tests/testthat/test-dbcreators.R

In chasemc/ghosts: Protein and small molecule analysis of bacteria by MALDI-TOF MS

context("test-dbcreators")

set.seed(42)
# Create version ----------------------------------------------------------


a <- basename(tempfile())
b <- tempdir()

pool <- ghosts::createPool(a, b)[[1]]

con <- pool::poolCheckout(pool)


test_that("no Version", {
  expect_false(DBI::dbExistsTable(con, "version"))
})

ghosts::sqlCreate_version(con)
a <-  DBI::dbGetQuery(con, "SELECT * FROM version")

test_that("Version database table creation", {
  expect_true(DBI::dbExistsTable(con, "version"))
  expect_identical(ncol(a), 2L)
  expect_identical(nrow(a), 1L)
})


# Create Meta -------------------------------------------------------------



test_that("no metaData", {
  expect_false(DBI::dbExistsTable(con, "metaData"))
})

ghosts::createMetaSQL(sampleID = c("hello", "hello", "hi"),
                        userDBCon = con)



a <-  DBI::dbGetQuery(con, "SELECT * FROM metaData")
b <- a[, -which(colnames(a) == "Strain_ID")]
b <- all(is.na(b))

test_that("metaData database table creation", {
  expect_true(DBI::dbExistsTable(con, "metaData"))
  expect_identical(a$Strain_ID, c("hello", "hi"))
  expect_true(b)
})



# Create XML --------------------------------------------------------------
# 
# test_that("no metaData", {
#   expect_false(DBI::dbExistsTable(con, "XML"))
# })
# 
# path <- system.file(file.path("extdata", "mzML","mzml.mzML"), package = 'ghosts')
# 
# mzcon <- mzR::openMSfile(path)
# 
# out <- ghosts::createXMLSQL(rawDataFilePath = path,
#                        userDBCon = con,
#                        mzML_con = mzcon)
# 
# ghosts::createXMLSQL(rawDataFilePath = path,
#                        userDBCon = con,
#                        mzML_con = mzcon)
# 
# a <-  DBI::dbGetQuery(con, "SELECT * FROM XML")
# b <- a$XML[[1]]
# b <- a$XML[[1]]
# 
# test_that("XML database table creation", {
#   expect_true(DBI::dbExistsTable(con, "XML"))
#   expect_identical(nrow(a), 1L)
#   expect_identical(ncol(a), 8L)
#   expect_identical(class(b), "raw")
#   expect_identical(out$mzMLHash, "3b3a0e4975b86523")
#   
# })
# 
# 
# 
# 
# 
# # Create Individual -------------------------------------------------------
# 
# 
# 
# 
pool::poolReturn(con)
pool::poolClose(pool)