test: create tests

README.md

@@ -2,5 +2,7 @@
 
 Code Ocean capsule: MOSuite - filter differential expression analysis results
 
+[![tests](https://github.com/NIDAP-Community/MOSuite-filter-diff/actions/workflows/tests.yml/badge.svg)](https://github.com/NIDAP-Community/MOSuite-filter-diff/actions/workflows/tests.yml)
+
 - [Code Ocean Capsule](https://poc-nci.codeocean.io/capsule/8221739/tree) | [Latest Release](https://poc-nci.codeocean.io/capsule/0936928/tree/latest)
 - [MOSuite R package docs](https://ccbr.github.io/MOSuite/)

code/main.R

@@ -1,5 +1,4 @@
 #!/usr/bin/env Rscript
-rlang::global_entrace()
 library(argparse)
 library(glue)
 library(MOSuite)
@@ -13,58 +12,173 @@ setup_capsule_environment()
 # parse CLI arguments
 parser <- ArgumentParser()
 
-parser$add_argument("--feature_id_colname", type="character", default=NULL, help="Column name for feature IDs")
-parser$add_argument("--significance_column", type="character", default="adjpval", help="Column name for significance")
-parser$add_argument("--significance_cutoff", type="double", default=0.05, help="Significance cutoff threshold")
-parser$add_argument("--change_column", type="character", default="logFC", help="Column name for change")
-parser$add_argument("--change_cutoff", type="double", default=1, help="Change cutoff threshold")
-parser$add_argument("--filtering_mode", type="character", default="any", help="Filter mode: any or all")
-parser$add_argument("--include_estimates", type="character", default="FC,logFC,tstat,pval,adjpval", help="Comma-separated list of estimates to include")
-parser$add_argument("--round_estimates", type="logical", default=TRUE, help="Round estimates")
-parser$add_argument("--rounding_decimal_for_percent_cells", type="integer", default=0, help="Decimal places for percent labels")
-parser$add_argument("--contrast_filter", type="character", default="none", help="Filter contrasts: keep, remove, or none")
-parser$add_argument("--contrasts", type="character", default="", help="Comma-separated list of contrasts")
-parser$add_argument("--groups", type="character", default="", help="Comma-separated list of groups")
-parser$add_argument("--groups_filter", type="character", default="none", help="Filter groups: keep, remove, or none")
-parser$add_argument("--label_font_size", type="double", default=6, help="Font size for labels")
-parser$add_argument("--label_distance", type="double", default=1, help="Distance of labels from bars")
-parser$add_argument("--y_axis_expansion", type="double", default=0.08, help="Y-axis expansion")
-parser$add_argument("--fill_colors", type="character", default="steelblue1,whitesmoke", help="Comma-separated fill colors")
-parser$add_argument("--pie_chart_in_3d", type="logical", default=TRUE, help="Draw pie charts in 3D")
-parser$add_argument("--bar_width", type="double", default=0.4, help="Bar width")
-parser$add_argument("--draw_bar_border", type="logical", default=TRUE, help="Draw bar borders")
-parser$add_argument("--plot_type", type="character", default="bar", help="Plot type: bar or pie")
-parser$add_argument("--plot_titles_fontsize", type="integer", default=12, help="Font size for plot titles")
+parser$add_argument(
+  "--feature_id_colname",
+  type = "character",
+  default = NULL,
+  help = "Column name for feature IDs"
+)
+parser$add_argument(
+  "--significance_column",
+  type = "character",
+  default = "adjpval",
+  help = "Column name for significance"
+)
+parser$add_argument(
+  "--significance_cutoff",
+  type = "double",
+  default = 0.05,
+  help = "Significance cutoff threshold"
+)
+parser$add_argument(
+  "--change_column",
+  type = "character",
+  default = "logFC",
+  help = "Column name for change"
+)
+parser$add_argument(
+  "--change_cutoff",
+  type = "double",
+  default = 1,
+  help = "Change cutoff threshold"
+)
+parser$add_argument(
+  "--filtering_mode",
+  type = "character",
+  default = "any",
+  help = "Filter mode: any or all"
+)
+parser$add_argument(
+  "--include_estimates",
+  type = "character",
+  default = "FC,logFC,tstat,pval,adjpval",
+  help = "Comma-separated list of estimates to include"
+)
+parser$add_argument(
+  "--round_estimates",
+  type = "logical",
+  default = TRUE,
+  help = "Round estimates"
+)
+parser$add_argument(
+  "--rounding_decimal_for_percent_cells",
+  type = "integer",
+  default = 0,
+  help = "Decimal places for percent labels"
+)
+parser$add_argument(
+  "--contrast_filter",
+  type = "character",
+  default = "none",
+  help = "Filter contrasts: keep, remove, or none"
+)
+parser$add_argument(
+  "--contrasts",
+  type = "character",
+  default = "",
+  help = "Comma-separated list of contrasts"
+)
+parser$add_argument(
+  "--groups",
+  type = "character",
+  default = "",
+  help = "Comma-separated list of groups"
+)
+parser$add_argument(
+  "--groups_filter",
+  type = "character",
+  default = "none",
+  help = "Filter groups: keep, remove, or none"
+)
+parser$add_argument(
+  "--label_font_size",
+  type = "double",
+  default = 6,
+  help = "Font size for labels"
+)
+parser$add_argument(
+  "--label_distance",
+  type = "double",
+  default = 1,
+  help = "Distance of labels from bars"
+)
+parser$add_argument(
+  "--y_axis_expansion",
+  type = "double",
+  default = 0.08,
+  help = "Y-axis expansion"
+)
+parser$add_argument(
+  "--fill_colors",
+  type = "character",
+  default = "steelblue1,whitesmoke",
+  help = "Comma-separated fill colors"
+)
+parser$add_argument(
+  "--pie_chart_in_3d",
+  type = "logical",
+  default = TRUE,
+  help = "Draw pie charts in 3D"
+)
+parser$add_argument(
+  "--bar_width",
+  type = "double",
+  default = 0.4,
+  help = "Bar width"
+)
+parser$add_argument(
+  "--draw_bar_border",
+  type = "logical",
+  default = TRUE,
+  help = "Draw bar borders"
+)
+parser$add_argument(
+  "--plot_type",
+  type = "character",
+  default = "bar",
+  help = "Plot type: bar or pie"
+)
+parser$add_argument(
+  "--plot_titles_fontsize",
+  type = "integer",
+  default = 12,
+  help = "Font size for plot titles"
+)
 
