tests/testthat/test-fetch_samples.R

In genieBPC: Project GENIE BioPharma Collaborative Data Processing Pipeline

test_that("missing input parameters", {
  # cohort name not specified
  expect_error(genieBPC:::fetch_samples())

  # record_id object not specified
  expect_error(genieBPC:::fetch_samples(cohort = "NSCLC"))

  # record_id object specified, but doesn't have variable record_id
  expect_error(genieBPC:::fetch_samples(
    cohort = "NSCLC",
    df_record_ids = tibble(
      cohort = "NSCLC",
      record_id = "123"
    )
  ))
})

test_that("function returns correct number of samples", {
  skip_if_not(genieBPC:::.is_connected_to_genie())

  nsclc_data <- pull_data_synapse("NSCLC", version = "v1.1-consortium")
  crc_data <- pull_data_synapse(c("CRC"), version = "v1.1-consortium")

  # NSCLC #
  ### all samples ###
  cohort_temp <- create_analytic_cohort(
    data_synapse = nsclc_data$NSCLC_v1.1,
    return_summary = FALSE
  )

  test1 <- genieBPC:::fetch_samples(
    cohort = "NSCLC",
    data_synapse = nsclc_data$NSCLC_v1.1,
    df_record_ids = cohort_temp$cohort_ca_dx
  )

  expect_true(tibble::is_tibble(test1))
  expect_equal(ncol(test1), 20)
  expect_equal(nrow(test1), 1992)
  expect_equal(length(unique(test1$record_id)), 1849)


  ### Stage IV ###
  cohort_temp <- create_analytic_cohort(
    data_synapse = nsclc_data$NSCLC_v1.1,
    stage_dx = c("Stage IV"),
    return_summary = FALSE
  )

  test2 <- genieBPC:::fetch_samples(
    cohort = "NSCLC",
    data_synapse = nsclc_data$NSCLC_v1.1,
    df_record_ids = cohort_temp$cohort_ca_dx
  )

  expect_true(tibble::is_tibble(test2))
  expect_equal(ncol(test2), 20)
  expect_equal(nrow(test2), 873)
  expect_equal(length(unique(test2$record_id)), 793)

  ### DFCI only ###
  cohort_temp <- create_analytic_cohort(
    data_synapse = nsclc_data$NSCLC_v1.1,
    return_summary = FALSE,
    institution = "DFCI"
  )

  test3 <- genieBPC:::fetch_samples(
    cohort = "NSCLC", data_synapse = nsclc_data$NSCLC_v1.1,
    df_record_ids = cohort_temp$cohort_ca_dx
  )
  expect_true(tibble::is_tibble(test3))
  expect_equal(ncol(test3), 20)
  expect_equal(nrow(test3), 736)
  expect_equal(length(unique(test3$record_id)), 699)
  expect_equal(unique(test3$institution), "DFCI")


  ##################################################################


  # CRC #

  ### all samples ###
  cohort_temp <- create_analytic_cohort(
    data_synapse = crc_data$CRC_v1.1,
    return_summary = FALSE
  )

  test1 <- genieBPC:::fetch_samples(
    cohort = "CRC", data_synapse = crc_data$CRC_v1.1,
    df_record_ids = cohort_temp$cohort_ca_dx
  )
  expect_true(tibble::is_tibble(test1))
  expect_equal(ncol(test1), 26)
  expect_equal(nrow(test1), 1566)
  expect_equal(length(unique(test1$record_id)), 1500)


  ### Stage IV ###
  cohort_temp <- create_analytic_cohort(
    stage_dx = c("Stage IV"),
    data_synapse = crc_data$CRC_v1.1,
    return_summary = FALSE
  )

  test2 <- genieBPC:::fetch_samples(
    cohort = "CRC", data_synapse = crc_data$CRC_v1.1,
    df_record_ids = cohort_temp$cohort_ca_dx
  )
  expect_true(tibble::is_tibble(test2))
  expect_equal(ncol(test2), 26)
  expect_equal(nrow(test2), 743)
  expect_equal(length(unique(test2$record_id)), 703)

  ### DFCI only ###
  cohort_temp <- create_analytic_cohort(
    data_synapse = crc_data$CRC_v1.1,
    return_summary = FALSE,
    institution = "DFCI"
  )

  test3 <- genieBPC:::fetch_samples(
    cohort = "CRC", data_synapse = crc_data$CRC_v1.1,
    df_record_ids = cohort_temp$cohort_ca_dx
  )

  expect_true(tibble::is_tibble(test3))
  expect_equal(ncol(test3), 26)
  expect_equal(nrow(test3), 577)
  expect_equal(length(unique(test3$record_id)), 570)
  expect_equal(unique(test3$institution), "DFCI")

  expect_error(test4 <- genieBPC:::fetch_samples(
    cohort = "CRC", data_synapse = crc_data$CRC_v1.1,
    df_record_ids = cohort_temp$cohort_ca_dx %>%
      rename(some_name = record_id)
  ))
})