R/attach_metadata.R
In ethanbass/chromConverter: Chromatographic File Converter
Defines functions
attach_metadata
#' Attaches metadata to chromatogram
#'
#' @name attach_metadata
#' @param x chromatogram
#' @param meta List object containing metadata.
#' @param format_in Chromatogram format
#' @param format_out R format. Either \code{matrix} or \code{data.frame}.
#' @param data_format Whether data is in wide or long format.
#' @param parser What parser was used to decode the data.
#' @param source_file The path to the source file.
#' @param scale Whether the data has been scaled.
#' @return A chromatogram with attached metadata.
#' @author Ethan Bass
#' @noRd
attach_metadata <- function(x, meta, format_in, format_out, data_format,
parser = NULL, source_file,
source_file_format = format_in,
scale = NULL){
if (grepl("chemstation", format_in)){
format_in <- "chemstation"
}
switch(format_in,
"raw" = {
structure(x, metadata = meta, data_format = data_format, parser = parser,
source_file = source_file,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE))
}, "asm" = {
structure(x,
sample_name = meta$`sample document`$written_name,
sample_id = meta$`sample document`$sample_identifier,
file_version = meta$file_version,
file_type = NA,
instrument = meta$`asset management identifier`,
detector_id = meta$detector_model_number,
detector_range = get_asm_wavelength(meta),
detector_y_unit = meta$detector_unit,
detector_reference = get_asm_wavelength(meta,
lab = "reference_wavelength_setting_value"),
software = NA,
software_version = NA,
software_revision = NA,
method = NA,
batch = NA,
operator = meta$operator,
run_datetime = as.POSIXct(strptime(meta$`injection document`$injection_time,
format = "%Y-%m-%dT%H:%M:%OS", tz = "UTC")),
sample_injection_volume = paste(meta$`injection document`$autosampler_injection_volume_setting_chromatography_value,
meta$`injection document`$autosampler_injection_volume_setting_chromatography_unit),
sample_amount = NA,
# time_range = meta$time_range,
# time_interval = NA,
time_unit = meta$time_unit,
intensity_multiplier = NA,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo = "sha1",
file = TRUE),
data_format = data_format,
parser = parser,
format_out = format_out)
}, "rainbow" = {
meta$date <- convert_timestamp(meta$date, datetime_formats =
c("%d %b %y %I:%M %p %z", "%d-%b-%Y %H:%M:%S",
"%d-%b-%y, %H:%M:%S", "%d %b %y %I:%M %p"))
structure(x,
sample_name = ifelse(is.null(meta$notebook),
fs::path_ext_remove(basename(source_file)),
meta$notebook),
sample_id = NA,
vial = meta$vialpos,
file_version = NA,
file_type = NA,
instrument = NA,
detector = meta$detector,
detector_range = NA,
detector_y_unit = meta$unit,
polarity = meta$polarity,
software = NA,
software_version = NA,
software_revision = NA,
method = meta$method,
batch = NA,
operator = NA,
run_datetime = meta$date,
sample_injection_volume = NA,
sample_amount = NA,
time_range = NA,
time_interval = NA,
time_unit = NA,
intensity_multiplier = NA,
scaled = NA,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = ifelse(fs::is_file(source_file),
digest::digest(source_file, algo = "sha1",
file = TRUE),
NA),
data_format = data_format,
parser = parser,
format_out = format_out)
}, "varian_sms" = {
meta$max_ionization_time <- sapply(meta$segment_metadata, function(x){
x$max_ionization_time
})
structure(x,
sample_name = ifelse(is.null(meta$sample_name),
fs::path_ext_remove(basename(source_file)),
meta$sample_name),
sample_id = NA,
sample_id = NA,
instrument = NA,
detector = "MS",
detector_id = NA,
software_name = get_metadata_field(meta, "software"),
software_version = get_metadata_field(meta, "version"),
method = NA,
batch = NA,
operator = NA,
run_datetime = c(meta$t1, meta$t2),
sample_injection_volume = NA,
sample_amount = NA,
time_start = sapply(meta$segment_metadata, function(x){
x$start_time}),
end_time = sapply(meta$segment_metadata, function(x){
x$end_time}),
no_scans = meta$n_scan,
ms_params = meta[c("ion_time", "emission_current", "max_ric_scan",
"max_ric_val", "max_ionization_time",
"temp_trap", "temp_manifold", "temp_transferline",
"axial_modulation")],
time_interval = NA,
time_interval_unit = NA,
time_unit = "Minutes",
time_multiplier = 1/60000,
wavelength = NA,
detector_y_unit = NA,
intensity_multiplier = 1,
mz_multiplier = 1/20,
scaled = FALSE,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo = "sha1", file = TRUE),
data_format = data_format,
parser = "chromconverter",
format_out = format_out)
}, "waters_arw" = {
structure(x, instrument = NA,
detector = get_metadata_field(meta, "Channel Type"),
software = get_metadata_field(meta, "Source S/W Info"),
method = get_metadata_field(meta, "Instrument Method Name"),
batch = get_metadata_field(meta, "Sample Set Name"),
operator = NA,
run_datetime = NA,
sample_name = ifelse(is.null(meta$SampleName),
fs::path_ext_remove(basename(source_file)),
meta$SampleName),
sample_id = NA,
sample_injection_volume = NA,
sample_amount = NA,
time_range = c(get_metadata_field(meta, "Data Start"),
get_metadata_field(meta, "Data End")),
time_interval = NA,
time_unit = NA,
detector_range = ifelse("Channel Description" %in% names(meta),
get_metadata_field(meta, "Channel Description"),
get_metadata_field(meta, "Channel")
),
detector_y_unit = get_metadata_field(meta, "Det. Units"),
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
data_format = data_format,
parser = "chromconverter",
format_out = format_out)
}, "waters_raw" = {
structure(x, instrument = get_metadata_field(meta, "Instrument"),
detector = NA,
software = NA,
method = NA,
batch = NA,
operator = get_metadata_field(meta, "User_Name"),
run_datetime = as.POSIXct(paste(meta$Acquired_Date, meta$Acquired_Time,
collapse = " "),
format = "%d-%b-%Y %I:%M:%S",
tz = "UTC"),
sample_name = ifelse(is.null(meta$`Acquired Name`),
fs::path_ext_remove(basename(source_file)),
meta$`Acquired Name`),
sample_id = NA,
sample_injection_volume = NA,
sample_amount = NA,
time_range = NA,
time_interval = NA,
time_unit = NA,
detector_range = NA,
detector_y_unit = get_metadata_field(meta, "Detector_Unit"),
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = NA,
data_format = data_format,
parser = "chromconverter",
format_out = format_out)
}, "shimadzu_dad" = {
structure(x,
instrument = get_metadata_field(meta, "Instrument Name"),
detector = "DAD",
detector_id = get_metadata_field(meta, "Detector Name"),
software_name = get_metadata_field(meta, "Application Name"),
software_version = get_metadata_field(meta, "Version"),
method = get_metadata_field(meta, "Method File"),
batch = get_metadata_field(meta, "Batch File"),
operator = get_metadata_field(meta, "Operator Name"),
run_datetime = as.POSIXct(meta$Acquired,
format = "%m/%d/%Y %I:%M:%S %p", tz = "UTC"),
sample_name = ifelse(is.null(meta[["Sample Name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["Sample Name"]]),
sample_id = get_metadata_field(meta, "Sample ID"),
sample_injection_volume = get_metadata_field(meta, "Injection Volume"),
sample_amount = get_metadata_field(meta, "Injection Volume"),
time_range = c(meta$`Start Time(min)`, meta$`End Time(min)`),
time_interval = meta$`Interval(msec)`,
time_interval_unit = get_time_unit(
grep("Interval", names(meta), value = TRUE)[1],
format_in = "shimadzu"),
time_unit = get_time_unit(
grep("Start Time", names(meta), value = TRUE)[1],
format_in = "shimadzu"),
detector_range = c(meta$`Start Wavelength(nm)`,
meta$`End Wavelength(nm)`),
detector_y_unit = NA,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