 args <- parser$parse_args()
 
 # load multiOmicDataSet from data directory
 moo <- load_moo_from_data_dir()
 
 # run MOSuite
-moo |> 
-    filter_diff(
-        feature_id_colname = args$feature_id_colname,
-        significance_column = args$significance_column,
-        significance_cutoff = args$significance_cutoff,
-        change_column = args$change_column,
-        change_cutoff = args$change_cutoff,
-        filtering_mode = args$filtering_mode,
-        include_estimates = parse_optional_vector(args$include_estimates),
-        round_estimates = args$round_estimates,
-        rounding_decimal_for_percent_cells = args$rounding_decimal_for_percent_cells,
-        contrast_filter = args$contrast_filter,
-        contrasts = parse_optional_vector(args$contrasts),
-        groups = parse_optional_vector(args$groups),
-        groups_filter = args$groups_filter,
-        label_font_size = args$label_font_size,
-        label_distance = args$label_distance,
-        y_axis_expansion = args$y_axis_expansion,
-        fill_colors = parse_optional_vector(args$fill_colors),
-        pie_chart_in_3d = args$pie_chart_in_3d,
-        bar_width = args$bar_width,
-        draw_bar_border = args$draw_bar_border,
-        plot_type = args$plot_type,
-        plot_titles_fontsize = args$plot_titles_fontsize
-        ) |> 
-    write_rds(file.path(getOption("moo_plots_dir"), "..", "moo", "moo.rds"))
+moo |>
+  filter_diff(
+    feature_id_colname = args$feature_id_colname,
+    significance_column = args$significance_column,
+    significance_cutoff = args$significance_cutoff,
+    change_column = args$change_column,
+    change_cutoff = args$change_cutoff,
+    filtering_mode = args$filtering_mode,
+    include_estimates = parse_optional_vector(args$include_estimates),
+    round_estimates = args$round_estimates,
+    rounding_decimal_for_percent_cells = args$rounding_decimal_for_percent_cells,
+    contrast_filter = args$contrast_filter,
+    contrasts = parse_optional_vector(args$contrasts),
+    groups = parse_optional_vector(args$groups),
+    groups_filter = args$groups_filter,
+    label_font_size = args$label_font_size,
+    label_distance = args$label_distance,
+    y_axis_expansion = args$y_axis_expansion,
+    fill_colors = parse_optional_vector(args$fill_colors),
+    pie_chart_in_3d = args$pie_chart_in_3d,
+    bar_width = args$bar_width,
+    draw_bar_border = args$draw_bar_border,
+    plot_type = args$plot_type,
+    plot_titles_fontsize = args$plot_titles_fontsize
+  ) |>
+  write_rds(file.path(
+    getOption("moo_plots_dir"),
+    "..",
+    "moo",
+    "moo-diff-filt.rds"
+  ))

tests/testthat.R

@@ -0,0 +1,2 @@
+library(testthat)
+test_dir(file.path('tests', 'testthat'), stop_on_failure = TRUE)

