tests/testthat/test-phenotype.R

In wuxi-nextcode/gorr: Genuity Science service API for R

context("test-phenotype.R")

init_phenotype_test <- function() {
    test_name <<- paste0("test_pheno", sample(1:1000,1))
    test_type <- "QT"
    test_desc <- "This is a test phenotype"
    test_phenotype <<- create_phenotype(name=test_name,
                                        result_type = test_type,
                                        description=test_desc,
                                        conn=conn)
}

init_phenotype_test()


test_that("phenotype_update_description works", {
    input <- "Update this"
    result <- phenotype_update_description(description=input, test_phenotype, conn=conn)

    expect_is(result, "phenotype")
})


test_that("phenotype_upload_data (list of lists) works", {
    input <- list(list("20001", "obese"), list("20002", "lean"))
    expect_error(phenotype_upload_data(data=input, test_phenotype, conn), NA) # Expect no error
})

test_that("phenotype_upload_data (data.frame) works", {
    input <- list(list("20001", "obese"), list("20002", "lean")) %>%
        do.call(rbind, . ) %>%
        as.data.frame()
    expect_error(phenotype_upload_data(data=input, test_phenotype, conn), NA) # Expect no error
})

#### Test phenotype tag services ####

test_that("phenotype_add_tags works", {
    test_phenotype <<- phenotype_add_tags(tag="test1,test2", test_phenotype)

    expect_is(test_phenotype, "phenotype")
    expect_equal(length(test_phenotype$tag_list), 2)
})

test_that("phenotype_set_tags works", {
    test_phenotype <<- phenotype_set_tags(tag="test3,test4,test5", test_phenotype)

    expect_is(test_phenotype, "phenotype")
    expect_equal(length(test_phenotype$tag_list), 3)
})

test_that("phenotype_delete_tags works", {
    test_phenotype <<- phenotype_delete_tags(tag="test4", test_phenotype)

    expect_is(test_phenotype, "phenotype")
    expect_equal(length(test_phenotype$tag_list), 2)
})

test_that("phenotype_get_tags works", {
    result <- phenotype_get_tags(test_phenotype)

    expect_is(result, "character")
    expect_equal(result, c("test3","test5"))

})


#### Test delete / clean up ####


test_that("phenotype_delete works", {
    expect_error(phenotype_delete(test_phenotype), NA) # Expect no error
})