data_format = data_format,
parser = "chromconverter",
format_out = format_out)
}, "shimadzu_chrom" = {
structure(x,
instrument = get_metadata_field(meta, "Instrument Name"),
detector_id = get_metadata_field(meta, "Detector Name"),
software_name = get_metadata_field(meta, "Application Name"),
software_version = get_metadata_field(meta, "Version"),
method = get_metadata_field(meta, "Method File"),
batch = get_metadata_field(meta, "Batch File"),
operator = get_metadata_field(meta, "Operator Name"),
run_datetime = as.POSIXct(meta$Acquired,
format = "%m/%d/%Y %I:%M:%S %p", tz = "UTC"),
sample_name = ifelse(is.null(meta[["Sample Name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["Sample Name"]]),
sample_id = get_metadata_field(meta, "Sample ID"),
sample_injection_volume = get_metadata_field(meta, "Injection Volume"),
sample_amount = get_metadata_field(meta, "Injection Volume"),
time_range = c(meta$`Start Time(min)`, meta$`End Time(min)`),
time_interval = meta$`Interval(msec)`,
time_interval_unit = get_time_unit(
grep("Interval", names(meta), value = TRUE)[1],
format_in = "shimadzu"),
time_unit = get_time_unit(
grep("Start Time", names(meta), value=TRUE)[1],
format_in = "shimadzu"),
wavelength = get_metadata_field(meta, "Wavelength(nm)"),
bandwidth = get_metadata_field(meta, "Bandwidth(nm)"),
detector_y_unit = get_metadata_field(meta, "Intensity Units"),
intensity_multiplier = as.numeric(get_metadata_field(meta, "Intensity Multiplier")),
scaled = scale,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
data_format = data_format,
parser = "chromconverter",
format_out = format_out)
}, "shimadzu_lcd" = {
structure(x,
instrument = get_metadata_field(meta, "DSN"),
detector = get_metadata_field(meta, "DETN"),
detector_id = get_metadata_field(meta, "DSID"),
# software_name = get_metadata_field(meta, "Application Name"),
software_version = get_metadata_field(meta, "DataFileProperty.szVersion"),
method = get_metadata_field(meta, "SampleInfoFile.methodfile"),
batch = get_metadata_field(meta, "SampleInfoFile.batchfile"),
operator = get_metadata_field(meta, "SampleInfo.operator_name"),
run_datetime = as.POSIXct(meta$time_acq, tz = "UTC"),
sample_name = ifelse(is.null(meta[["SampleInfo.smpl_name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["SampleInfo.smpl_name"]]),
sample_id = get_metadata_field(meta, "SampleInfo.smpl_id"),
vial = get_metadata_field(meta, 'SampleInfo.smpl_vial'),
sample_type = get_metadata_field(meta, "SampleInfo.smpl_type"),
sample_dilution = get_metadata_field(meta, "SampleInfo.dil_factor"),
sample_injection_volume = get_metadata_field(meta, "SampleInfo.inj_vol"),
sample_amount = get_metadata_field(meta, "SampleInfo.smpl_amount"),
time_range = c(get_metadata_field(meta, "DLT"),
get_metadata_field(meta, "AT")),
time_interval = get_metadata_field(meta, "Rate"),
time_interval_unit = get_metadata_field(meta, "time.unit"),
time_unit = get_metadata_field(meta, "time.unit"),
time_multiplier = get_metadata_field(meta, "time.vf"),
wavelength = get_sz_wv(meta),
detector_y_unit = get_metadata_field(meta, "detector.unit"),
intensity_multiplier = get_metadata_field(meta, "detector.vf"),
scaled = scale,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
data_format = data_format,
parser = "chromconverter",
format_out = format_out)
}, "chromeleon" = {
if (is.null(meta$`Inject Time`)){
datetime.idx <- unlist(sapply(c("Date$", "Time$"), function(str){
grep(str, names(meta))
})
)
datetime <- unlist(meta[datetime.idx])
if (length(datetime > 1)){
datetime <- paste(datetime, collapse = " ")
}
datetime <- as.POSIXct(datetime, format = c("%m/%d/%Y %H:%M:%S",
"%d.%m.%Y %H:%M:%S",
"%m/%d/%Y %H:%M:%S %p %z"),
tz = "UTC")
datetime <- datetime[!is.na(datetime)]
} else {
datetime <- sub("(\\+\\d{2}):(\\d{2})$", "\\1\\2", meta$`Inject Time`)
datetime <- as.POSIXct(strptime(datetime, format = "%d/%m/%Y %H:%M:%S %z"),
tz="UTC")
}
time_interval_unit <- tryCatch({
get_time_unit(grep("Average Step", names(meta), value = TRUE)[1],
format_in = "chromeleon")}, error = function(err) NA)
time_unit <- tryCatch({
get_time_unit(grep("Time Min.", names(meta), value = TRUE)[1],
format_in = "chromeleon")}, error = function(err) NA)
if (is.null(meta$Name) && !is.null(meta$Injection)){
meta$Name <- meta$Injection
}
if (is.null(meta$`Signal Unit`)){
unit <- grep("Signal Min", names(meta), value = TRUE)
unit <- sub(".*(?:\\((.*)\\)).*|.*", "\\1", unit)
meta$`Signal Unit` <- unit
}
structure(x, instrument = NA,
detector = meta$Detector,
software = meta$`Generating Data System`,
method = meta$`Instrument Method`,
batch = meta$Sequence,
operator = meta$`Operator`,
run_datetime = datetime,
sample_name = ifelse(is.null(meta$Name),
fs::path_ext_remove(basename(source_file)),
meta$Name),
sample_id = NA,
vial = meta$Position,
sample_injection_volume = meta[[which(grepl("Volume",names(meta)))]],
sample_amount = NA,
sample_dilution = meta$`Dilution Factor`,
sample_type = get_metadata_field(meta, "Type"),
time_range = c(get_metadata_field(meta, "Time Min. (min)"),
get_metadata_field(meta, "Time Max. (min)")),
time_interval = tryCatch({
meta[[grep("Average Step", names(meta))]]
}, error = function(err) NA),
time_interval_unit = time_interval_unit,
time_unit = time_unit,
detector_range = ifelse(meta$`Spectral Field` == "3DFIELD",
c(get_metadata_field(meta, "Scan Min. (nm)"),
get_metadata_field(meta, "Scan Max. (nm)")),
NA),
detector_y_unit = meta$`Signal Unit`,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo = "sha1",
file = TRUE),
format_out = format_out,
data_format = data_format,
parser = "chromconverter"
)
}, "chemstation" = {
meta$date <- convert_timestamp(meta$date, datetime_formats =
c("%d-%b-%y, %H:%M:%S", "%m/%d/%Y %I:%M:%S %p",
"%d/%m/%Y %I:%M:%S %p"))
structure(x, sample_name = iconv(meta$sample_name, sub = ""),
sample_id = meta$vial,
file_version = meta$version,
file_type = meta$file_type,
instrument = meta$AcqInstName,
detector = meta$detector,
detector_id = meta$detector_model,
detector_range = meta$signal,
detector_y_unit = meta$units,
detector_x_unit = meta$detector_x_unit,
software = meta$software,
software_version = meta$software_version,
software_revision = meta$software_revision,
# software = meta$Version,
method = meta$method,
batch = meta$SeqPathAndFile,
operator = meta$operator,
run_datetime = meta$date,
sample_injection_volume = meta$InjVolume,
sample_amount = meta$InjVolume,
time_range = meta$time_range,
time_interval = NA,
time_unit = "Minutes",
intensity_multiplier = meta$intensity_multiplier,
scaled = scale,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo = "sha1",
file = TRUE),
data_format = data_format,
parser = parser,
format_out = format_out)
}, "chemstation_peaklist" = {
structure(x, instrument = meta$`Acq. Instrument`,
detector = NA,
software = NA,
method = meta$Method,
batch = NA,
operator = meta$`Acq. Operator`,
run_datetime = NA,
sample_name = ifelse(is.null(meta[["Sample Name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["Sample Name"]]),
sample_id = NA,
sample_injection_volume = meta$`Inj Volume`,
sample_amount = meta$`Inj Volume`,
time_range = NA,
time_interval = NA,
time_unit = NA,
detector_range = NA,
detector_y_unit = NA,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
data_format = data_format,
parser = parser,
format_out = format_out)
}, "masshunter_dad" = {
structure(x, instrument = meta$Instrument,
detector = "DAD",
software = NA,
method = meta$Method,