tests/testthat/test-main.R

@@ -0,0 +1,148 @@
+test_that("code/run executes successfully with default CLI arguments", {
+  # Create temporary workspace
+  workspace <- tempfile("mosuite_filter_diff_test_")
+  dir.create(workspace)
+  on.exit(unlink(workspace, recursive = TRUE), add = TRUE)
+
+  # Set up directory structure
+  code_dir <- file.path(workspace, "code")
+  data_dir <- file.path(workspace, "data")
+  results_dir <- file.path(code_dir, "..", "results")
+  dir.create(code_dir)
+  dir.create(data_dir)
+  dir.create(results_dir)
+
+  # Get test data from package tests directory
+  repo_root <- normalizePath(file.path(dirname(getwd()), ".."))
+  test_data_file <- file.path(repo_root, "tests", "data", "moo-diff.rds")
+
+  expect_true(
+    file.exists(test_data_file),
+    info = paste("Test data file should exist at", test_data_file)
+  )
+  file.copy(test_data_file, file.path(data_dir, "moo.rds"))
+
+  # Copy main.R and run script to workspace
+  file.copy(
+    file.path(repo_root, "code", "main.R"),
+    file.path(code_dir, "main.R")
+  )
+  file.copy(
+    file.path(repo_root, "code", "run"),
+    file.path(code_dir, "run")
+  )
+
+  # Run the script from code directory
+  old_wd <- getwd()
+  setwd(code_dir)
+  on.exit(setwd(old_wd), add = TRUE)
+
+  # Execute run script with default CLI arguments
+  exit_code <- system2(
+    "bash",
+    args = c(
+      "run",
+      "--significance_column=adjpval",
+      "--significance_cutoff=0.05",
+      "--change_column=logFC",
+      "--change_cutoff=1",
+      "--filtering_mode=any"
+    )
+  )
+
+  # Check for successful execution
+  expect_equal(exit_code, 0, info = "run script should execute without error")
+  expect_true(
+    file.exists(file.path(results_dir, "moo", "moo-diff-filt.rds")),
+    info = "Output file moo-diff-filt.rds should be created"
+  )
+
+  # Validate output is a valid MOO object
+  moo <- readr::read_rds(file.path(results_dir, "moo", "moo-diff-filt.rds"))
+  expect_true(
+    S7::S7_inherits(moo, MOSuite::multiOmicDataSet),
+    info = "Output should be an S7 multiOmicDataSet object"
+  )
+
+  # Validate diff results exist
+  expect_true(
+    "diff" %in% names(moo@analyses),
+    info = "Output should have diff results in moo@analyses"
+  )
+})
+
+test_that("code/run executes with custom CLI arguments", {
+  # Create temporary workspace
+  workspace <- tempfile("mosuite_filter_diff_custom_test_")
+  dir.create(workspace)
+  on.exit(unlink(workspace, recursive = TRUE), add = TRUE)
+
+  # Set up directory structure
+  code_dir <- file.path(workspace, "code")
+  data_dir <- file.path(workspace, "data")
+  results_dir <- file.path(code_dir, "..", "results")
+  dir.create(code_dir)
+  dir.create(data_dir)
+  dir.create(results_dir)
+
+  # Get test data from package tests directory
+  repo_root <- normalizePath(file.path(dirname(getwd()), ".."))
+  test_data_file <- file.path(repo_root, "tests", "data", "moo-diff.rds")
+
+  # Copy test data to workspace
+  file.copy(test_data_file, file.path(data_dir, "moo.rds"))
+
+  # Copy main.R and run script to workspace
+  file.copy(
+    file.path(repo_root, "code", "main.R"),
+    file.path(code_dir, "main.R")
+  )
+  file.copy(
+    file.path(repo_root, "code", "run"),
+    file.path(code_dir, "run")
+  )
+
+  # Run the script from code directory
+  old_wd <- getwd()
+  setwd(code_dir)
+  on.exit(setwd(old_wd), add = TRUE)
+
+  # Execute run script with custom CLI arguments
+  exit_code <- system2(
+    "bash",
+    args = c(
+      "run",
+      "--significance_column=pval",
+      "--significance_cutoff=0.01",
+      "--change_column=logFC",
+      "--change_cutoff=2",
+      "--filtering_mode=all",
+      "--round_estimates=TRUE",
+      "--plot_type=bar"
+    )
+  )
+
+  # Check for successful execution
+  expect_equal(
+    exit_code,
+    0,
+    info = "run script with custom args should execute without error"
+  )
+  expect_true(
+    file.exists(file.path(results_dir, "moo", "moo-diff-filt.rds")),
+    info = "Output file moo-diff-filt.rds should be created with custom args"
+  )
+
+  # Validate output is a valid MOO object
+  moo <- readr::read_rds(file.path(results_dir, "moo", "moo-diff-filt.rds"))
+  expect_true(
+    S7::S7_inherits(moo, MOSuite::multiOmicDataSet),
+    info = "Output should be an S7 multiOmicDataSet object"
+  )
+
+  # Validate diff results exist
+  expect_true(
+    "diff" %in% names(moo@analyses),
+    info = "Output should have diff results in moo@analyses"
+  )
+})