data(enterotype)
data(data_fungi)

test_that("list_fastq_files function works fine", {
  expect_type(
    list_fastq_files(
      "inst/extdata",
      paired_end = FALSE,
      pattern_R1 = ""
    ),
    "list"
  )
  expect_equal(length(unlist(
    list_fastq_files(
      "inst/extdata",
      paired_end = FALSE,
      pattern_R1 = ""
    )
  )), 3)
  expect_equal(length(unlist(
    list_fastq_files(
      "inst/extdata",
      paired_end = FALSE,
      pattern_R1 = "",
      nb_files = 2
    )
  )), 2)
  expect_type(list_fastq_files("inst/extdata/"), "list")
  expect_equal(length(list_fastq_files("inst/extdata/")), 2)
})

test_that("rename_samples_otu_table function works fine when taxa_are_rows", {
  expect_s4_class(
    rename_samples_otu_table(data_fungi, as.character(1:nsamples(data_fungi))),
    "otu_table"
  )
  expect_equal(nrow(rename_samples_otu_table(data_fungi, as.character(
    1:nsamples(data_fungi)
  ))), nsamples(data_fungi))
  expect_equal(ncol(rename_samples_otu_table(data_fungi, as.character(
    1:nsamples(data_fungi)
  ))), ntaxa(data_fungi))
  expect_equal(
    sample_names(rename_samples_otu_table(data_fungi, as.character(
      1:nsamples(data_fungi)
    ))),
    as.character(1:nsamples(data_fungi))
  )
  expect_error(rename_samples_otu_table(data_fungi, as.character(2:nsamples(data_fungi))))
})

data_fungi_row <- clean_pq(data_fungi, force_taxa_as_rows = TRUE)

test_that("rename_samples_otu_table function works fine when taxa_are_columns", {
  expect_s4_class(
    rename_samples_otu_table(data_fungi_row, as.character(1:nsamples(data_fungi_row))),
    "otu_table"
  )
  expect_equal(ncol(rename_samples_otu_table(
    data_fungi_row, as.character(1:nsamples(data_fungi_row))
  )), nsamples(data_fungi_row))
  expect_equal(nrow(rename_samples_otu_table(
    data_fungi_row, as.character(1:nsamples(data_fungi_row))
  )), ntaxa(data_fungi_row))
  expect_equal(
    sample_names(rename_samples_otu_table(
      data_fungi_row, as.character(1:nsamples(data_fungi_row))
    )),
    as.character(1:nsamples(data_fungi))
  )
  expect_error(rename_samples_otu_table(data_fungi_row, as.character(2:nsamples(data_fungi_row))))
})

data_fungi_test <- data_fungi
data_fungi_test@otu_table[, 1] <-
  rep(0, nrow(data_fungi_test@otu_table))
data_fungi_test@otu_table[10, ] <-
  rep(0, ncol(data_fungi_test@otu_table))

test_that("track_wkflow function works fine", {
  skip_on_os("windows")
  expect_message(track_wkflow(list(
    unlist(list_fastq_files("inst/extdata/")), data_fungi, enterotype
  )))
  expect_s3_class(track_wkflow(list(
    unlist(list_fastq_files("inst/extdata/")), data_fungi, enterotype
  )), "data.frame")
  expect_s3_class(track_wkflow(
    list(unlist(list_fastq_files("inst/extdata/")), data_fungi, enterotype),
    obj_names = c("Fastq.files", "data_fungi", "Enterotype")
  ), "data.frame")
  expect_s3_class(track_wkflow(list(
    unlist(list_fastq_files("inst/extdata/")), data_fungi, data_fungi_test
  ), clean_pq = TRUE), "data.frame")
})

test_that("track_wkflow function works fine with taxonomy_rank", {
  expect_error(track_wkflow(list(
    unlist(list_fastq_files("inst/extdata/")), data_fungi, enterotype
  ), taxonomy_rank = c(3, 5)))
  expect_s3_class(track_wkflow(list(data_fungi, enterotype), taxonomy_rank = c(3, 5)), "data.frame")
})

tree_A10_005 <- subset_samples(data_fungi, Tree_name == "A10-005")

