tests/testthat/test-env.R

In FASTGenomics/fastgenomicsR: Facilitates the use of the FASTGenomics backend.

context("test-env")

mapping = "{
    \"some_input\": \"$SOME_ENV_VARIABLE\",
    \"cells\": \"cell_metadata.csv\",
    \"genes\": \"gene_metadata.csv\",
    \"some_optional_input\": \"optional_existing\"
}
"

setup({
    Sys.setenv(FG_DATA_ROOT="../data/$WORKING_ENV")
    Sys.setenv(INPUT_FILE_MAPPING=mapping)
    Sys.setenv(SOME_ENV_VARIABLE="expression_matrix.csv")
    Sys.setenv(WORKING_ENV="working_env")})

teardown({
    Sys.unsetenv("FG_DATA_ROOT")
    Sys.unsetenv("INPUT_FILE_MAPPING")
    Sys.unsetenv("SOME_ENV_VARIABLE")
    Sys.unsetenv("WORKING_ENV")})

APP <- file.path("../apps/working")

test_that("Runtime environmental variables work", {
    expect_error(fastgenomicsR::Process(app_dir=APP), NA)
})