Nothing
context("Testing rank-based query")
test_that("Rank-based query", {
skip_if_offline() # offline or on CRAN
skip_if(ccdb_down()) # ccdb api 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"))
})
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