batch = NA,
operator = meta$OperatorName,
run_datetime = meta$AcqTime,
sample_name = ifelse(is.null(meta[["Sample Name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["Sample Name"]]),
sample_id = meta$`Sample ID`,
sample_injection_volume = meta$`Inj Vol`,
sample_amount = meta$`Inj Vol`,
time_range = NA,
time_interval = NA,
time_unit = NA,
detector_range = NA,
detector_y_unit = NA,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
data_format = data_format,
parser = parser,
format_out = format_out)
}, "andi_chrom" = {
structure(x, instrument = NA,
detector = get_metadata_field(meta, "detector"),
detector_id = get_metadata_field(meta, "detector_name"),
software = NA,
method = NA,
batch = get_metadata_field(meta, "experiment_title"),
operator = get_metadata_field(meta, "operator_name"),
run_datetime = as.POSIXct(
get_metadata_field(meta, "injection_date_time_stamp"),
format = "%Y%m%d%H%M%S%z", tz = "UTC"),
sample_name = ifelse(is.null(meta[["sample_name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["sample_name"]]),
sample_id = get_metadata_field(meta, "sample_id"),
sample_type = get_metadata_field(meta, "sample_type"),
sample_injection_volume = get_metadata_field(meta, "sample_injection_volume"),
sample_amount = get_metadata_field(meta, "sample_amount"),
time_start = NA,
time_end = NA,
time_interval = NA,
time_unit = get_metadata_field(meta, "retention_unit"),
detector_range = NA,
# detector_end = NA,
detector_y_unit = get_metadata_field(meta, "detector_y_unit"),
detector_x_unit = NA,
source_file = ifelse(missing(source_file), NA, source_file),
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
format_out = ifelse(missing(format_out), NA, format_out),
data_format = ifelse(missing(data_format), NA, data_format),
parser = "chromconverter")
}, "andi_ms" = {
structure(x, instrument = NA,
detector = get_metadata_field(meta, "detector"),
detector_id = get_metadata_field(meta, "detector_name"),
software = NA,
method = NA,
batch = get_metadata_field(meta, "experiment_title"),
operator = get_metadata_field(meta, "operator_name"),
run_datetime = as.POSIXct(
get_metadata_field(meta, "experiment_date_time_stamp"),
format = "%Y%m%d%H%M%S%z", tz = "UTC"),
sample_name = ifelse(is.null(meta[["sample_name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["sample_name"]]),
sample_id = get_metadata_field(meta, "sample_id"),
sample_type = get_metadata_field(meta, "sample_type"),
sample_injection_volume = get_metadata_field(meta, "sample_injection_volume"),
sample_amount = get_metadata_field(meta, "sample_amount"),
time_start = NA,
time_end = NA,
time_interval = NA,
time_unit = get_metadata_field(meta, "raw_data_time_units"),
detector_range = NA,
detector_y_unit = get_metadata_field(meta, "detector_y_unit"),
detector_x_unit = get_metadata_field(meta, "raw_data_mass_units"),
intensity_multiplier = get_metadata_field(meta, "raw_data_intensity_factor"),
intensity_offset = get_metadata_field(meta, "raw_data_intensity_offset"),
ms_params = list(n_scans = get_metadata_field(meta, "raw_data_nscans"),
ionization_mode = get_metadata_field(meta, "test_ionization_mode"),
polarity = get_metadata_field(meta, "test_ionization_polarity"),
detector_type = get_metadata_field(meta, "test_detector_type")),
source_file = ifelse(missing(source_file), NA, source_file),
source_file_format = get_metadata_field(meta, "source_file_format"),
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
format_out = ifelse(missing(format_out), NA, format_out),
data_format = ifelse(missing(data_format), NA, data_format),
parser = "chromconverter")
}, "mdf" = {
structure(x, instrument = meta[meta$Property == "Instrument", "Value"],
detector = "Variable Wavelength Detector",
software = NA,
method = NA,
batch = get_metadata_field(meta, "experiment_title"),
operator = meta[meta$Property == "Operator", "Value"],
run_datetime = as.POSIXct(
meta[meta$Property == "Time", "Value"],
format = "%d.%m.%Y %H:%M:%S", tz = "UTC"),
sample_name = ifelse(is.null(meta[["sample_name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["sample_name"]]),
sample_id = get_metadata_field(meta, "sample_id"),
sample_type = "unknown",
sample_injection_volume = 1,
sample_amount = 1,
time_start = meta[meta$Group == "Interval Time" &
meta$Property == "From", "Value"],
time_end = meta[meta$Group == "Interval Time" &
meta$Property == "To", "Value"],
time_interval = meta[meta$Group == "Interval Time" &
meta$Property == "Step", "Value"],
time_unit = meta[meta$Group == "Interval Time" &
meta$Property == "Units", "Value"],
detector_range = meta[meta$Property == "Wave", "Value"],
# detector_end = meta[meta$Property == "Wave", "Value"],
detector_y_unit = meta[meta$Group == "Array photometric" &
meta$Property == "Units", "Value"],
source_file = ifelse(missing(source_file), NA, source_file),
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
format_out = ifelse(missing(format_out), NA, format_out),
data_format = ifelse(missing(data_format), NA, data_format),
parser = "chromconverter")
}, "thermoraw" = {
structure(x, instrument = c(meta$`Instrument model`, meta$`Instrument name`,
meta$`Instrument serial number`),
detector = NA,
software = meta$`Software version`,
method = NA,
batch = NA,
operator = NA,
run_date = meta$`Creation date`,
sample_name = fs::path_ext_remove(basename(meta$`RAW file path`)),
sample_id = meta$`Sample id`,
vial = meta$`Sample vial`,
injection_volume = meta$`Sample injection volume`,
sample_dilution = meta$`Sample dilution factor`,
time_range = meta$`Time range`,
time_interval = meta$`Interval(msec)`,
source_file = ifelse(missing(source_file), NA, source_file),
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
format_out = ifelse(missing(format_out), NA, format_out),
data_format = "long",
parser = "ThermoRawFileParser"
)
}, "default" = {
structure(x, instrument = meta$Instrument,
detector = NA,
software = NA,
method = meta$Method,
batch = NA,
operator = meta$OperatorName,
run_datetime = meta$AcqTime,
sample_name = ifelse(is.null(meta[["Sample Name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["Sample Name"]]),
sample_id = meta$`Sample ID`,
sample_injection_volume = meta$`Inj Vol`,
sample_amount = meta$`Inj Vol`,
time_range = NA,
time_interval = NA,
time_unit = NA,
detector_range = NA,
detector_y_unit = NA,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
format_out = ifelse(missing(format_out), NA, format_out),
data_format = ifelse(missing(data_format), NA, data_format),
parser = ifelse(missing(parser), NA, parser)
)
}
)
}
#' @noRd
get_metadata_field <- function(x, field, num = FALSE, null_val = NA){
ifelse(!is.null(x[[field]]),
ifelse(num, as.numeric(x[[field]]), x[[field]]),
null_val)
}
#' @noRd
get_metadata_field2 <- function(x, field, class = c("char","float","int"),
null_val = NA){
class <- match.arg(class, c("char","float","int"))
conv <- switch(class, char = as.character, float = as.numeric,
int = as.integer)
ifelse(!is.null(attr(x,field)) && !is.na(attr(x,field)),
conv(attr(x, field)), null_val)
}
#' @noRd
get_time_unit <- function(string, format_in){
if (length(string) == 0 || is.na(string)){
NA
} else{
if (format_in %in% c("chromeleon", "shimadzu")){
pattern <- "\\((.*?)\\)"
unit <- gsub("\\(|\\)", "", regmatches(string, regexpr(pattern, string))[[1]])
switch(unit, "min" = "Minutes", "sec" = "Seconds")
} else NA
}
}
#' @name read_chemstation_metadata
#' @param file file
#' @param what Whether to return \code{metadata} or \code{peaktable}.
