test: create tests

.github/workflows/test.yml → .github/workflows/tests.yml

@@ -1,4 +1,4 @@
-name: test
+name: tests
 
 on:
   push:
@@ -7,7 +7,7 @@ on:
     branches: [ main, dev ]
 
 jobs:
-  test:
+  tests:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3

README.md

@@ -2,5 +2,7 @@
 
 Code Ocean capsule: MOSuite - normalize counts
 
+[![tests](https://github.com/NIDAP-Community/MOSuite-normalize-counts/actions/workflows/tests.yml/badge.svg)](https://github.com/NIDAP-Community/MOSuite-normalize-counts/actions/workflows/tests.yml)
+
 - [Code Ocean Capsule](https://poc-nci.codeocean.io/capsule/6680510/tree) | [Latest Release](https://poc-nci.codeocean.io/capsule/9169525/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)
@@ -13,70 +12,200 @@ setup_capsule_environment()
 # parse CLI arguments
 parser <- ArgumentParser()
 
-parser$add_argument("--count_type", type="character", default="filt")
-parser$add_argument("--norm_type", type="character", default="voom")
-parser$add_argument("--feature_id_colname", type="character", default=NULL, help="Column name for feature IDs")
-parser$add_argument("--samples_to_include", type="character", default="", help="Comma-separated list of samples to include")
-parser$add_argument("--sample_id_colname", type="character", default=NULL, help="Column name for sample IDs")
-parser$add_argument("--group_colname", type="character", default="Group", help="Column name for sample groups")
-parser$add_argument("--label_colname", type="character", default=NULL, help="Column name for sample labels")
-parser$add_argument("--input_in_log_counts", type="logical", default=FALSE, help="Counts are already log2-transformed")
-parser$add_argument("--voom_normalization_method", type="character", default="quantile", help="Normalization method for limma::voom")
-parser$add_argument("--samples_to_rename", type="character", default="", help="Sample renaming pairs: old:new,old2:new2")
-parser$add_argument("--add_label_to_pca", type="logical", default=TRUE, help="Label points on the PCA plot")
-parser$add_argument("--principal_component_on_x_axis", type="integer", default=1, help="PCA component on x-axis")
-parser$add_argument("--principal_component_on_y_axis", type="integer", default=2, help="PCA component on y-axis")
-parser$add_argument("--legend_position_for_pca", type="character", default="top", help="Legend position for PCA plot")
-parser$add_argument("--label_offset_x_", type="double", default=2, help="Label offset x for PCA plot")
-parser$add_argument("--label_offset_y_", type="double", default=2, help="Label offset y for PCA plot")
-parser$add_argument("--label_font_size", type="double", default=3, help="Label font size for PCA plot")
-parser$add_argument("--point_size_for_pca", type="double", default=8, help="Point size for PCA plot")
-parser$add_argument("--color_histogram_by_group", type="logical", default=TRUE, help="Color histogram by group")
-parser$add_argument("--set_min_max_for_x_axis_for_histogram", type="logical", default=FALSE, help="Set min/max x-axis for histogram")
-parser$add_argument("--minimum_for_x_axis_for_histogram", type="double", default=-1, help="Histogram x-axis minimum")
-parser$add_argument("--maximum_for_x_axis_for_histogram", type="double", default=1, help="Histogram x-axis maximum")
-parser$add_argument("--legend_font_size_for_histogram", type="double", default=10, help="Legend font size for histogram")
-parser$add_argument("--legend_position_for_histogram", type="character", default="top", help="Legend position for histogram")
-parser$add_argument("--number_of_histogram_legend_columns", type="integer", default=6, help="Number of legend columns for histogram")
-parser$add_argument("--plot_corr_matrix_heatmap", type="logical", default=TRUE, help="Plot correlation heatmap")
-parser$add_argument("--colors_for_plots", type="character", default="", help="Comma-separated list of colors for plots")
