tests/testthat/test-Accession_Search_Functions.R

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

context("Accession Search Functions")


#' Main objectives tested
#' 
#' Search all (.searchForAccessionAcrossDBsDF())
#' - wrong or incomplete accession identifiers
#' 
#' 
#' Search SRA / GEO
#' - wrong type of accessions
#' - wrong column names


test_that(".searchForAccessionAcrossDBsDF", {
  
  # Wrong / incomplete accession identifiers
  expect_error(.searchForAccessionAcrossDBsDF("", "*")) #Should throw error via digitSort
  expect_error(.searchForAccessionAcrossDBsDF("abc", "*")) #Should throw error via digitSort
  
  # SRA-like
  expect_error(.searchForAccessionAcrossDBsDF("SR", "*")) #Should throw error via digitSort
  expect_error(.searchForAccessionAcrossDBsDF("SRO", "*")) #Should throw error via digitSort
  expect_error(.searchForAccessionAcrossDBsDF("SR11", "*")) #Should throw error via digitSort
  expect_error(.searchForAccessionAcrossDBsDF("SR.", "*")) #Should throw error via digitSort
  expect_error(suppressWarnings(.searchForAccessionAcrossDBsDF("SRR11", "*"))) #Should throw error via digitSort
  expect_error(.searchForAccessionAcrossDBsDF("SRX11", "*")) #Should throw error via digitSort
  expect_error(.searchForAccessionAcrossDBsDF("SRS11", "*")) #Should throw error via digitSort
  expect_error(.searchForAccessionAcrossDBsDF("SRP11", "*")) #Should throw error via digitSort

  
  # GEO-like
  expect_error(.searchForAccessionAcrossDBsDF("GEO", "*")) #Should throw error via digitSort
  expect_error(.searchForAccessionAcrossDBsDF("GS", "*")) #Should throw error via digitSort
  expect_error(.searchForAccessionAcrossDBsDF("GSM", "*")) #Should throw error via digitSort
  expect_error(.searchForAccessionAcrossDBsDF("GSM11", "*")) #Should throw error via digitSort
  expect_error(.searchForAccessionAcrossDBsDF("GE", "*")) #Should throw error via digitSort
  expect_error(.searchForAccessionAcrossDBsDF("GSE", "*")) #Should throw error via digitSort
  expect_error(.searchForAccessionAcrossDBsDF("GSE11", "*")) #Should throw error via digitSort
  
  
})





# .searchSRAForAccession ####

test_that(".searchSRAForAccession", {
  
  #Check that non-existent accessions
  # DELETED: 1. throw a warning
  # 2. do not return matches
  # expect_warning(.searchSRAForAccession("SRR1", "*"))
  expect_equal(dim(suppressWarnings(.searchSRAForAccession("SRR1", "*")))[1], 0)
  
  #Check that other accessions are not accepted
  expect_error(.searchSRAForAccession("GSM1000", "*"))
  expect_error(.searchSRAForAccession("GSE1000", "*"))
  
  
  #Check that non-existent columns are not accepted and throw an error
  expect_error(.searchSRAForAccession("SRR988139", "nth"))
  expect_error(.searchSRAForAccession("SRR988139", "sth"))
  
  
  
})


# .searchGEOForGSE ####
test_that(".searchGEOForGSE", {
  
  # Check that non-existent accessions
  # DELETED: 1. throw a warning
  # 2. do not return matches
  # expect_warning(.searchSRAForAccession("SRR1", "*"))
  expect_equal(dim(suppressWarnings(.searchGEOForGSE("GSE1", "*", "*")))[1], 0)
  
  # Check that other accessions are not accepted
  expect_error(.searchGEOForGSE("GSM1000", "*", "*"))
  expect_error(.searchGEOForGSE("SRP1000", "*", "*"))
  expect_error(.searchGEOForGSE("SRR1000", "*", "*"))
  
  
  
  # Check that non-existent columns are not accepted and throw an error
  expect_error(.searchGEOForGSE("GSE1000", "nth"))
  expect_error(.searchGEOForGSE("GSE1000", "sth"))
  
  
})




# .searchGEOForGSM ####
test_that(".searchGEOForGSM", {
  
  # Check that non-existent accessions
  # DELETED: 1. throw a warning
  # 2. do not return matches
  # expect_warning(.searchSRAForAccession("SRR1", "*"))
  expect_equal(dim(suppressWarnings(.searchGEOForGSM("GSM1", "*", "*")))[1], 0)
  
  # Check that other accessions are not accepted
  expect_error(.searchGEOForGSM("GSE1000", "*", "*"))
  expect_error(.searchGEOForGSM("SRP1000", "*", "*"))
  expect_error(.searchGEOForGSM("SRR1000", "*", "*"))
  
  
  
  # Check that non-existent columns are not accepted and throw an error
  expect_error(.searchGEOForGSM("GSM1000", "nth"))
  expect_error(.searchGEOForGSM("GSM1000", "sth"))
  
  
})