#' @importFrom readxl read_xls
#' @return A list containing extracted metadata.
#' @author Ethan Bass
#' @noRd
read_chemstation_metadata <- function(file, what = c("metadata", "peaktable")){
what <- match.arg(what, c("metadata", "peaktable"))
# find xls csv files
folder <- gsub(basename(file), "", file)
# check for .D folder
if (grepl("\\.D/$", folder, ignore.case = TRUE)){
# find xls/csv
reps <- list.files(folder, pattern = '.xls',
ignore.case = TRUE, full.names = TRUE)
if (length(reps) > 0){
if (what == "metadata"){
meta <- as.data.frame(readxl::read_xls(reps[1], sheet = 1, skip = 1))
meta2<-as.list(meta$Results)
names(meta2) <- meta$Title
meta2
} else if (what == "peaktable"){
pktab <- as.data.frame(readxl::read_xls(rep, sheet = "Peak"))
pktab <- pktab[, -c(1:2)]
pktab
}
}
}
}
#' @name read_masshunter_metadata
#' @param file file
#' @importFrom xml2 read_xml xml_find_all xml_text
#' @return A list containing extracted metadata.
#' @author Ethan Bass
#' @noRd
read_masshunter_metadata <- function(file){
# check for .D folder
folder <- gsub(basename(file), "", file)
if (grepl("\\.D/|\\.d/$", folder, ignore.case = TRUE)){
# find xml
rep <- list.files(folder, pattern = '.xml',
ignore.case = TRUE, full.names = TRUE)
if (length(rep) > 0){
path_devices <- rep[basename(rep) == "Devices.xml"]
path_sample <- rep[basename(rep) == "sample_info.xml"]
if (length(path_sample) == 1){
meta_sample <- xml2::read_xml(path_sample)
name <- xml2::xml_text(xml2::xml_find_all(meta_sample, xpath = "//Name"))
meta_sample <- as.list(xml2::xml_text(
xml2::xml_find_all(meta_sample, xpath = "//Value")
))
names(meta_sample) <- name
}
if (length(path_devices) == 1){
meta_devices <- xml2::read_xml(path_devices)
name <- xml_text(xml_find_all(meta_devices, xpath = "//Name"))
meta_devices <- as.character(xml_text(
xml_find_all(meta_devices, xpath = "//ModelNumber")
))
names(meta_devices) <- name
}
meta_sample$Instrument <- meta_devices
}
}
meta_sample
}
#' @name read_waters_metadata
#' @param file file
#' @return A list containing extracted metadata.
#' @author Ethan Bass
#' @noRd
read_waters_metadata <- function(file){
ll <- readLines(file, n = 2)
ll <- iconv(ll,from = "ISO-8859-1", to = "UTF-8")
meta <- gsub("\\\"", "", do.call(cbind, strsplit(ll, "\t")))
rownames(meta) <- meta[, 1]
meta <- as.list(meta[, -1])
}
#' Extract metadata
#'
#' Extract metadata as a data.frame from a list of chromatograms.
#'
#' @param chrom_list A list of chromatograms with attached metadata (as returned
#' by \code{read_chroms} with \code{read_metadata = TRUE}).
#' @param what A character vector specifying the metadata elements to extract.
#' @param format_out Format of object. Either \code{data.frame} or \code{tibble}.
#' @return A data.frame or tibble (according to the value of \code{format_out}),
#' with samples as rows and the specified metadata elements as columns.
#' @export
extract_metadata <- function(chrom_list,
what = c("instrument", "detector", "detector_id",
"software", "method", "batch", "operator",
"run_datetime",
"sample_name", "sample_id",
"injection_volume", "time_range",
"time_interval", "time_unit", "detector_range",
"detector_y_unit", "detector_x_unit",
"intensity_multiplier", "scaled", "source_file",
"source_file_format", "source_sha1",
"data_format", "parser", "format_out"),
format_out = c("data.frame", "tibble")
){
if (inherits(chrom_list, c("matrix", "data.table", "data.frame"))){
chrom_list <- list(chrom_list)
use_names <- FALSE
} else use_names <- TRUE
what <- match.arg(what, several.ok = TRUE)
format_out <- match.arg(format_out, c("data.frame", "tibble"))
metadata <- purrr::map_df(chrom_list, function(chrom){
unlist(sapply(what, function(w){
attr(chrom, which = w)
}, simplify = FALSE))
})
metadata$run_datetime <- as.POSIXct(as.numeric(metadata$run_datetime),tz = "UTC")
if (use_names && format_out == "tibble"){
metadata <- tibble::add_column(.data = metadata,
data.frame(name = names(chrom_list)),
.before=TRUE)
} else if (use_names && format_out == "data.frame"){
metadata <- data.frame(name = names(chrom_list), metadata,
row.names = names(chrom_list))
}
metadata
}
#' Transfer metadata
#'@noRd
transfer_metadata <- function (new_object, old_object,
exclude = c("names", "row.names",
"class", "dim", "dimnames")){
a <- attributes(old_object)
a[exclude] <- NULL
attributes(new_object) <- c(attributes(new_object), a)
new_object
}
#' Get 'Shimadzu' Wavelength
#' @noRd
get_sz_wv <- function(meta){
if ("WVB" %in% names(meta)){
c(get_metadata_field(meta, "WVB"),
get_metadata_field(meta, "WVE"))
} else{
get_metadata_field(meta, "ADN")
}
}
#' Extract ASM wavelength from metadata list
#' @author Ethan Bass
#' @noRd
get_asm_wavelength <- function(meta, lab = "absorbance_wavelength_setting.value"){
wv_idx <- grep(lab, names(meta$`device control aggregate document`))
unique(unlist(meta$`device control aggregate document`[wv_idx]))
}
#' Convert date-time string to POSIXct
#' @author Ethan Bass
#' @noRd
convert_timestamp <- function(string, datetime_formats){
tryCatch({
as.POSIXct(string, tz = "UTC", tryFormats = datetime_formats)
}, error = function(cond){
warning("Run date-time could not be converted to POSIXct format, returning string instead.")
string
})
}
ethanbass/chromConverter documentation built on Jan. 14, 2025, 2:11 a.m.
