConn <- biodb$getFactory()$createConn('comp.sqlite', url=COMP.SQLITE.URL)
testthat::expect_identical(character(), sqlConn$getEntryIds())
# Make sure we have no residual cache entries from previous tests
biodb$getPersistentCache()$deleteAllFiles(sqlConn$getCacheId(), fail=FALSE)
# Check CSV conn
ids <- csvConn$getEntryIds()
testthat::expect_is(ids, 'character')
testthat::expect_true(length(ids) > 0)
testthat::expect_false(any(is.na(ids)))
# Copy CSV db into SQLite db
sqlConn$allowEditing()
biodb$copyDb(csvConn, sqlConn)
sqlConn$allowWriting()
sqlConn$write()
# Test
testthat::expect_identical(csvConn$getEntryIds(), sqlConn$getEntryIds())
# Delete connectors
biodb$getFactory()$deleteConn(csvConn)
biodb$getFactory()$deleteConn(sqlConn)
testthat::expect_true(file.exists(COMP.SQLITE.URL))
}
test_createMassSQLiteDbFromCsvFile <- function(biodb) {
testthat::expect_false(file.exists(MASS.SQLITE.URL))
# Create folder
folder <- dirname(MASS.SQLITE.URL)
if ( ! dir.exists(folder))
dir.create(folder, recursive=TRUE)
# Create connectors
csvConn <- biodb$getFactory()$createConn('mass.csv.file',
url=MASSFILEDB.URL,
fail.if.exists=FALSE)
sqlConn <- biodb$getFactory()$createConn('mass.sqlite', url=MASS.SQLITE.URL)
testthat::expect_identical(character(), sqlConn$getEntryIds())
# Make sure we have no residual cache entries from previous tests
biodb$getPersistentCache()$deleteAllFiles(sqlConn$getCacheId(), fail=FALSE)
# Check CSV conn
ids <- csvConn$getEntryIds()
testthat::expect_is(ids, 'character')
testthat::expect_true(length(ids) > 0)
testthat::expect_false(any(is.na(ids)))
# Copy CSV db into SQLite db
sqlConn$allowEditing()
biodb$copyDb(csvConn, sqlConn)
sqlConn$allowWriting()
sqlConn$write()
# Test
testthat::expect_identical(csvConn$getEntryIds(), sqlConn$getEntryIds())
# Delete connectors
biodb$getFactory()$deleteConn(csvConn)
biodb$getFactory()$deleteConn(sqlConn)
testthat::expect_true(file.exists(MASS.SQLITE.URL))
}
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