tests/testthat/test-rank-query.R

In chromer: Interface to Chromosome Counts Database API

context("Testing rank-based query")

test_that("Rank-based query", {

    skip_if_offline()    # offline or on CRAN
    skip_if(ccdb_down()) # ccdb.tau.ac.il is down

    ## Query for genus Lachemilla for testing purposes
    cp <- chrom_counts(taxa="Lachemilla", rank="genus", full=FALSE)
    cf <- chrom_counts(taxa="Lachemilla", rank="genus", full=TRUE)

    ## Call function for making short species name
    short_species_name <- chromer:::short_species_name

    # Main function returns the correct format
    expect_that(cp, is_a("data.frame"))
    expect_that(cf, is_a("data.frame"))
    expect_equal(ncol(cp), 4)
    expect_equal(ncol(cf), 13)   # previously said to be 15
    expect_equal(nrow(cp), nrow(cf))

    ##############################

    # No match returns empty data frame

    dum <- chrom_counts(taxa="Notagenus", rank="genus")
    expect_equal(nrow(dum), 0)
    expect_equal(ncol(dum), 0)

    ##############################


    # Querying multiple taxa works

    mp <- chrom_counts(taxa=c("Lachemilla", "Lachemilla"), rank="genus",
                       full=FALSE)
    expect_that(mp, is_a("data.frame"))
    expect_equal(nrow(mp), 2*nrow(cp))
    mp <- chrom_counts(taxa=list("Lachemilla", "Lachemilla"), rank="genus",
                       full=FALSE)
    expect_that(mp, is_a("data.frame"))
    expect_equal(nrow(mp), 2*nrow(cp))

    ##############################

    # Query worked properly

    ## Full records
    gen <- unique(cf$genus)
    fam <- unique(cf$family)
    expect_equal(gen, "Lachemilla")
    expect_equal(fam, "Rosaceae")

    ## Partial records
    gen <- unique(sapply(cp$resolved_binomial, function(x)
                         {strsplit(x, split="_")[[1]][1]}))
    expect_equal(gen, "Lachemilla")

    ##############################

    # Species querying works properly for both possible queries

    ## With space
    min_spc <- data.frame(chrom_counts("Castilleja minata", "species"))
    min_und <- data.frame(chrom_counts("Castilleja_minata", "species"))

    expect_equal(min_spc, min_und)

    ##############################

    # Building species name worked properly

    spf <- cf$resolved_binomial
    spp <- cp$resolved_binomial
    expect_equal(spf, spp)

    sp_tmp <- cf$resolved_name[1]
    expect_equal(short_species_name(sp_tmp), spf[1])

    ## Make sure strsplit is working properly
    sp_dum <- "Dummy species (Tax. auth.) Name"
    sh_dum <- short_species_name(sp_dum)
    expect_equal(sh_dum, "Dummy_species")

    ## Varieties
    sp_var <- "Dummy species var. x (Tax. auth.) Name"
    sh_var <- short_species_name(sp_var)
    expect_equal(sh_var, "Dummy_species_var._x")

    ## Subspecies
    sp_sub <- "Dummy species subsp. x (Tax. auth.) Name"
    sh_sub <- short_species_name(sp_sub)
    expect_equal(sh_sub, "Dummy_species_subsp._x")

    ##############################

    # Bad input throws error
    expect_error(chrom_counts("foo", c("genus", "family")))
    expect_error(chrom_counts("foo", "foo"))

})