tests/testthat/test_040_chebi.ex.R

In pkrog/biodb: biodb, a library and a development framework for connecting to chemical and biological databases

test_chebiex_getEntryPageUrl <- function(conn) {
    
    myUrl <- conn$getEntryPageUrl('17001')
    testthat::expect_is(myUrl, 'character')
    testthat::expect_true(length(myUrl) == 1)
    testthat::expect_true( ! is.na(myUrl))
}

test_chebiex_getEntryImageUrl <- function(conn) {
    
    myUrl <- conn$getEntryImageUrl('17001')
    testthat::expect_is(myUrl, 'character')
    testthat::expect_true(length(myUrl) == 1)
    testthat::expect_true( ! is.na(myUrl))
}

test_getEntry <- function(conn) {

    entry <- conn$getEntry('17001')
    testthat::expect_is(entry, 'BiodbEntry')
    conn$deleteAllEntriesFromVolatileCache()
    entry <- conn$getEntry('17001')
    testthat::expect_is(entry, 'BiodbEntry')
    entry <- conn$getEntry('foo')
    testthat::expect_null(entry)
    ids <- c('foo', '17001', '2528', '15440', '7799')
    entries <- conn$getEntry(ids)
    testthat::expect_is(entries, 'list')
    testthat::expect_length(entries, length(ids))
    testthat::expect_null(entries[[1]])
    for (i in seq(2, length(ids))) {
        e <- entries[[i]]
        testthat::expect_is(e, 'BiodbEntry')
        testthat::expect_equal(e$getFieldValue('accession'), ids[[i]])
    }
}

test_urlChange <- function(conn) {
    key <- 'my.new.url'
    value <- '/some/path/to/local/file'
    conn$setPropValSlot('urls', key, value)
    v <- conn$getPropValSlot('urls', key)
    testthat::expect_equal(value, v)
}

# Set context
biodb::testContext("Test chebi.ex connector.")

# Instantiate Biodb
biodb <- biodb::createBiodbTestInstance()

# Delete existing connectors
biodb$getFactory()$deleteAllConnectors()
testthat::expect_length(biodb$getFactory()$getAllConnectors(), 0)
testthat::expect_length(biodb$getRequestScheduler()$getAllRules(), 0)

# Test with ChEBI
defFile <- system.file("extdata", "chebi_ex.yml", package="biodb")
connFile <- system.file("extdata", "ChebiExConn.R", package="biodb")
entryFile <- system.file("extdata", "ChebiExEntry.R", package="biodb")
biodb$loadDefinitions(defFile)
source(connFile)
source(entryFile)
conn <- biodb$getFactory()$createConn('chebi.ex')
testthat::expect_is(conn, 'BiodbConn')

# Run tests
biodb::testThat("getEntryPageUrl() works.", test_chebiex_getEntryPageUrl,
    conn=conn)
biodb::testThat("getEntryImageUrl() works.", test_chebiex_getEntryImageUrl,
    conn=conn)
biodb::testThat("We can retrieve entries.", test_getEntry, conn=conn)
biodb::testThat("We can add or change URLs.", test_urlChange, conn=conn)

# Terminate Biodb
biodb$terminate()