R Package Documentation
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Defines functions attach_metadata
#' Attaches metadata to chromatogram
#'
#' @name attach_metadata
#' @param x chromatogram
#' @param meta List object containing metadata.
#' @param format_in Chromatogram format
#' @param format_out R format. Either \code{matrix} or \code{data.frame}.
#' @param data_format Whether data is in wide or long format.
#' @param parser What parser was used to decode the data.
#' @param source_file The path to the source file.
#' @param scale Whether the data has been scaled.
#' @return A chromatogram with attached metadata.
#' @author Ethan Bass
#' @noRd
attach_metadata <- function(x, meta, format_in, format_out, data_format,
parser = NULL, source_file,
source_file_format = format_in,
scale = NULL){
if (grepl("chemstation", format_in)){
format_in <- "chemstation"
}
switch(format_in,
"raw" = {
structure(x, metadata = meta, data_format = data_format, parser = parser,
source_file = source_file,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE))
}, "asm" = {
structure(x,
sample_name = meta$`sample document`$written_name,
sample_id = meta$`sample document`$sample_identifier,
file_version = meta$file_version,
file_type = NA,
instrument = meta$`asset management identifier`,
detector_id = meta$detector_model_number,
detector_range = get_asm_wavelength(meta),
detector_y_unit = meta$detector_unit,
detector_reference = get_asm_wavelength(meta,
lab = "reference_wavelength_setting_value"),
software = NA,
software_version = NA,
software_revision = NA,
method = NA,
batch = NA,
operator = meta$operator,
run_datetime = as.POSIXct(strptime(meta$`injection document`$injection_time,
format = "%Y-%m-%dT%H:%M:%OS", tz = "UTC")),
sample_injection_volume = paste(meta$`injection document`$autosampler_injection_volume_setting_chromatography_value,
meta$`injection document`$autosampler_injection_volume_setting_chromatography_unit),
sample_amount = NA,
# time_range = meta$time_range,
# time_interval = NA,
time_unit = meta$time_unit,
intensity_multiplier = NA,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo = "sha1",
file = TRUE),
data_format = data_format,
parser = parser,
format_out = format_out)
}, "rainbow" = {
meta$date <- convert_timestamp(meta$date, datetime_formats =
c("%d %b %y %I:%M %p %z", "%d-%b-%Y %H:%M:%S",
"%d-%b-%y, %H:%M:%S", "%d %b %y %I:%M %p"))
structure(x,
sample_name = ifelse(is.null(meta$notebook),
fs::path_ext_remove(basename(source_file)),
meta$notebook),
sample_id = NA,
vial = meta$vialpos,
file_version = NA,
file_type = NA,
instrument = NA,
detector = meta$detector,
detector_range = NA,
detector_y_unit = meta$unit,
polarity = meta$polarity,
software = NA,
software_version = NA,
software_revision = NA,
method = meta$method,
batch = NA,
operator = NA,
run_datetime = meta$date,
sample_injection_volume = NA,
sample_amount = NA,
time_range = NA,
time_interval = NA,
time_unit = NA,
intensity_multiplier = NA,
scaled = NA,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = ifelse(fs::is_file(source_file),
digest::digest(source_file, algo = "sha1",
file = TRUE),
NA),
data_format = data_format,
parser = parser,
format_out = format_out)
}, "varian_sms" = {
meta$max_ionization_time <- sapply(meta$segment_metadata, function(x){
x$max_ionization_time
})
structure(x,
sample_name = ifelse(is.null(meta$sample_name),
fs::path_ext_remove(basename(source_file)),
meta$sample_name),
sample_id = NA,
sample_id = NA,
instrument = NA,
detector = "MS",
detector_id = NA,
software_name = get_metadata_field(meta, "software"),
software_version = get_metadata_field(meta, "version"),
method = NA,
batch = NA,
operator = NA,
run_datetime = c(meta$t1, meta$t2),
sample_injection_volume = NA,
sample_amount = NA,
time_start = sapply(meta$segment_metadata, function(x){
x$start_time}),
end_time = sapply(meta$segment_metadata, function(x){
x$end_time}),
no_scans = meta$n_scan,
ms_params = meta[c("ion_time", "emission_current", "max_ric_scan",
"max_ric_val", "max_ionization_time",
"temp_trap", "temp_manifold", "temp_transferline",
"axial_modulation")],
time_interval = NA,
time_interval_unit = NA,
time_unit = "Minutes",
time_multiplier = 1/60000,
wavelength = NA,
detector_y_unit = NA,
intensity_multiplier = 1,
mz_multiplier = 1/20,
scaled = FALSE,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo = "sha1", file = TRUE),
data_format = data_format,
parser = "chromconverter",
format_out = format_out)
}, "waters_arw" = {
structure(x, instrument = NA,
detector = get_metadata_field(meta, "Channel Type"),
software = get_metadata_field(meta, "Source S/W Info"),
method = get_metadata_field(meta, "Instrument Method Name"),
batch = get_metadata_field(meta, "Sample Set Name"),
operator = NA,
run_datetime = NA,
sample_name = ifelse(is.null(meta$SampleName),
fs::path_ext_remove(basename(source_file)),
meta$SampleName),
sample_id = NA,
sample_injection_volume = NA,
sample_amount = NA,
time_range = c(get_metadata_field(meta, "Data Start"),
get_metadata_field(meta, "Data End")),
time_interval = NA,
time_unit = NA,
detector_range = ifelse("Channel Description" %in% names(meta),
get_metadata_field(meta, "Channel Description"),
get_metadata_field(meta, "Channel")
),
detector_y_unit = get_metadata_field(meta, "Det. Units"),
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
data_format = data_format,
parser = "chromconverter",
format_out = format_out)
}, "waters_raw" = {
structure(x, instrument = get_metadata_field(meta, "Instrument"),
detector = NA,
software = NA,
method = NA,
batch = NA,
operator = get_metadata_field(meta, "User_Name"),
run_datetime = as.POSIXct(paste(meta$Acquired_Date, meta$Acquired_Time,
collapse = " "),
format = "%d-%b-%Y %I:%M:%S",
tz = "UTC"),
sample_name = ifelse(is.null(meta$`Acquired Name`),
fs::path_ext_remove(basename(source_file)),
meta$`Acquired Name`),
sample_id = NA,
sample_injection_volume = NA,
sample_amount = NA,
time_range = NA,
time_interval = NA,
time_unit = NA,
detector_range = NA,
detector_y_unit = get_metadata_field(meta, "Detector_Unit"),
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = NA,
data_format = data_format,
parser = "chromconverter",
format_out = format_out)
}, "shimadzu_dad" = {
structure(x,
instrument = get_metadata_field(meta, "Instrument Name"),
detector = "DAD",
detector_id = get_metadata_field(meta, "Detector Name"),
software_name = get_metadata_field(meta, "Application Name"),
software_version = get_metadata_field(meta, "Version"),
method = get_metadata_field(meta, "Method File"),
batch = get_metadata_field(meta, "Batch File"),
operator = get_metadata_field(meta, "Operator Name"),
run_datetime = as.POSIXct(meta$Acquired,
format = "%m/%d/%Y %I:%M:%S %p", tz = "UTC"),
sample_name = ifelse(is.null(meta[["Sample Name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["Sample Name"]]),
sample_id = get_metadata_field(meta, "Sample ID"),
sample_injection_volume = get_metadata_field(meta, "Injection Volume"),
sample_amount = get_metadata_field(meta, "Injection Volume"),
time_range = c(meta$`Start Time(min)`, meta$`End Time(min)`),
time_interval = meta$`Interval(msec)`,
time_interval_unit = get_time_unit(
grep("Interval", names(meta), value = TRUE)[1],
format_in = "shimadzu"),
time_unit = get_time_unit(
grep("Start Time", names(meta), value = TRUE)[1],
format_in = "shimadzu"),
detector_range = c(meta$`Start Wavelength(nm)`,
meta$`End Wavelength(nm)`),
detector_y_unit = NA,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