test_that("track_wkflow_samples function works fine", {
  expect_message(track_wkflow_samples(tree_A10_005))
  expect_equal(length(track_wkflow_samples(tree_A10_005)), 3)
  expect_type(track_wkflow_samples(tree_A10_005), "list")
  expect_s3_class(track_wkflow_samples(tree_A10_005)[[1]], "data.frame")
})


derep_R1_001 <- dada2::derepFastq("inst/extdata/ex_R1_001.fastq.gz")
dada_R1_001 <-
  dada(derep_R1_001, selfConsist = TRUE, multithread = TRUE)
derep_R_001 <-
  dada2::derepFastq(c(
    "inst/extdata/ex_R1_001.fastq.gz",
    "inst/extdata/ex_R2_001.fastq.gz"
  ))
test_that("track_wkflow_samples function works fine with object of class matrix, dada and derep", {
  skip_on_os("windows")
  expect_s3_class(track_wkflow(
    list(
      data_fungi@otu_table,
      derep_R1_001,
      derep_R_001,
      "inst/extdata/ex_R1_001.fastq.gz",
      dada_R1_001
    )
  ), "data.frame")
})

test_that("select_one_sample function works fine", {
  expect_message(A8_005 <-
    select_one_sample(data_fungi, "A8-005_S4_MERGED.fastq.gz"))
  expect_s4_class(A8_005, "phyloseq")
  expect_error(select_one_sample(data_fungi, "A8-005_S.fastq.gz"))
})

test_that("subsample_fastq function works fine", {
  expect_silent(subsample_fastq("inst/extdata/ex_R1_001.fastq.gz", "your_path_to_output"))
  file.exists("your_path_to_output/ex_R1_001.fastq.gz")
  unlink("your_path_to_output", recursive = TRUE)
  expect_silent(subsample_fastq(
    list_fastq_files("inst/extdata"),
    "your_path_to_output2",
    nb_seq = 10
  ))
  file.exists("your_path_to_output2/ex_R1_001.fastq.gz")
  unlink("your_path_to_output2", recursive = TRUE)
})

test_that("sample_data_with_new_names function works fine", {
  sam_file <- system.file("extdata", "sam_data.csv", package = "MiscMetabar")
  expect_silent(newdf <- sample_data_with_new_names(sam_file, paste0("Samples_", seq(1, 185))))
  expect_equal(dim(newdf)[1], 185)
  expect_equal(dim(newdf)[2], 7)
})


test_that("sample_data_with_new_names function works fine", {
  testFastqs_fw <- c(
    system.file("extdata", "sam1F.fastq.gz", package = "dada2"),
    system.file("extdata", "sam2F.fastq.gz", package = "dada2")
  )
  testFastqs_rev <- c(
    system.file("extdata", "sam1R.fastq.gz", package = "dada2"),
    system.file("extdata", "sam2R.fastq.gz", package = "dada2")
  )
  expect_silent(filt_fastq_fw <- filter_trim(testFastqs_fw, output_fw = tempdir()))
  expect_equal(length(derepFastq(filt_fastq_fw[1])), 2)
  expect_silent(filt_fastq_pe <- filter_trim(testFastqs_fw,
    testFastqs_rev,
    output_fw = tempdir("fw"),
    output_rev = tempdir("rev")
  ))
  expect_equal(length(derepFastq(filt_fastq_pe[[1]])), 4)
  expect_equal(length(derepFastq(filt_fastq_pe[[2]])), 4)
})

test_that("add_info_to_sam_data function works fine with data_fungi", {
  new_df <- data.frame(
    variable_1 = runif(n = nsamples(data_fungi), min = 1, max = 20),
    variable_2 = runif(n = nsamples(data_fungi), min = 1, max = 2)
  )
  rownames(new_df) <- sample_names(data_fungi)
  expect_silent(data_fungi2 <- add_info_to_sam_data(data_fungi, new_df))
  expect_equal(dim(data_fungi2@sam_data)[2], 11)
  expect_equal(length(data_fungi2@sam_data$nb_seq), 185)
  expect_equal(length(data_fungi2@sam_data$nb_otu), 185)
})