tests/testthat/test-chained_function_snapshot_value.R

In EdwardJGillian/GilOG: This package shows how to deal with file input in R Shiny

library(GilOG)
library(testthat)

test_chained_functions <- function(csv_file1, csv_file2) {
  testthat::local_edition(3)
  test_that("check file values for parameters", {

    # create file path to csv file examples

    csv_path1 <-
      paste0(home, "/data/snapshot_csv_input/", csv_file1)
    csv <- stringr::str_remove(csv_file1, ".csv")
    df1 <- as.data.frame(read.csv(file=csv_path1, na.strings = ""))

    csv_path2 <-
      paste0(home, "/data/snapshot_csv_input/", csv_file2)
    df2 <- as.data.frame(read.csv(file=csv_path2, na.strings = ""))

    organism <- df1


    testthat::expect_snapshot_value(
      organism, style = "json2")

    genes <- df2


    testthat::expect_snapshot_value(
      genes, style = "json2")

    # dplyr needs to be run inside testthat for function to work
    # generates a warning
    suppressWarnings(library(dplyr))
    summary_count_df <- GilOG::summary_count_processing(organism, genes)

    testthat::expect_snapshot_value(
      summary_count_df, style = "json2")

    gpo_length_size <- GilOG::gene_length_size_calc(organism, genes)

    testthat::expect_snapshot_value(
      gpo_length_size, style = "json2")

    co_ef_df <- GilOG::cor_processing(gpo_length_size)

    # round r values in co_ef_df for snapshot testing
    co_ef_df <- co_ef_df %>% dplyr::mutate(across(where(is.numeric), round, 5))

    testthat::expect_snapshot_value(
     co_ef_df, style = "json2")

    gpo_length_size_top_5 <- GilOG::cor_processing_top_5(gpo_length_size)

    testthat::expect_snapshot_value(
      gpo_length_size_top_5, style = "json2")

    group_id <- as.double(1)
    gpo_1 <- GilOG::gpo_output_processing(gpo_length_size_top_5, group_id)

    testthat::expect_snapshot_value(
      gpo_1, style = "json2")

    group_id <- as.double(2)
    gpo_2 <- GilOG::gpo_output_processing(gpo_length_size_top_5, group_id)

    testthat::expect_snapshot_value(
      gpo_2, style = "json2")

    group_id <- as.double(3)
    gpo_3 <- GilOG::gpo_output_processing(gpo_length_size_top_5, group_id)

    testthat::expect_snapshot_value(
      gpo_3, style = "json2")

    group_id <- as.double(4)
    gpo_4 <- GilOG::gpo_output_processing(gpo_length_size_top_5, group_id)

    testthat::expect_snapshot_value(
      gpo_4, style = "json2")

    group_id <- as.double(5)
    gpo_5 <- GilOG::gpo_output_processing(gpo_length_size_top_5, group_id)

    testthat::expect_snapshot_value(
      gpo_5, style = "json2")

  })
}

# create the ALS file path
home <- setwd(Sys.getenv("HOME"))


csv_file_path <- file.path(getwd())
csv_file_path <- file.path(home, "data/snapshot_csv_input")

# create organism as test1.csv and genes as test2
csv_files_list1 <- list.files(path = csv_file_path, pattern = "organisms*", full.names = FALSE)
csv_files_list2 <- list.files(path = csv_file_path, pattern = "genes*", full.names = FALSE)

# apply 1 list vector to the function
# apply 2 list vector to function +
purrr::map2(csv_files_list1, csv_files_list2, test_chained_functions)