tests/testthat.R

In rformassspectrometry/MsqlBackend: SQL-based Mass Spectrometry Data Backend

library(testthat)
library(MsBackendSql)
library(Spectra)
library(RSQLite)
library(msdata)

setClass("DummySQL",
         contains = "SQLiteConnection")

setMethod("dbExecute", c("DummySQL", "character"),
          function(conn, statement, ...) {
              TRUE
          })

mm8_file <- system.file("microtofq", "MM8.mzML", package = "msdata")
mm8_sps <- Spectra(mm8_file)
mm8_db_long <- dbConnect(SQLite(), tempfile())
createMsBackendSqlDatabase(mm8_db_long, mm8_file, blob = FALSE,
                           peaksStorageMode = "long")
mm8_be_long <- backendInitialize(MsBackendSql(), mm8_db_long)

mm8_db_blob <- dbConnect(SQLite(), tempfile())
createMsBackendSqlDatabase(mm8_db_blob, mm8_file, blob = TRUE,
                           peaksStorageMode = "blob")
mm8_be_blob <- backendInitialize(MsBackendSql(), mm8_db_blob)

mm8_db_blob2 <- dbConnect(SQLite(), tempfile())
createMsBackendSqlDatabase(mm8_db_blob2, mm8_file, blob = TRUE,
                           peaksStorageMode = "blob2")
mm8_be_blob2 <- backendInitialize(MsBackendSql(), mm8_db_blob2)

mm14_file <- system.file("microtofq", "MM14.mzML", package = "msdata")
mm_db <- dbConnect(SQLite(), tempfile())
createMsBackendSqlDatabase(mm_db, c(mm8_file, mm14_file), blob = FALSE)
mm_be <- backendInitialize(MsBackendSql(), mm_db)

tmt_file <- proteomics(full.names = TRUE)[4L]
tmt_mzr <- backendInitialize(MsBackendMzR(), tmt_file)
tmt_db <- dbConnect(SQLite(), tempfile())
createMsBackendSqlDatabase(tmt_db, tmt_file, blob = FALSE)
tmt_be <- backendInitialize(MsBackendSql(), tmt_db)

test_check("MsBackendSql")

test_suite <- system.file("test_backends", "test_MsBackend",
                          package = "Spectra")

be <- mm8_be_blob
test_dir(test_suite, stop_on_failure = TRUE)

be <- tmt_be[sample(seq_along(tmt_be), 300)]
test_dir(test_suite, stop_on_failure = TRUE)

dbDisconnect(mm8_db_long)
dbDisconnect(mm8_db_blob)
dbDisconnect(mm8_db_blob2)
dbDisconnect(mm_db)
dbDisconnect(tmt_db)