library(testthat)

test_that("no CDs are added if add_cds is FALSE", {
    d <- data.frame(NAME = "A", SMILES = "CC", RT = 1)
    out <- preprocess_data(d, add_cds = FALSE, verbose = 0)
    expect_equal(out, d)
})

test_that("polynomial features are added correctly", {
    M <- data.frame(NAME = c("A", "B"), SMILES = c("CC", "CCC"), RT = c(1, 2))
    X <- data.frame(Fsp3 = c(1, 2))
    d <- cbind(M, X)
    out <- preprocess_data(d, add_cds = FALSE, degree_polynomial = 3, verbose = 0)
    expect_equal(colnames(out), c("NAME", "SMILES", "RT", "Fsp3", "Fsp3^2", "Fsp3^3"))
})

test_that("interaction terms are added correctly", {
    M <- data.frame(NAME = c("A", "B"), SMILES = c("CC", "CCC"), RT = c(1, 2))
    X <- data.frame(Fsp3 = c(1, 2), apol = c(3, 4))
    d <- cbind(M, X)
    out <- preprocess_data(d, add_cds = FALSE, interaction_terms = TRUE, verbose = 0)
    expect_equal(colnames(out), c("NAME", "SMILES", "RT", "Fsp3", "apol", "Fsp3:apol"))
})

test_that("NA removal works", {
    M <- data.frame(NAME = c("A", "B"), SMILES = c("CC", "CCC"), RT = c(1, 2))
    X <- data.frame(Fsp3 = c(1, NA), apol = c(3, 4))
    d <- cbind(M, X)
    out <- preprocess_data(d, add_cds = FALSE, rm_na = TRUE, verbose = 0)
    expect_equal(colnames(out), c("NAME", "SMILES", "RT", "apol"))
})

test_that("near-zero variance removal works", {
    M <- data.frame(NAME = c("A", "B", "C"), SMILES = c("CC", "CCC", "CCCC"), RT = c(1, 2, 3))
    X <- data.frame(Fsp3 = c(1, 1, 1), apol = c(3, 4, 5))
    d <- cbind(M, X)
    out <- preprocess_data(d, add_cds = FALSE, rm_near_zero_var = TRUE, verbose = 0)
    expect_equal(colnames(out), c("NAME", "SMILES", "RT", "apol"))
})

test_that("adding interaction terms requires >=2 predictors", {
    M <- data.frame(NAME = c("A", "B"), SMILES = c("CC", "CCC"), RT = c(1, 2))
    X <- data.frame(Fsp3 = c(1, 2))
    d <- cbind(M, X)
    out <- preprocess_data(d, add_cds = FALSE, interaction_terms = TRUE, verbose = 0)
    expect_equal(colnames(out), c("NAME", "SMILES", "RT", "Fsp3"))
})

test_that("function removes unsupported columns", {
    d <- data.frame(NAME = "A", SMILES = "CC", RT = 1, OTHER = 5)
    out <- preprocess_data(d, add_cds = FALSE, verbose = 0)
    expect_equal(colnames(out), c("NAME", "SMILES", "RT"))
})

test_that("polynomial terms are ignored when constructing interaction terms", {
    M <- data.frame(NAME = c("A", "B"), SMILES = c("CC", "CCC"), RT = c(1, 2))
    X <- data.frame(Fsp3 = c(1, 2), apol = c(3, 4), nAtom = c(5, 6))
    d <- cbind(M, X)
    out <- preprocess_data(
        data = d, add_cds = FALSE, degree_polynomial = 2,
        interaction_terms = TRUE, verbose = 0
    )
    expect_equal(colnames(out), c(
        "NAME", "SMILES", "RT",
        "Fsp3", "apol", "nAtom",
        "Fsp3^2", "apol^2", "nAtom^2",
        "Fsp3:apol", "Fsp3:nAtom", "apol:nAtom"
    ))
})