tests/testthat/test-convertAccession.R

In ss-lab-cancerunit/SpiderSeqR: A Tool for Integration of Big Bio Data

context("Accession Conversion")

#' Testing conversion between databases
#' Things to be verified
#' - (demo) commutative - searching in SRA first = searching in GEO first (and vice versa)
#' - (demo) associative - searching for accessions individually yields same results as searching for all at the same time
#' - (demo) count - count of accessions in the database is equal to count as a result of the conversion
#' NOTE: only done on demo version of the databases; previous version worked also on real ones, but was removed due to speed and portability issues
#' ===*=== further expand 






# Setup ####

n_tests <- 5




# Helper functions ####




#' Generate random accessions from SRA
#' 
#' @param x Character with accession type
#' @param n Number of accessions desired
#' @param max_runs Maximum number of runs per accession allowed (will keep iterating until accession within the maximum is found)
#' @return A character vector with the randomly generated accessions
#' 
randomSRA <- function(x, n = 1, max_runs = 100){
  z <- character(length = n)
  for (i in 1:n){
    y <- character()
    y <- DBI::dbGetQuery(sra_con, paste0("SELECT ", x, " FROM sra GROUP BY RANDOM() LIMIT ", 1))
    y <- y[,1]
    acc_number <- as.numeric(DBI::dbGetQuery(sra_con, paste0("SELECT count(*) FROM sra WHERE ", x, " = '", y, "'")))
    print(y)
    z[i] <- y
    
    while(acc_number > max_runs){
      y <- DBI::dbGetQuery(sra_con, paste0("SELECT ", x, " FROM sra GROUP BY RANDOM() LIMIT ", 1))
      y <- y[,1]
      acc_number <- as.numeric(DBI::dbGetQuery(sra_con, paste0("SELECT count(*) FROM sra WHERE ", x, " = '", y, "'")))
      print(y)
      z[i] <- y
    }
  }
  
  return(z)
}


randomGEO <- function(x = c("gsm", "gse"), n = 1, max_gsms = 100){
  x <- match.arg(x)
  
  if (x == "gsm"){
    z <- DBI::dbGetQuery(geo_con, paste0("SELECT gsm FROM gsm GROUP BY RANDOM() LIMIT ", n))
    z <- z[,1]
  }
  
  if (x == "gse"){
    z <- character(length = n)
    for (i in 1:n){
      y <- DBI::dbGetQuery(geo_con, paste0("SELECT gse FROM gse GROUP BY RANDOM() LIMIT 1"))
      y <- y[,1]
      
      gsm_count <- DBI::dbGetQuery(geo_con, paste0("SELECT count(*) FROM gsm WHERE series_id LIKE '%",  y, "' OR series_id LIKE '%", y, ",%'" ))
      gsm_count <- as.numeric(gsm_count)
      
      while (gsm_count > 100){
        y <- DBI::dbGetQuery(geo_con, paste0("SELECT gse FROM gse GROUP BY RANDOM() LIMIT 1"))
        y <- y[,1]
        print(y)
        
        gsm_count <- DBI::dbGetQuery(geo_con, paste0("SELECT count(*) FROM gsm WHERE series_id LIKE '%",  y, "' OR series_id LIKE '%", y, ",%'" ))
        gsm_count <- as.numeric(gsm_count)
        
      }
      
      z[i] <- y
      
      
    }
    
  }
  
  
  return(z)
}





# Commutative ####


test_that("Commutative conversion SRA -> GEO", {
  
  i <- 0
  while (i < n_tests){
  # while (i < get("n_tests", env = parent.env(environment()))){
    x <- sample(unique(sra_demo$study_accession), 1)
    
    sra_input <- convertAccession(x)
    
    if (sum(grepl("GSM\\d\\d\\d+", sra_input$gsm))>0){
      i <- i + 1
      geo_input <- convertAccession(sra_input$gsm)
      expect_identical(sra_input, geo_input)
    }
  }

})

test_that("Commutative conversion GEO -> SRA", {
  i <- 0
  while (i < n_tests){
  # while (i < get("n_tests", env = parent.env(environment()))){ # Seems unnecessary
    x <- sample(unique(unlist(strsplit(gsm_demo$series_id, split = ","))), 1)
    
    geo_input <- convertAccession(x)
    
    if (sum(grepl("SRR\\d\\d\\d+", geo_input$run_accession))>0){
      i <- i + 1
      sra_input <- convertAccession(geo_input$run_accession)
      expect_identical(sra_input, geo_input)
    }
  }
})




# Associative ####

# SRA first

test_that("Associative SRA -> GEO", {
  
  # for (i in 1:get("n_tests", env = parent.env(environment()))
  for (i in 1:n_tests){
    x <- sample(unique(sra_demo$study_accession), 3)
    
    x1 <- convertAccession(x[1])
    x2 <- convertAccession(x[2])
    x3 <- convertAccession(x[3])
    
    x_123 <- rbind(x1, x2, x3)
    
    x_123 <- .unifyDFFormat(x_123)
    
    x_all <- convertAccession(x)
    expect_identical(x_123, x_all)
  }
})




# GEO first

test_that("Associative GEO -> SRA", {
  for (i in 1:n_tests){
    x <- sample(unique(gse_demo$gse), 3)
    
    x1 <- convertAccession(x[1])
    x2 <- convertAccession(x[2])
    x3 <- convertAccession(x[3])
    
    x_123 <- rbind(x1, x2, x3)
    
    x_123 <- .unifyDFFormat(x_123)
    
    x_all <- convertAccession(x)
    
    expect_identical(x_123, x_all)
  }
})





# Count check ####

# SRA (study_accession ONLY)


test_that("Equal count SRA", {
  
  for (i in 1:n_tests){
    x <- sample(sra_demo$study_accession, 1)
    
    x_count <- as.numeric(DBI::dbGetQuery(sra_con, paste0("SELECT count(DISTINCT run_accession) FROM sra WHERE study_accession = '", x, "'")))
    
    x_conv <- convertAccession(x)
    
    
    expect_equal(x_count, length(unique(x_conv$run_accession)))
    
    
  }
  
  
})





# GEO (series_id ONLY)


test_that("Equal count GEO", {
  
  for (i in 1:n_tests){
    x <- sample(gse_demo$gse, 1)
    
    x_count <- as.numeric(DBI::dbGetQuery(geo_con, paste0("SELECT count(DISTINCT gsm) FROM gsm WHERE series_id LIKE '%", x, ",%' OR series_id LIKE '%", x, "'")))
    
    x_conv <- convertAccession(x)
    
    expect_equal(x_count, length(unique(x_conv$gsm)))
    
  }
  
  
})