R：如何使用testthat测试依赖外部程序的函数？

Question

I have a function bowtieIndex(bowtieBuildLocation, filename) that calls bowtie2-build. It's parameters are the bowtie2-build location on my system and the output filename.

How do I write a test for this function without hard-coding the bowtie2-build location?

Answer 1

If all you are doing inside the function is calling an external program, then you can't test if that works directly. Without the code itself, this is hard to answer specifically, but if, for example, bowtieIndex is calling system to run an external program, you can mock what system will do, pretending that it worked, or failed. Look at the documentation for testthat::with_mock .

Three examples follow. The first parameter is the new code that will be executed instead of the real system function. The parameters that the system function was called with are available as normal in a function definition, if you want to do very specific things. I find it easier to test repeatedly rather than write a complex replacement function. Everything inside the second parameter, a code block { }, is executed with a context that see only the replacement system function, including all nested function calls. After this code block, the with_mock function exits and the real base::system is back in scope automatically. There are some limits to what functions can be mocked, but a surprising number of base functions can be over-ridden.

# Pretend that the system call exited with a specific error
with_mock(
    `base::system`= function(...) {
        stop("It didn't work");
    }, {
    expect_error( bowtieIndex( bowtieBuildLocation, filename ),
                  "It didn't work"
    )
})

# Pretend that the system call exited with a specific return value
with_mock(
    `base::system`= function(...) {
        return(127);
    }, {
    expect_error( bowtieIndex( bowtieBuildLocation, filename ),
                  "Error from your function on bad return value." )
    expect_false( file.exists( "someNotGeneratedFile" ))
})

# Pretend that the system call worked in a specific way
with_mock(
    `base::system`= function(...) {
        file.create("someGeneratedFile")
        return(0);
    }, {
    # No error
    expect_error( got <- bowtieIndex(bowtieBuildLocation, filename), NA )

    # File was created
    expect_true( file.exists( "someGeneratedFile" ))
})

# got variable holding results is actually available here, outside
# with_mock, so don't need to test everything within the function.
test_equal( got, c( "I", "was", "returned" ))