data_format = data_format,
parser = "chromconverter",
format_out = format_out)
}, "shimadzu_chrom" = {
structure(x,
instrument = get_metadata_field(meta, "Instrument Name"),
detector_id = get_metadata_field(meta, "Detector Name"),
software_name = get_metadata_field(meta, "Application Name"),
software_version = get_metadata_field(meta, "Version"),
method = get_metadata_field(meta, "Method File"),
batch = get_metadata_field(meta, "Batch File"),
operator = get_metadata_field(meta, "Operator Name"),
run_datetime = as.POSIXct(meta$Acquired,
format = "%m/%d/%Y %I:%M:%S %p", tz = "UTC"),
sample_name = ifelse(is.null(meta[["Sample Name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["Sample Name"]]),
sample_id = get_metadata_field(meta, "Sample ID"),
sample_injection_volume = get_metadata_field(meta, "Injection Volume"),
sample_amount = get_metadata_field(meta, "Injection Volume"),
time_range = c(meta$`Start Time(min)`, meta$`End Time(min)`),
time_interval = meta$`Interval(msec)`,
time_interval_unit = get_time_unit(
grep("Interval", names(meta), value = TRUE)[1],
format_in = "shimadzu"),
time_unit = get_time_unit(
grep("Start Time", names(meta), value=TRUE)[1],
format_in = "shimadzu"),
wavelength = get_metadata_field(meta, "Wavelength(nm)"),
bandwidth = get_metadata_field(meta, "Bandwidth(nm)"),
detector_y_unit = get_metadata_field(meta, "Intensity Units"),
intensity_multiplier = as.numeric(get_metadata_field(meta, "Intensity Multiplier")),
scaled = scale,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
data_format = data_format,
parser = "chromconverter",
format_out = format_out)
}, "shimadzu_lcd" = {
structure(x,
instrument = get_metadata_field(meta, "DSN"),
detector = get_metadata_field(meta, "DETN"),
detector_id = get_metadata_field(meta, "DSID"),
# software_name = get_metadata_field(meta, "Application Name"),
software_version = get_metadata_field(meta, "DataFileProperty.szVersion"),
method = get_metadata_field(meta, "SampleInfoFile.methodfile"),
batch = get_metadata_field(meta, "SampleInfoFile.batchfile"),
operator = get_metadata_field(meta, "SampleInfo.operator_name"),
run_datetime = as.POSIXct(meta$time_acq, tz = "UTC"),
sample_name = ifelse(is.null(meta[["SampleInfo.smpl_name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["SampleInfo.smpl_name"]]),
sample_id = get_metadata_field(meta, "SampleInfo.smpl_id"),
vial = get_metadata_field(meta, 'SampleInfo.smpl_vial'),
sample_type = get_metadata_field(meta, "SampleInfo.smpl_type"),
sample_dilution = get_metadata_field(meta, "SampleInfo.dil_factor"),
sample_injection_volume = get_metadata_field(meta, "SampleInfo.inj_vol"),
sample_amount = get_metadata_field(meta, "SampleInfo.smpl_amount"),
time_range = c(get_metadata_field(meta, "DLT"),
get_metadata_field(meta, "AT")),
time_interval = get_metadata_field(meta, "Rate"),
time_interval_unit = get_metadata_field(meta, "time.unit"),
time_unit = get_metadata_field(meta, "time.unit"),
time_multiplier = get_metadata_field(meta, "time.vf"),
wavelength = get_sz_wv(meta),
detector_y_unit = get_metadata_field(meta, "detector.unit"),
intensity_multiplier = get_metadata_field(meta, "detector.vf"),
scaled = scale,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
data_format = data_format,
parser = "chromconverter",
format_out = format_out)
}, "chromeleon" = {
if (is.null(meta$`Inject Time`)){
datetime.idx <- unlist(sapply(c("Date$", "Time$"), function(str){
grep(str, names(meta))
})
)
datetime <- unlist(meta[datetime.idx])
if (length(datetime > 1)){
datetime <- paste(datetime, collapse = " ")
}
datetime <- as.POSIXct(datetime, format = c("%m/%d/%Y %H:%M:%S",
"%d.%m.%Y %H:%M:%S",
"%m/%d/%Y %H:%M:%S %p %z"),
tz = "UTC")
datetime <- datetime[!is.na(datetime)]
} else {
datetime <- sub("(\\+\\d{2}):(\\d{2})$", "\\1\\2", meta$`Inject Time`)
datetime <- as.POSIXct(strptime(datetime, format = "%d/%m/%Y %H:%M:%S %z"),
tz="UTC")
}
time_interval_unit <- tryCatch({
get_time_unit(grep("Average Step", names(meta), value = TRUE)[1],
format_in = "chromeleon")}, error = function(err) NA)
time_unit <- tryCatch({
get_time_unit(grep("Time Min.", names(meta), value = TRUE)[1],
format_in = "chromeleon")}, error = function(err) NA)
if (is.null(meta$Name) && !is.null(meta$Injection)){
meta$Name <- meta$Injection
}
if (is.null(meta$`Signal Unit`)){
unit <- grep("Signal Min", names(meta), value = TRUE)
unit <- sub(".*(?:\\((.*)\\)).*|.*", "\\1", unit)
meta$`Signal Unit` <- unit
}
structure(x, instrument = NA,
detector = meta$Detector,
software = meta$`Generating Data System`,
method = meta$`Instrument Method`,
batch = meta$Sequence,
operator = meta$`Operator`,
run_datetime = datetime,
sample_name = ifelse(is.null(meta$Name),
fs::path_ext_remove(basename(source_file)),
meta$Name),
sample_id = NA,
vial = meta$Position,
sample_injection_volume = meta[[which(grepl("Volume",names(meta)))]],
sample_amount = NA,
sample_dilution = meta$`Dilution Factor`,
sample_type = get_metadata_field(meta, "Type"),
time_range = c(get_metadata_field(meta, "Time Min. (min)"),
get_metadata_field(meta, "Time Max. (min)")),
time_interval = tryCatch({
meta[[grep("Average Step", names(meta))]]
}, error = function(err) NA),
time_interval_unit = time_interval_unit,
time_unit = time_unit,
detector_range = ifelse(meta$`Spectral Field` == "3DFIELD",
c(get_metadata_field(meta, "Scan Min. (nm)"),
get_metadata_field(meta, "Scan Max. (nm)")),
NA),
detector_y_unit = meta$`Signal Unit`,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo = "sha1",
file = TRUE),
format_out = format_out,
data_format = data_format,
parser = "chromconverter"
)
}, "chemstation" = {
meta$date <- convert_timestamp(meta$date, datetime_formats =
c("%d-%b-%y, %H:%M:%S", "%m/%d/%Y %I:%M:%S %p",
"%d/%m/%Y %I:%M:%S %p"))
structure(x, sample_name = iconv(meta$sample_name, sub = ""),
sample_id = meta$vial,
file_version = meta$version,
file_type = meta$file_type,
instrument = meta$AcqInstName,
detector = meta$detector,
detector_id = meta$detector_model,
detector_range = meta$signal,
detector_y_unit = meta$units,
detector_x_unit = meta$detector_x_unit,
software = meta$software,
software_version = meta$software_version,
software_revision = meta$software_revision,
# software = meta$Version,
method = meta$method,
batch = meta$SeqPathAndFile,
operator = meta$operator,
run_datetime = meta$date,
sample_injection_volume = meta$InjVolume,
sample_amount = meta$InjVolume,
time_range = meta$time_range,
time_interval = NA,
time_unit = "Minutes",
intensity_multiplier = meta$intensity_multiplier,
scaled = scale,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo = "sha1",
file = TRUE),
data_format = data_format,
parser = parser,
format_out = format_out)
}, "chemstation_peaklist" = {
structure(x, instrument = meta$`Acq. Instrument`,
detector = NA,
software = NA,
method = meta$Method,
batch = NA,
operator = meta$`Acq. Operator`,
run_datetime = NA,
sample_name = ifelse(is.null(meta[["Sample Name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["Sample Name"]]),
sample_id = NA,
sample_injection_volume = meta$`Inj Volume`,
sample_amount = meta$`Inj Volume`,
time_range = NA,
time_interval = NA,
time_unit = NA,
detector_range = NA,
detector_y_unit = NA,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
data_format = data_format,
parser = parser,
format_out = format_out)
}, "masshunter_dad" = {
structure(x, instrument = meta$Instrument,
detector = "DAD",
software = NA,
method = meta$Method,
batch = NA,
operator = meta$OperatorName,