-parser$add_argument("--interactive_plots", type="logical", default=FALSE, help="Create interactive plots with plotly")
+parser$add_argument("--count_type", type = "character", default = "filt")
+parser$add_argument("--norm_type", type = "character", default = "voom")
+parser$add_argument(
+  "--feature_id_colname",
+  type = "character",
+  default = NULL,
+  help = "Column name for feature IDs"
+)
+parser$add_argument(
+  "--samples_to_include",
+  type = "character",
+  default = "",
+  help = "Comma-separated list of samples to include"
+)
+parser$add_argument(
+  "--sample_id_colname",
+  type = "character",
+  default = NULL,
+  help = "Column name for sample IDs"
+)
+parser$add_argument(
+  "--group_colname",
+  type = "character",
+  default = "Group",
+  help = "Column name for sample groups"
+)
+parser$add_argument(
+  "--label_colname",
+  type = "character",
+  default = NULL,
+  help = "Column name for sample labels"
+)
+parser$add_argument(
+  "--input_in_log_counts",
+  type = "logical",
+  default = FALSE,
+  help = "Counts are already log2-transformed"
+)
+parser$add_argument(
+  "--voom_normalization_method",
+  type = "character",
+  default = "quantile",
+  help = "Normalization method for limma::voom"
+)
+parser$add_argument(
+  "--samples_to_rename",
+  type = "character",
+  default = "",
+  help = "Sample renaming pairs: old:new,old2:new2"
+)
+parser$add_argument(
+  "--add_label_to_pca",
+  type = "logical",
+  default = TRUE,
+  help = "Label points on the PCA plot"
+)
+parser$add_argument(
+  "--principal_component_on_x_axis",
+  type = "integer",
+  default = 1,
+  help = "PCA component on x-axis"
+)
+parser$add_argument(
+  "--principal_component_on_y_axis",
+  type = "integer",
+  default = 2,
+  help = "PCA component on y-axis"
+)
+parser$add_argument(
+  "--legend_position_for_pca",
+  type = "character",
+  default = "top",
+  help = "Legend position for PCA plot"
+)
+parser$add_argument(
+  "--label_offset_x_",
+  type = "double",
+  default = 2,
+  help = "Label offset x for PCA plot"
+)
+parser$add_argument(
+  "--label_offset_y_",
+  type = "double",
+  default = 2,
+  help = "Label offset y for PCA plot"
+)
+parser$add_argument(
+  "--label_font_size",
+  type = "double",
+  default = 3,
+  help = "Label font size for PCA plot"
+)
+parser$add_argument(
+  "--point_size_for_pca",
+  type = "double",
+  default = 8,
+  help = "Point size for PCA plot"
+)
+parser$add_argument(
+  "--color_histogram_by_group",
+  type = "logical",
+  default = TRUE,
+  help = "Color histogram by group"
+)
+parser$add_argument(
+  "--set_min_max_for_x_axis_for_histogram",
+  type = "logical",
+  default = FALSE,
+  help = "Set min/max x-axis for histogram"
+)
+parser$add_argument(
+  "--minimum_for_x_axis_for_histogram",
+  type = "double",
+  default = -1,
+  help = "Histogram x-axis minimum"
+)
+parser$add_argument(
+  "--maximum_for_x_axis_for_histogram",
+  type = "double",
+  default = 1,
+  help = "Histogram x-axis maximum"
+)
+parser$add_argument(
+  "--legend_font_size_for_histogram",
+  type = "double",
+  default = 10,
+  help = "Legend font size for histogram"
+)
+parser$add_argument(
+  "--legend_position_for_histogram",
+  type = "character",
+  default = "top",
+  help = "Legend position for histogram"
+)
+parser$add_argument(
+  "--number_of_histogram_legend_columns",
+  type = "integer",
+  default = 6,
+  help = "Number of legend columns for histogram"
+)
+parser$add_argument(
+  "--plot_corr_matrix_heatmap",
+  type = "logical",
+  default = TRUE,
+  help = "Plot correlation heatmap"
+)
+parser$add_argument(
+  "--colors_for_plots",
+  type = "character",
+  default = "",
+  help = "Comma-separated list of colors for plots"
+)
+parser$add_argument(
+  "--interactive_plots",
+  type = "logical",
+  default = FALSE,
+  help = "Create interactive plots with plotly"
+)
 
