R/getAcquisitionDatemzML.R

In peakPantheR: Peak Picking and Annotation of High Resolution Experiments

#' @title Parse acquisition date from a mzML file
#'
#' @description Extract acquisition date (`'startTimeStamp'``) from a mzML file.
#' In case of failure (or the file is not a \code{mzML}) returns NULL
#'
#' @param mzMLPath (str) path to mzML raw data file
#' @param verbose (bool) if TRUE message progress
#'
#' @return POSIXct or NA
getAcquisitionDatemzML <- function(mzMLPath, verbose = TRUE) {
    
    ## Check input
    mzMLPath <- normalizePath(mzMLPath, mustWork = FALSE)
    # not a mzML extension
    if (tolower(stringr::str_sub(basename(mzMLPath), start = -5)) != ".mzml") {
        if (verbose) {
            message("Check input, mzMLPath must be a .mzML")
        }
        return(NA)
    }
    
    stime <- Sys.time()
    
    ## Parse XML
    acqTime <- tryCatch({
        ## try
        xmlfile <- XML::xmlParse(mzMLPath)
        xmltop <- XML::xmlRoot(xmlfile)
        # check top level structure
        if (XML::xmlName(xmltop) != "indexedmzML") {
            if (verbose) {
                message("Check input, mzMLPath is not a valid mzML file")
            }
            return(NA)
        } else {
            acqTime <- strptime(XML::xmlGetAttr(xmltop[["mzML"]][["run"]],
                                                "startTimeStamp"),
                                format = "%Y-%m-%dT%H:%M:%S")
        }
    }, error = function(cond) {
        ## catch
        if (verbose) {
            message("Check input, failure while parsing mzMLPath")}
        return(NA)
    })
    
    ## Output
    etime <- Sys.time()
    if (verbose) {
        message("Acquisition date parsed in: ",
                round(as.double(difftime(etime, stime)), 2),
                " ", units(difftime(etime, stime)))
    }
    
    return(acqTime)
}