run_datetime = meta$AcqTime,
sample_name = ifelse(is.null(meta[["Sample Name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["Sample Name"]]),
sample_id = meta$`Sample ID`,
sample_injection_volume = meta$`Inj Vol`,
sample_amount = meta$`Inj Vol`,
time_range = NA,
time_interval = NA,
time_unit = NA,
detector_range = NA,
detector_y_unit = NA,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
data_format = data_format,
parser = parser,
format_out = format_out)
}, "andi_chrom" = {
structure(x, instrument = NA,
detector = get_metadata_field(meta, "detector"),
detector_id = get_metadata_field(meta, "detector_name"),
software = NA,
method = NA,
batch = get_metadata_field(meta, "experiment_title"),
operator = get_metadata_field(meta, "operator_name"),
run_datetime = as.POSIXct(
get_metadata_field(meta, "injection_date_time_stamp"),
format = "%Y%m%d%H%M%S%z", tz = "UTC"),
sample_name = ifelse(is.null(meta[["sample_name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["sample_name"]]),
sample_id = get_metadata_field(meta, "sample_id"),
sample_type = get_metadata_field(meta, "sample_type"),
sample_injection_volume = get_metadata_field(meta, "sample_injection_volume"),
sample_amount = get_metadata_field(meta, "sample_amount"),
time_start = NA,
time_end = NA,
time_interval = NA,
time_unit = get_metadata_field(meta, "retention_unit"),
detector_range = NA,
# detector_end = NA,
detector_y_unit = get_metadata_field(meta, "detector_y_unit"),
detector_x_unit = NA,
source_file = ifelse(missing(source_file), NA, source_file),
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
format_out = ifelse(missing(format_out), NA, format_out),
data_format = ifelse(missing(data_format), NA, data_format),
parser = "chromconverter")
}, "andi_ms" = {
structure(x, instrument = NA,
detector = get_metadata_field(meta, "detector"),
detector_id = get_metadata_field(meta, "detector_name"),
software = NA,
method = NA,
batch = get_metadata_field(meta, "experiment_title"),
operator = get_metadata_field(meta, "operator_name"),
run_datetime = as.POSIXct(
get_metadata_field(meta, "experiment_date_time_stamp"),
format = "%Y%m%d%H%M%S%z", tz = "UTC"),
sample_name = ifelse(is.null(meta[["sample_name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["sample_name"]]),
sample_id = get_metadata_field(meta, "sample_id"),
sample_type = get_metadata_field(meta, "sample_type"),
sample_injection_volume = get_metadata_field(meta, "sample_injection_volume"),
sample_amount = get_metadata_field(meta, "sample_amount"),
time_start = NA,
time_end = NA,
time_interval = NA,
time_unit = get_metadata_field(meta, "raw_data_time_units"),
detector_range = NA,
detector_y_unit = get_metadata_field(meta, "detector_y_unit"),
detector_x_unit = get_metadata_field(meta, "raw_data_mass_units"),
intensity_multiplier = get_metadata_field(meta, "raw_data_intensity_factor"),
intensity_offset = get_metadata_field(meta, "raw_data_intensity_offset"),
ms_params = list(n_scans = get_metadata_field(meta, "raw_data_nscans"),
ionization_mode = get_metadata_field(meta, "test_ionization_mode"),
polarity = get_metadata_field(meta, "test_ionization_polarity"),
detector_type = get_metadata_field(meta, "test_detector_type")),
source_file = ifelse(missing(source_file), NA, source_file),
source_file_format = get_metadata_field(meta, "source_file_format"),
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
format_out = ifelse(missing(format_out), NA, format_out),
data_format = ifelse(missing(data_format), NA, data_format),
parser = "chromconverter")
}, "mdf" = {
structure(x, instrument = meta[meta$Property == "Instrument", "Value"],
detector = "Variable Wavelength Detector",
software = NA,
method = NA,
batch = get_metadata_field(meta, "experiment_title"),
operator = meta[meta$Property == "Operator", "Value"],
run_datetime = as.POSIXct(
meta[meta$Property == "Time", "Value"],
format = "%d.%m.%Y %H:%M:%S", tz = "UTC"),
sample_name = ifelse(is.null(meta[["sample_name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["sample_name"]]),
sample_id = get_metadata_field(meta, "sample_id"),
sample_type = "unknown",
sample_injection_volume = 1,
sample_amount = 1,
time_start = meta[meta$Group == "Interval Time" &
meta$Property == "From", "Value"],
time_end = meta[meta$Group == "Interval Time" &
meta$Property == "To", "Value"],
time_interval = meta[meta$Group == "Interval Time" &
meta$Property == "Step", "Value"],
time_unit = meta[meta$Group == "Interval Time" &
meta$Property == "Units", "Value"],
detector_range = meta[meta$Property == "Wave", "Value"],
# detector_end = meta[meta$Property == "Wave", "Value"],
detector_y_unit = meta[meta$Group == "Array photometric" &
meta$Property == "Units", "Value"],
source_file = ifelse(missing(source_file), NA, source_file),
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
format_out = ifelse(missing(format_out), NA, format_out),
data_format = ifelse(missing(data_format), NA, data_format),
parser = "chromconverter")
}, "thermoraw" = {
structure(x, instrument = c(meta$`Instrument model`, meta$`Instrument name`,
meta$`Instrument serial number`),
detector = NA,
software = meta$`Software version`,
method = NA,
batch = NA,
operator = NA,
run_date = meta$`Creation date`,
sample_name = fs::path_ext_remove(basename(meta$`RAW file path`)),
sample_id = meta$`Sample id`,
vial = meta$`Sample vial`,
injection_volume = meta$`Sample injection volume`,
sample_dilution = meta$`Sample dilution factor`,
time_range = meta$`Time range`,
time_interval = meta$`Interval(msec)`,
source_file = ifelse(missing(source_file), NA, source_file),
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
format_out = ifelse(missing(format_out), NA, format_out),
data_format = "long",
parser = "ThermoRawFileParser"
)
}, "default" = {
structure(x, instrument = meta$Instrument,
detector = NA,
software = NA,
method = meta$Method,
batch = NA,
operator = meta$OperatorName,
run_datetime = meta$AcqTime,
sample_name = ifelse(is.null(meta[["Sample Name"]]),
fs::path_ext_remove(basename(source_file)),
meta[["Sample Name"]]),
sample_id = meta$`Sample ID`,
sample_injection_volume = meta$`Inj Vol`,
sample_amount = meta$`Inj Vol`,
time_range = NA,
time_interval = NA,
time_unit = NA,
detector_range = NA,
detector_y_unit = NA,
source_file = source_file,
source_file_format = source_file_format,
source_sha1 = digest::digest(source_file, algo="sha1", file=TRUE),
format_out = ifelse(missing(format_out), NA, format_out),
data_format = ifelse(missing(data_format), NA, data_format),
parser = ifelse(missing(parser), NA, parser)
)
}
)
}
#' @noRd
get_metadata_field <- function(x, field, num = FALSE, null_val = NA){
ifelse(!is.null(x[[field]]),
ifelse(num, as.numeric(x[[field]]), x[[field]]),
null_val)
}
#' @noRd
get_metadata_field2 <- function(x, field, class = c("char","float","int"),
null_val = NA){
class <- match.arg(class, c("char","float","int"))
conv <- switch(class, char = as.character, float = as.numeric,
int = as.integer)
ifelse(!is.null(attr(x,field)) && !is.na(attr(x,field)),
conv(attr(x, field)), null_val)
}
#' @noRd
get_time_unit <- function(string, format_in){
if (length(string) == 0 || is.na(string)){
NA
} else{
if (format_in %in% c("chromeleon", "shimadzu")){
pattern <- "\\((.*?)\\)"
unit <- gsub("\\(|\\)", "", regmatches(string, regexpr(pattern, string))[[1]])
switch(unit, "min" = "Minutes", "sec" = "Seconds")
} else NA
}
}
#' @name read_chemstation_metadata
#' @param file file
#' @param what Whether to return \code{metadata} or \code{peaktable}.