 args <- parser$parse_args()
 
 # load multiOmicDataSet from data directory
 moo <- load_moo_from_data_dir()
 
 # run MOSuite
-moo |> 
-    normalize_counts(
-        count_type = args$count_type,
-        norm_type = args$norm_type,
-        feature_id_colname = args$feature_id_colname,
-        samples_to_include = parse_optional_vector(args$samples_to_include),
-        sample_id_colname = args$sample_id_colname,
-        group_colname = args$group_colname,
-        label_colname = args$label_colname,
-        input_in_log_counts = args$input_in_log_counts,
-        voom_normalization_method = args$voom_normalization_method,
-        samples_to_rename = parse_samples_to_rename(args$samples_to_rename),
-        add_label_to_pca = args$add_label_to_pca,
-        principal_component_on_x_axis = args$principal_component_on_x_axis,
-        principal_component_on_y_axis = args$principal_component_on_y_axis,
-        legend_position_for_pca = args$legend_position_for_pca,
-        label_offset_x_ = args$label_offset_x_,
-        label_offset_y_ = args$label_offset_y_,
-        label_font_size = args$label_font_size,
-        point_size_for_pca = args$point_size_for_pca,
-        color_histogram_by_group = args$color_histogram_by_group,
-        set_min_max_for_x_axis_for_histogram = args$set_min_max_for_x_axis_for_histogram,
-        minimum_for_x_axis_for_histogram = args$minimum_for_x_axis_for_histogram,
-        maximum_for_x_axis_for_histogram = args$maximum_for_x_axis_for_histogram,
-        legend_font_size_for_histogram = args$legend_font_size_for_histogram,
-        legend_position_for_histogram = args$legend_position_for_histogram,
-        number_of_histogram_legend_columns = args$number_of_histogram_legend_columns,
-        plot_corr_matrix_heatmap = args$plot_corr_matrix_heatmap,
-        colors_for_plots = parse_optional_vector(args$colors_for_plots),
-        interactive_plots = args$interactive_plots
-        ) |> 
-    write_rds(file.path(getOption("moo_plots_dir"), "..", "moo", "moo.rds"))
+moo |>
+  normalize_counts(
+    count_type = args$count_type,
+    norm_type = args$norm_type,
+    feature_id_colname = args$feature_id_colname,
+    samples_to_include = parse_optional_vector(args$samples_to_include),
+    sample_id_colname = args$sample_id_colname,
+    group_colname = args$group_colname,
+    label_colname = args$label_colname,
+    input_in_log_counts = args$input_in_log_counts,
+    voom_normalization_method = args$voom_normalization_method,
+    samples_to_rename = parse_samples_to_rename(args$samples_to_rename),
+    add_label_to_pca = args$add_label_to_pca,
+    principal_component_on_x_axis = args$principal_component_on_x_axis,
+    principal_component_on_y_axis = args$principal_component_on_y_axis,
+    legend_position_for_pca = args$legend_position_for_pca,
+    label_offset_x_ = args$label_offset_x_,
+    label_offset_y_ = args$label_offset_y_,
+    label_font_size = args$label_font_size,
+    point_size_for_pca = args$point_size_for_pca,
+    color_histogram_by_group = args$color_histogram_by_group,
+    set_min_max_for_x_axis_for_histogram = args$set_min_max_for_x_axis_for_histogram,
+    minimum_for_x_axis_for_histogram = args$minimum_for_x_axis_for_histogram,
+    maximum_for_x_axis_for_histogram = args$maximum_for_x_axis_for_histogram,
+    legend_font_size_for_histogram = args$legend_font_size_for_histogram,
+    legend_position_for_histogram = args$legend_position_for_histogram,
+    number_of_histogram_legend_columns = args$number_of_histogram_legend_columns,
+    plot_corr_matrix_heatmap = args$plot_corr_matrix_heatmap,
+    colors_for_plots = parse_optional_vector(args$colors_for_plots),
+    interactive_plots = args$interactive_plots
+  ) |>
+  write_rds(file.path(getOption("moo_plots_dir"), "..", "moo", "moo-norm.rds"))

tests/test-setup.R

@@ -0,0 +1,45 @@
+#!/usr/bin/env Rscript
+
+# Simple test to verify the test setup and data exists
+cat("Testing basic test setup...\n")
+
+# Get the current working directory during test execution
+cwd <- getwd()
+cat("Current directory:", cwd, "\n")
+
+# Calculate repo root the same way the test does in tests/testthat/test-main.R
+# When running from tests/testthat, dirname(getwd()) goes to tests/
+repo_root_test_calculation <- normalizePath(file.path(dirname(cwd), ".."))
+cat(
+  "Calculated repo_root (test calculation):",
+  repo_root_test_calculation,
+  "\n"
+)
+
+# From script running in tests directory:
+# When this script is in tests/ directory, repo_root should be dirname(getwd())
+repo_root_script <- normalizePath(dirname(cwd))
+cat("Calculated repo_root (script location):", repo_root_script, "\n")
+
+# Check if test data exists using test calculation
+test_data_file <- file.path(repo_root_script, "data", "moo-batch.rds")
+cat("\nLooking for test data at:", test_data_file, "\n")
+cat("Test data exists:", file.exists(test_data_file), "\n")
+
+# Check code files
+code_main <- file.path(repo_root_script, "..", "code", "main.R")
+code_run <- file.path(repo_root_script, "..", "code", "run")
+cat("code/main.R exists:", file.exists(code_main), "\n")
+cat("code/run exists:", file.exists(code_run), "\n")
+
+# Try to load the MOO object
+if (file.exists(test_data_file)) {
+  cat("\nTrying to load MOO object...\n")
+  library(readr)
+  moo <- readr::read_rds(test_data_file)
+  cat("MOO object loaded successfully!\n")
+  cat("MOO class:", class(moo), "\n")
+  if (hasSlot(moo, "counts")) {
+    cat("MOO columns in counts:", names(moo@counts), "\n")
+  }
+}

tests/testthat.R

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