Add end-to-end test with mocked executable (#26)

Author: esiegel

R/eula.R

@@ -18,12 +18,18 @@ eula <- function() {
     return(FALSE)
   }
 
-  dir.create(eula_data_dir(), showWarnings=FALSE, recursive = TRUE)
-  file.create(eula_lock_file())
+  eula_create()
 
   invisible(TRUE)
 }
 
+#' Create Eula lock file
+#' @noRd
+eula_create <- function() {
+  dir.create(eula_data_dir(), showWarnings=FALSE, recursive = TRUE)
+  file.create(eula_lock_file())
+}
+
 #' Reset Eula by removing lock file
 #' @noRd
 eula_reset <- function() {

tests/testthat/helper.R

@@ -1,7 +1,12 @@
+#' Create random barcode
+random_barcode <- function(size = 10) {
+  paste0(sample(c("A", "C", "T", "G"), size, replace=TRUE), collapse="")
+}
+
 #' Create a sparse count_mat
 #'
 #' @importFrom Matrix rsparsematrix
-create_count_mat <- function(rows, cols) {
+create_count_mat <- function(rows, cols, valid_barcodes = FALSE) {
   mat <- Matrix::rsparsematrix(rows, cols, 0.5, rand.x = function(n) as.integer(100*runif(n)))
 
   rownames <- as.character()
@@ -11,15 +16,46 @@ create_count_mat <- function(rows, cols) {
 
   colnames <- as.character()
   if (cols > 0) {
-    colnames <- paste0("col", 1:cols)
+    if (valid_barcodes) {
+      colnames <- lapply(rep(10, cols), random_barcode)
+    } else {
+      colnames <- paste0("col", 1:cols)
+    }
   }
 
   dimnames(mat) <- list(rownames, colnames)
   mat
 }
 
+#' Create a dimensional reduction (projection) object
+create_dim_reduction <- function(count_mat, key) {
+  barcode_count <- dim(count_mat)[2]
+
+  proj <- create_dense_mat(barcode_count, 2)
+
+  rownames(proj) <- colnames(count_mat)
+  colnames(proj) <- c(paste0(key, 1), paste0(key, 2))
+
+  Seurat::CreateDimReducObject(
+    embeddings = proj,
+    key = paste0(key, "_"),
+    assay = "rna",
+    global = TRUE
+  )
+}
+
 #' Create a dense matrix
 create_dense_mat <- function(rows, cols) {
   count <- rows * cols
   matrix(runif(count), nrow=rows)
 }
+
+get_executable_path <- function() {
+  wd <- getwd()
+  os <- get_system_os()
+  if (os == "windows") {
+    return(file.path(wd, "mock_louper.bat"))
+  } else {
+    return(file.path(wd, "mock_louper"))
+  }
+}

tests/testthat/mock_louper

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+echo "-----------RUNNING MOCK LOUPER EXECUTABLE--------------"
+echo Arguments passed to the script: "$@"
+echo "-------------------------------------------------------"

tests/testthat/mock_louper.bat

@@ -0,0 +1,5 @@
+@echo off
+
+echo "-----------RUNNING MOCK LOUPER.BAT EXECUTABLE--------------"
+echo Arguments passed to the script: %*
+echo "-----------------------------------------------------------"

tests/testthat/test-lib.R

@@ -0,0 +1,31 @@
+test_that("can run create_loupe_from_seurat", {
+  barcode_count <- 3
+
+  count_mat <- create_count_mat(100, barcode_count, valid_barcodes = TRUE)
+  proj <- create_dim_reduction(count_mat, "proj1")
+  cluster <- factor(seq(barcode_count))
+
+  obj <- Seurat::CreateSeuratObject(count_mat, assay="rna")
+  obj[["proj1"]] <- proj
+  obj[["cluster1"]] <- cluster
+
+  # create eula lock file to avoid interactive setup
+  eula_create()
+
+  x <- create_loupe_from_seurat(obj, executable_path = get_executable_path())
+  expect(x, "create_loupe_from_seurat returns TRUE")
+})
+
+test_that("can run create_loupe", {
+  barcode_count <- 5
+  count_mat <- create_count_mat(100, barcode_count, valid_barcodes = TRUE)
+  proj <- create_dense_mat(barcode_count, 2)
+  clusters <- list("f1" = factor(c("a", "c", "b", "a", "b"), levels=c("a", "b", "c"), ordered=TRUE))
+  projections <- list("p1" = proj)
+
+  # create eula lock file to avoid interactive setup
+  eula_create()
+
+  x <- create_loupe(count_mat, clusters = clusters, projections = projections, executable_path = get_executable_path())
+  expect(x, "create_loupe returns TRUE")
+})