tests/testthat/test-dbcreators.R

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

#sql_fill_version_table

# 
# temp <- tempfile()
# 
# con <- pool::dbPool(drv = RSQLite::SQLite(),
#                     dbname = ":memory:")
# 
# sql_fill_version_table(con)
# test_that("create database 'version' table", {
#   expect_true("version" %in% DBI::dbListTables(con))
#   
#   expect_equal(dim((DBI::dbGetQuery(con, "SELECT * FROM version"))),
#                c(1,2))
#   
#   expect_equal(colnames(DBI::dbGetQuery(con, "SELECT * FROM version")),
#                c("IDBacVersion", "rVersion"))
#   
#   expect_equal(DBI::dbGetQuery(con, "SELECT * FROM version")[[1]],
#                getNamespaceVersion("IDBacApp")[[1]])
# })
# 
# 
# # insertLocale ------------------------------------------------------------
# 
# insertLocale(con)
# 
# test_that("create database 'locale' table", {
#   expect_true("locale" %in% DBI::dbListTables(con))
#   
#   expect_equal(dim((DBI::dbGetQuery(con, "SELECT * FROM locale"))),
#                c(1,1))
#   expect_equal(class(DBI::dbGetQuery(con, "SELECT * FROM locale")[[1]]),
#                "character")
#   expect_equal(colnames(DBI::dbGetQuery(con, "SELECT * FROM locale")),
#                "locale")
#   expect_true(nchar(DBI::dbGetQuery(con, "SELECT * FROM locale")[[1]]) > 10)
# })
# 
# 
# 
# # createMetaSQL -----------------------------------------------------------
# 
# createMetaSQL(sampleID = c("samIam", "greenEggs"),
#                         userDBCon = con)
# 
# test_that("create database 'metadata' table", {
#   expect_true("metaData" %in% DBI::dbListTables(con))
#   
#   expect_equal( dim((DBI::dbGetQuery(con, "SELECT * FROM metadata"))),
#                 c(2, 20))
# })
# 
# test_that("create database 'metadata' table; check columns", {
#   expect_equal(colnames(DBI::dbGetQuery(con, "SELECT * FROM metaData")),
#                c("Strain_ID",
#                  "Genbank_Accession",
#                  "NCBI_TaxID",
#                  "Kingdom",
#                  "Phylum",
#                  "Class",
#                  "Order",
#                  "Family",
#                  "Genus",
#                  "Species",
#                  "MALDI_Matrix",
#                  "DSM_Agar_Media",
#                  "Cultivation_Temp_Celsius",
#                  "Cultivation_Time_Days",
#                  "Cultivation_Other",
#                  "User",
#                  "User_ORCID",
#                  "PI_FirstName_LastName",
#                  "PI_ORCID",
#                  "dna_16S")
#   )
# })
# 
# 
# 
# 
# test_that("create database 'metadata' table: sample name", {
#   
#   expect_equal(DBI::dbGetQuery(con, "SELECT * FROM metaData")[,1],
#                c("samIam","greenEggs"))
# })
# 
# 
# 
# 
# # createXMLSQL ------------------------------------------------------------
# 
# 
# mzML_con <- mzR::openMSfile(system.file(file.path("extdata",
#                                                   "mzml",
#                                                   "mzml.mzML"),
#                                         package = "IDBacApp"),
#                             backend = "pwiz")
# 
# result <- createXMLSQL(rawDataFilePath = system.file(file.path("extdata",
#                                                                          "mzml",
#                                                                          "mzml.mzML"),
#                                                                package = "IDBacApp"),
#                                  userDBCon = con,
#                                  mzML_con = mzML_con)
# 
# 
# test_that("create database 'XML' table", {
#   expect_true("XML" %in% DBI::dbListTables(con))
#   expect_known_hash(result, 
#                     "233c42a5d9")
# })
# 
# 
# 
# 
# # createSpectraSQL --------------------------------------------------------
# scanNumber <- nrow(mzR::header(mzML_con))
# 
# createSpectraSQL(mzML_con = mzML_con, 
#                  scanNumber = 1,
#                  userDBCon = con,
#                  sampleID = "hello",
#                  XMLinfo = result,
#                  smallRangeEnd = 6000,
#                  acquisitionInfo = NULL)