tests/testthat/test-databasetransfer.R

In chasemc/IDBacApp: MALDI-TOF MS Protien and Small Molecule Analysis

# context("test-databasetransfer")
# 
# a1 <- tempfile()
# b1 <- createPool(basename(a1),
#                            gsub("\\\\", "/", dirname(a1)))
# bb1 <- pool::poolCheckout(b1[[1]])
# bb1path <- gsub("\\\\", "/", bb1@dbname)
# 
# a2 <- tempfile()
# b2 <- createPool(basename(a2),
#                            gsub("\\\\", "/", dirname(a2)))
# bb2 <- pool::poolCheckout(b2[[1]])
# bb2path <- gsub("\\\\", "/", bb2@dbname)
# 
# 
# 
# test_that("SQL warning on attach", {
#   expect_warning(copyDB_dbAttach(bb1path, bb2))
# })
# 
# z2 <- DBI::dbGetQuery(bb2, "PRAGMA database_list;")
# 
# # -------------------------------------------------------------------------
# 
# old <- z2$file[[1]]
# new <- z2$file[[3]]
# 
# test_that("SQL db was attached", {
#   expect_identical(basename(old), paste0(basename(a2), ".sqlite"))
#   expect_identical(basename(new), paste0(basename(a1), ".sqlite"))
# })
# 
# 
# 
# 
# pool::poolReturn(bb1)
# pool::poolReturn(bb2)
# pool::poolClose(b1[[1]])
# pool::poolClose(b2[[1]])
# 
# 
# # Setup new db ------------------------------------------------------------
# 
# a1 <- tempfile()
# b1 <- createPool(basename(a1),
#                            gsub("\\\\", "/", dirname(a1)))
# bb1 <- pool::poolCheckout(b1[[1]])
# bb1path <- gsub("\\\\", "/", bb1@dbname)
# 
# a2 <- system.file(file.path("extdata", "sqlite","sample.sqlite"), package = 'IDBacApp')
# b2 <- createPool(basename(a2),
#                            gsub("\\\\", "/", dirname(a2)))
# bb2 <- pool::poolCheckout(b2[[1]])
# bb2path <- gsub("\\\\", "/", bb2@dbname)
# 
# 
# 
# test_that("Provided and test sqlite DBs have correct tables", {
#   expect_identical(DBI::dbListTables(bb2), c("IndividualSpectra", "XML", "metaData", "version"))
#   expect_identical(DBI::dbListTables(bb1), character(0))
# })
# 
# 
# # metaData setup -------------------------------------------------------
# 
# copyDB_setupMeta(newDBconn = bb1,
#                            existingDBconn = bb2,
#                            arch = sqlTableArchitecture(1)
#                            )
# a <- DBI::dbGetQuery(bb1,"SELECT * FROM metaData")
# 
# test_that("Correctly transferred 'metaData' table", {
#   expect_identical(DBI::dbListTables(bb2), c("IndividualSpectra", "XML", "metaData", "version"))
#   expect_identical(DBI::dbListTables(bb1), c("metaData"))
#   expect_identical(nrow(a), 0L)
#   expect_identical(ncol(a), 20L)
# })
# 
# # XML setup ------------------------------------------------------------
# 
# sql_CreatexmlTable(sqlConnection = bb1)
# 
# 
# a <- DBI::dbGetQuery(bb1,"SELECT * FROM XML")
# 
# test_that("Correctly setup 'XML' table", {
#   expect_identical(DBI::dbListTables(bb2), c("IndividualSpectra", "XML", "metaData", "version"))
#   expect_identical(DBI::dbListTables(bb1), c("XML", "metaData"))
#   expect_identical(nrow(a), 0L)
#   expect_identical(ncol(a), 8L)
# })
# 
# 
# 
# # masstable ---------------------------------------------------------------
# 
# sql_CreatemassTable(sqlConnection = db1)
# 
# a <- DBI::dbGetQuery(bb1,"SELECT * FROM massTable")
# 
# 
# 
# 
# 
# 
# 
# # IndividualSpectra -------------------------------------------------------
# 
# 
# copyDB_setupIndividualSpectra(newDBconn = bb1,
#                                         existingDBconn = bb2,
#                                         arch = sqlTableArchitecture(1)
# )
# a <- DBI::dbGetQuery(bb1,"SELECT * FROM XML")
# 
# test_that("Correctly setup 'IndividualSpectra' table", {
#   expect_identical(DBI::dbListTables(bb2), c("IndividualSpectra", "XML", "metaData", "version"))
#   expect_identical(DBI::dbListTables(bb1), c("metaData", "XML", "IndividualSpectra"))
#   expect_identical(nrow(a), 1L)
#   expect_identical(ncol(a), 8L)
#   expect_identical(sum(is.na(a)), 8L)
# 
# })
# 
#