tests/testthat/testtaigr2.R

In broadinstitute/taigr: Load taiga data with cache functionality

library(testthat)
library(taigr)

mat.data.id <- "b9a6c877-37cb-4ebb-8c05-3385ff9a5ec7"
mat.data.name <- "depcon-binary-context-matrix"
df.data.id <- "0b8e280b-472c-42d4-b047-42cba9ed8e4c"
df.data.name <- "lineage-colors"
data.version <- 1

options(default.taiga.api.version=2)
options(default.taiga.url="https://cds.team/taiga")

test_that("loading by id works", {
    expect_is(load.from.taiga(mat.data.id),
              "matrix")

    expect_is(load.from.taiga(df.data.id),
              "data.frame")
})

test_that("loading a specific file works", {
    expect_is(load.from.taiga(mat.data.id, data.file="data"),
              "matrix")
})

test_that("loading by name works", {
    expect_is(load.from.taiga(data.name=df.data.name, data.version=1),
              "data.frame")

    expect_is(load.from.taiga(data.name=mat.data.name, data.version=1),
              "matrix")
})

test_that("loading missing results in null", {
    suppressWarnings( {
    expect_null(load.from.taiga(data.id="invalid"))

    expect_null(load.from.taiga(data.name="invalid"))

    expect_null(load.from.taiga(data.name=df.data.name, data.version=100))

    #currently stops if data.file doesn't exist.  I could argue we actually want all of these to result
    #in an error instead of NULL.  May need to revist
    #expect_null(load.from.taiga(mat.data.id, data.file="invalid"))
    } )
})

test_that("Different files from same data version get cached differently", {
    tiny.matrix <- load.from.taiga(data.name='taigr-data-40f2', data.version=1, data.file='tiny_matrix')
    expect_equal(nrow(tiny.matrix), 2)
    expect_equal(ncol(tiny.matrix), 3)

    tiny.table <- load.from.taiga(data.name='taigr-data-40f2', data.version=1, data.file='tiny_table')
    expect_equal(nrow(tiny.table), 3)
    expect_equal(ncol(tiny.table), 4)

    # now try again, using the cached values
    tiny.matrix <- load.from.taiga(data.name='taigr-data-40f2', data.version=1, data.file='tiny_matrix')
    expect_equal(nrow(tiny.matrix), 2)
    expect_equal(ncol(tiny.matrix), 3)

    tiny.table <- load.from.taiga(data.name='taigr-data-40f2', data.version=1, data.file='tiny_table')
    expect_equal(nrow(tiny.table), 3)
    expect_equal(ncol(tiny.table), 4)
})

test_that("alt data.id formats work", {
    tiny.matrix <- load.from.taiga('taigr-data-40f2.1', data.file='tiny_matrix')
    expect_equal(nrow(tiny.matrix), 2)
    expect_equal(ncol(tiny.matrix), 3)

    tiny.matrix <- load.from.taiga('taigr-data-40f2.1/tiny_matrix')
    expect_equal(nrow(tiny.matrix), 2)
    expect_equal(ncol(tiny.matrix), 3)
})

test_that("Transpose is honored", {
    tiny.matrix <- load.from.taiga(data.name='taigr-data-40f2', data.version=1, data.file='tiny_matrix')
    expect_equal(nrow(tiny.matrix), 2)
    expect_equal(ncol(tiny.matrix), 3)

    tiny.matrix <- load.from.taiga(data.name='taigr-data-40f2', data.version=1, data.file='tiny_matrix', transpose = T)
    expect_equal(nrow(tiny.matrix), 3)
    expect_equal(ncol(tiny.matrix), 2)
})

test_that("Loading raw works", {
    fn <- download.raw.from.taiga(data.name='tiny-raw-d7e2', data.version=1)
    expect_equal(readLines(fn), "sample")
})

#tiny.matrix <- load.from.taiga(data.id="f20ef5fb44794e52867e2e9ff6165822", data.file='tiny_matrix')
#expect_equal(nrow(tiny.matrix), 2)
#expect_equal(ncol(tiny.matrix), 3)