tests/testthat/test_variants.R

In progenetix/pgxRpi: R wrapper for Progenetix

context("Retrieve variants")
require(httr)
require(dplyr)
url_1 <- "http://progenetix.org/beacon/biosamples/pgxbs-kftvh94d/g_variants"
url_2 <- "https://progenetix.org/services/pgxsegvariants/?biosampleIds=pgxbs-kftvlaih,pgxbs-kftvjgcc"
url_3 <- "https://progenetix.org/services/variantsbedfile/?output=igv&biosampleIds=pgxbs-kftvlaih,pgxbs-kftvjgcc"
url_4 <- "https://progenetix.org/services/samplematrix/?biosampleIds=pgxbs-kftvlaih,pgxbs-kftvjgcc"
url_5 <- "https://progenetix.org/services/samplematrix/?individualIds=pgxind-kftx3565,pgxind-kftx5g4v"
url_6 <- "https://progenetix.org/services/samplematrix/?filters=pgx:icdom-88503"
url_7 <- "https://progenetix.org/services/cnvstats/?biosampleIds=pgxbs-kftvh94d,pgxbs-kftvh94g,pgxbs-kftvh972"
url_8 <- "https://progenetix.org/services/cnvstats/?individualIds=pgxind-kftx3565,pgxind-kftx5g4v"
url_9 <- "https://progenetix.org/services/cnvstats/?filters=pgx:icdom-88503"
url_10 <- "https://cancercelllines.org/beacon/biosamples/cellzbs-kftvksak/g_variants"

test_that("retrieve variants with JSON",{
        cat(paste("\n trying:",url_1,"\n"))
        result <-  content(GET(url_1))
        expect_equal(result$responseSummary$exists,TRUE)
        table <- lapply(result$response$resultSets[[1]]$results,unlist)
        table <- as.data.frame(bind_rows(table))
        expect_gt(nrow(table),0)
})


test_that("retrieve variants with pgxseg",{
    cat(paste("\n trying:",url_2,"\n"))
    r <- GET(url_2)
    expect_equal(http_type(r), "text/plain")
    expect_no_error(result <- read.table(url_2, stringsAsFactors = FALSE, sep = "\t",fill=TRUE,header=T))
    expect_gt(nrow(result),0)
    expect_gt(ncol(result),5)
})

test_that("retrieve variants with igv-bed",{
    cat(paste("\n trying:",url_3,"\n"))
    r <- GET(url_3)
    expect_equal(http_type(r), "application/vnd.realvnc.bed")
    expect_no_error(result <- read.table(url_3, stringsAsFactors = FALSE, sep = "\t",fill=TRUE,header=T))
    expect_gt(nrow(result),0)
    expect_gt(ncol(result),5)
})

test_that("retrieve pgxmatrix variant with biosample id",{
    cat(paste("\n trying:",url_4,"\n"))
    r <- GET(url_4)
    expect_equal(http_type(r), "text/plain")
    expect_no_error(result <- read.table(url_4, stringsAsFactors = FALSE, sep = "\t",fill=TRUE,header=T))
    expect_gt(nrow(result),0)
    expect_gt(ncol(result),6212)
})

test_that("retrieve pgxmatrix variant with individual id",{
    cat(paste("\n trying:",url_5,"\n"))
    r <- GET(url_5)
    expect_equal(http_type(r), "text/plain")
    expect_no_error(result <- read.table(url_5, stringsAsFactors = FALSE, sep = "\t",fill=TRUE,header=T))
    expect_gt(nrow(result),0)
    expect_gt(ncol(result),6212)
})

test_that("retrieve pgxmatrix variant with filters",{
    cat(paste("\n trying:",url_6,"\n"))
    r <- GET(url_6)
    expect_equal(http_type(r), "text/plain")
    expect_no_error(result <- read.table(url_6, stringsAsFactors = FALSE, sep = "\t",fill=TRUE,header=T))
    expect_gt(nrow(result),0)
    expect_gt(ncol(result),6212)
})

test_that("retrieve fraction variant with biosample id",{
    cat(paste("\n trying:",url_7,"\n")) 
    result <-  content(GET(url_7))
    expect_equal(result$responseSummary$exists,TRUE)
    table <- lapply(result$response$resultSets[[1]]$results,unlist)
    table <- as.data.frame(bind_rows(table))
    expect_gt(nrow(table),0)
})

test_that("retrieve fraction variant with individual id",{
    cat(paste("\n trying:",url_8,"\n"))
    result <-  content(GET(url_8))
    expect_equal(result$responseSummary$exists,TRUE)
    table <- lapply(result$response$resultSets[[1]]$results,unlist)
    table <- as.data.frame(bind_rows(table))
    expect_gt(nrow(table),0)
})

test_that("retrieve fraction variant with filters",{
    cat(paste("\n trying:",url_9,"\n"))
    result <-  content(GET(url_9))
    expect_equal(result$responseSummary$exists,TRUE)
    table <- lapply(result$response$resultSets[[1]]$results,unlist)
    table <- as.data.frame(bind_rows(table))
    expect_gt(nrow(table),0)
})

test_that("retrieve variants with JSON in cellz",{
        cat(paste("\n trying:",url_10,"\n"))
        result <-  content(GET(url_10))
        expect_equal(result$responseSummary$exists,TRUE)
        table <- lapply(result$response$resultSets[[1]]$results,unlist)
        table <- as.data.frame(bind_rows(table))
        expect_gt(nrow(table),0)
})