tests/testthat/test_get_transcriptome_id_from_genome_id.R

In avidaR: A Computational Biologist’s Toolkit To Get Data From 'avidaDB'

test_that("get_transcriptome_id_from_genome_id", {
  
  skip_if_offline(host = "graphdb.fortunalab.org")
  
  suppressMessages({
    triplestore <- triplestore_access$new()
    
    response <- triplestore$set_access_options(
      url = "https://graphdb.fortunalab.org",
      user = "public_avida",
      password = "public_avida",
      repository = "avidaDB_test"
    )
    
    found1 <- get_transcriptome_id_from_genome_id(
      genome_id = 1,
      triplestore = triplestore
    )
  
    found2 <- get_transcriptome_id_from_genome_id(
      genome_id = c(1, 2),
      seed_id = c(2,1),
      transcriptome_seq = TRUE,
      transcriptome_pos = FALSE,
      triplestore = triplestore
    )
  
    found3 <- get_transcriptome_id_from_genome_id(
      genome_id = c(1, 2),
      seed_id = c(2,1),
      transcriptome_seq = FALSE,
      transcriptome_pos = TRUE,
      triplestore = triplestore
    )
  
    found4 <- get_transcriptome_id_from_genome_id(
      genome_id = 2,
      genome_seq = TRUE,
      transcriptome_seq = TRUE,
      transcriptome_pos = TRUE,
      triplestore = triplestore
    )
    
    skip_if(is.null(response) || is.null(found1) || is.null(found2) || is.null(found3) || is.null(found4))
  
    expect_match(class(found1), "data.frame")
    expect_true(nrow(found1) > 0)
    expect_equal(colnames(found1), c("genome_id", "transcriptome_id"))
    expect_equal(found1$transcriptome_id[1], "transcriptome_32406326")
  
    expect_match(class(found2), "data.frame")
    expect_true(nrow(found2) > 0)
    expect_equal(colnames(found2), c("seed_id", "genome_id", "transcriptome_id", "transcriptome_seq"))
    expect_equal(found2$seed_id[1], "seed_2")
  
    expect_match(class(found3), "data.frame")
    expect_true(nrow(found3) > 0)
    expect_equal(colnames(found3), c("seed_id", "genome_id", "transcriptome_id", "transcriptome_pos"))
    expect_equal(grepl("|", found3$transcriptome_pos[1]), TRUE)
  
    expect_match(class(found4), "data.frame")
    expect_true(nrow(found4) > 0)
    expect_equal(colnames(found4), c("genome_id", "genome_seq", "transcriptome_id", "transcriptome_seq", "transcriptome_pos"))
    expect_equal(found4$transcriptome_id[1], "transcriptome_13267653")    
  })


})