#' @importFrom readxl read_xls
#' @return A list containing extracted metadata.
#' @author Ethan Bass
#' @noRd
read_chemstation_metadata <- function(file, what = c("metadata", "peaktable")){
what <- match.arg(what, c("metadata", "peaktable"))
# find xls csv files
folder <- gsub(basename(file), "", file)
# check for .D folder
if (grepl("\\.D/$", folder, ignore.case = TRUE)){
# find xls/csv
reps <- list.files(folder, pattern = '.xls',
ignore.case = TRUE, full.names = TRUE)
if (length(reps) > 0){
if (what == "metadata"){
meta <- as.data.frame(readxl::read_xls(reps[1], sheet = 1, skip = 1))
meta2<-as.list(meta$Results)
names(meta2) <- meta$Title
meta2
} else if (what == "peaktable"){
pktab <- as.data.frame(readxl::read_xls(rep, sheet = "Peak"))
pktab <- pktab[, -c(1:2)]
pktab
}
}
}
}
#' @name read_masshunter_metadata
#' @param file file
#' @importFrom xml2 read_xml xml_find_all xml_text
#' @return A list containing extracted metadata.
#' @author Ethan Bass
#' @noRd
read_masshunter_metadata <- function(file){
# check for .D folder
folder <- gsub(basename(file), "", file)
if (grepl("\\.D/|\\.d/$", folder, ignore.case = TRUE)){
# find xml
rep <- list.files(folder, pattern = '.xml',
ignore.case = TRUE, full.names = TRUE)
if (length(rep) > 0){
path_devices <- rep[basename(rep) == "Devices.xml"]
path_sample <- rep[basename(rep) == "sample_info.xml"]
if (length(path_sample) == 1){
meta_sample <- xml2::read_xml(path_sample)
name <- xml2::xml_text(xml2::xml_find_all(meta_sample, xpath = "//Name"))
meta_sample <- as.list(xml2::xml_text(
xml2::xml_find_all(meta_sample, xpath = "//Value")
))
names(meta_sample) <- name
}
if (length(path_devices) == 1){
meta_devices <- xml2::read_xml(path_devices)
name <- xml_text(xml_find_all(meta_devices, xpath = "//Name"))
meta_devices <- as.character(xml_text(
xml_find_all(meta_devices, xpath = "//ModelNumber")
))
names(meta_devices) <- name
}
meta_sample$Instrument <- meta_devices
}
}
meta_sample
}
#' @name read_waters_metadata
#' @param file file
#' @return A list containing extracted metadata.
#' @author Ethan Bass
#' @noRd
read_waters_metadata <- function(file){
ll <- readLines(file, n = 2)
ll <- iconv(ll,from = "ISO-8859-1", to = "UTF-8")
meta <- gsub("\\\"", "", do.call(cbind, strsplit(ll, "\t")))
rownames(meta) <- meta[, 1]
meta <- as.list(meta[, -1])
}
#' Extract metadata
#'
#' Extract metadata as a data.frame from a list of chromatograms.
#'
#' @param chrom_list A list of chromatograms with attached metadata (as returned
#' by \code{read_chroms} with \code{read_metadata = TRUE}).
#' @param what A character vector specifying the metadata elements to extract.
#' @param format_out Format of object. Either \code{data.frame} or \code{tibble}.
#' @return A data.frame or tibble (according to the value of \code{format_out}),
#' with samples as rows and the specified metadata elements as columns.
#' @export
extract_metadata <- function(chrom_list,
what = c("instrument", "detector", "detector_id",
"software", "method", "batch", "operator",
"run_datetime",
"sample_name", "sample_id",
"injection_volume", "time_range",
"time_interval", "time_unit", "detector_range",
"detector_y_unit", "detector_x_unit",
"intensity_multiplier", "scaled", "source_file",
"source_file_format", "source_sha1",
"data_format", "parser", "format_out"),
format_out = c("data.frame", "tibble")
){
if (inherits(chrom_list, c("matrix", "data.table", "data.frame"))){
chrom_list <- list(chrom_list)
use_names <- FALSE
} else use_names <- TRUE
what <- match.arg(what, several.ok = TRUE)
format_out <- match.arg(format_out, c("data.frame", "tibble"))
metadata <- purrr::map_df(chrom_list, function(chrom){
unlist(sapply(what, function(w){
attr(chrom, which = w)
}, simplify = FALSE))
})
metadata$run_datetime <- as.POSIXct(as.numeric(metadata$run_datetime),tz = "UTC")
if (use_names && format_out == "tibble"){
metadata <- tibble::add_column(.data = metadata,
data.frame(name = names(chrom_list)),
.before=TRUE)
} else if (use_names && format_out == "data.frame"){
metadata <- data.frame(name = names(chrom_list), metadata,
row.names = names(chrom_list))
}
metadata
}
#' Transfer metadata
#'@noRd
transfer_metadata <- function (new_object, old_object,
exclude = c("names", "row.names",
"class", "dim", "dimnames")){
a <- attributes(old_object)
a[exclude] <- NULL
attributes(new_object) <- c(attributes(new_object), a)
new_object
}
#' Get 'Shimadzu' Wavelength
#' @noRd
get_sz_wv <- function(meta){
if ("WVB" %in% names(meta)){
c(get_metadata_field(meta, "WVB"),
get_metadata_field(meta, "WVE"))
} else{
get_metadata_field(meta, "ADN")
}
}
#' Extract ASM wavelength from metadata list
#' @author Ethan Bass
#' @noRd
get_asm_wavelength <- function(meta, lab = "absorbance_wavelength_setting.value"){
wv_idx <- grep(lab, names(meta$`device control aggregate document`))
unique(unlist(meta$`device control aggregate document`[wv_idx]))
}
#' Convert date-time string to POSIXct
#' @author Ethan Bass
#' @noRd
convert_timestamp <- function(string, datetime_formats){
tryCatch({
as.POSIXct(string, tz = "UTC", tryFormats = datetime_formats)
}, error = function(cond){
warning("Run date-time could not be converted to POSIXct format, returning string instead.")
string
})
}
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