#' processMZML
#'
#' @param mzFilePaths file paths of the mzml files
#' @param sampleIds sampleIds that are in the same order as the paths
#' @param sqlDirectory sqlDirectory
#' @param newExperimentName newExperimentName
#'
#' @return Nothing direct, creates a sqlite database
#' @export
#'
processMZML <- function(mzFilePaths,
sampleIds,
sqlDirectory,
newExperimentName){
# validate(need(length(mzFilePaths) == length(sampleIds),
# "Temp mzML files and sample ID lengths don't match."
# ))
#
lengthProgress <- length(mzFilePaths)
userDB <- tempRepo::createNewSQLITEdb(newExperimentName = newExperimentName,
sqlDirectory = sqlDirectory)[[1]]
userDB <- pool::poolCheckout(userDB)
progLength <- base::length(mzFilePaths)
withProgress(message = 'Processing in progress',
value = 0,
max = progLength, {
for (i in base::seq_along(mzFilePaths)) {
setProgress(value = i,
message = 'Processing in progress',
detail = glue::glue(" \n Sample: {sampleIds[[i]]},
{i} of {progLength}"),
session = getDefaultReactiveDomain())
tempRepo::spectraProcessingFunction(rawDataFilePath = mzFilePaths[[i]],
sampleID = sampleIds[[i]],
userDBCon = userDB) # pool connection
}
})
pool::poolReturn(userDB)
}
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