Merge pull request #5 from ethanbass/dev

add openchrom_parser function

DESCRIPTION

@@ -16,7 +16,9 @@ Imports:
     reticulate,
     stringr,
     tidyr,
-    utils
+    utils,
+    magrittr,
+    xml2
 Suggests: 
     entab,
     mzR,

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(entab_reader)
+export(read_chemstation_csv)
 export(read_chromeleon)
 export(read_chroms)
 export(read_fid)
@@ -10,7 +11,9 @@ export(read_thermoraw)
 export(read_waters_arw)
 export(sp_converter)
 export(uv_converter)
+import(magrittr)
 import(reticulate)
+import(xml2)
 importFrom(purrr,partial)
 importFrom(readr,read_lines)
 importFrom(readr,read_tsv)

NEWS.md

@@ -6,6 +6,7 @@
 * Added `read_entab` function for calling Entab parsers.
 * Added `read_thermoraw` function to convert ThermoRawFiles by calling the ThermoRawFileParser.
 * Added `read_mzml` function to extract UV data from mzML files using `mzR`.
+* Added `openchrom_parser` to call OpenChrom parsers through the commandline interface.
 
 All of the above functions can also be called from `read_chroms` by setting the `format_in` and `parser` arguments.  
 

R/openchrom_parser.R

@@ -0,0 +1,135 @@
+#' Parse files with OpenChrom
+#'
+#' To use this function [OpenChrom](https://lablicate.com/platform/openchrom) must be manually installed.
+#'
+#' The \code{openchrom_parser} works by creating an \code{xml} batchfile and
+#' feeding it to the OpenChrom commandline interface. OpenChrom batchfiles
+#' consist of \code{InputEntries} (the files you want to convert) and \code{
+#' ProcessEntries} (what you want to do to the files). The parsers are organized
+#' into broad categories by detector-type and output format. The detector-types
+#' are \code{msd} (mass selective detectors), \code{csd} (current selective
+#' detectors, such as FID, ECD, NPD), and \code{wsd} (wavelength selective
+#' detectors, such as  DAD, and UV/VIS). Thus, when calling the OpenChrom parsers,
+#' you must select one of these three options for the input format (\code{format_in}).
+
+#' @import xml2
+#' @import magrittr
+#' @param files files to parse
+#' @param path_out directory to export converted files.
+#' @param format_in Either `msd` for mass spectrometry data, `csd` for flame ionization data, or `wsd` for DAD/UV data.
+#' @param export_format Either \code{mzml}, \code{cdf}, \code{animl}, or \code{csv}.
+#' @return If \code{export_format} is \code{csv}, the function will return a list
+#' of chromatograms in \code{data.frame} format. Otherwise it will not return anything.
+#' @section Side effects: Chromatograms will be exported in the format specified
+#' by \code{export_format} in the folder specified by \code{path_out}.
+#' @author Ethan Bass
+#' @export openchrom_parser
+#' If you want to use the OpenChrom GUI, it is recommended to create a separate
+#' command-line version of OpenChrom to call from R.
+#'
+
+openchrom_parser <- function(files, path_out, format_in,
+                             export_format=c("mzml", "cdf", "animl", "csv"),
+                             export_paths = FALSE){
+  if (missing(format_in))
+    stop("Format must be specified. The options are `msd` for mass spectrometry, `csd` for flame ionization (FID),
+    or `wsd` for DAD/UV data.")
+  export_format <- match.arg(export_format, c("mzml", "cdf", "animl", "csv"))
+  if (missing(path_out)){
+    path_out <- set_temp_directory()
+  }
+  if(!file.exists(path_out)){
+    stop("'path_out' not found. Make sure directory exists.")
+  }
+  openchrom_path <- configure_openchrom_parser()
+  path_template <- system.file("openchrom_template.xml", package = "chromConverter")
+  x <- xml2::read_xml(x = path_template)
+  # add files to InputEntries
+  for (file in files){
+  x %>% xml_children %>% .[[3]] %>%
+    xml_add_child(.value = "InputEntry")  %>% xml_add_child(xml_cdata(file))
+  }
+  # add parser to ProcessEntries
+  msd_mzml_converter<-'ProcessEntry id="msd.export.org.eclipse.chemclipse.msd.converter.supplier.mzml" name="mzML Chromatogram (*.mzML)" description="Reads mzML Chromatograms" jsonSettings="{&quot;Filename&quot;:&quot;{chromatogram_name}{extension}&quot;,&quot;Export Folder&quot;:&quot;path_out&quot;}" symbolicName="" className="" dataTypes=""'
+  msd_netcdf_converter<-'ProcessEntry id="msd.export.net.openchrom.msd.converter.supplier.cdf" name="ANDI/AIA CDF Chromatogram (*.CDF)" description="Reads an writes ANDI/AIA CDF Chromatograms." jsonSettings="{&quot;Filename&quot;:&quot;{chromatogram_name}{extension}&quot;,&quot;Export Folder&quot;:&quot;path_out&quot;}" symbolicName="" className="" dataTypes=""'
+  msd_animl_converter <- 'ProcessEntry id="msd.export.net.openchrom.msd.converter.supplier.animl.chromatogram" name="AnIML MSD Chromatogram (*.animl)" description="Reads and writes Analytical Information Markup Language Chromatograms" jsonSettings="{&quot;Filename&quot;:&quot;{chromatogram_name}{extension}&quot;,&quot;Export Folder&quot;:&quot;path_out&quot;}" symbolicName="" className="" dataTypes=""'
+  msd_csv_converter <- 'ProcessEntry id="msd.export.org.eclipse.chemclipse.msd.converter.supplier.csv" name="CSV Chromatogram (*.csv)" description="Reads and Writes Chromatograms to CSV." jsonSettings="{&quot;Filename&quot;:&quot;{chromatogram_name}{extension}&quot;,&quot;Export Folder&quot;:&quot;path_out&quot;}" symbolicName="" className="" dataTypes=""'
+  csd_csv_converter <- 'ProcessEntry id="csd.export.org.eclipse.chemclipse.csd.converter.supplier.csv" name="CSV Chromatogram (*.csv)" description="Reads and Writes Chromatograms to CSV." jsonSettings="{&quot;Filename&quot;:&quot;{chromatogram_name}{extension}&quot;,&quot;Export Folder&quot;:&quot;path_out&quot;}" symbolicName="" className="" dataTypes=""'
+  csd_animl_converter <- 'ProcessEntry id="csd.export.net.openchrom.csd.converter.supplier.animl" name="AnIML FID Chromatogram (*.animl)" description="Writes AnIML Chromatograms." jsonSettings="{&quot;Filename&quot;:&quot;{chromatogram_name}{extension}&quot;,&quot;Export Folder&quot;:&quot;path_out&quot;}" symbolicName="" className="" dataTypes=""'
+  wsd_animl_converter <- 'ProcessEntry id="wsd.export.net.openchrom.wsd.converter.supplier.animl.chromatogram" name="AnIML UV-Vis Chromatogram (*.animl)" description="Reads Analytical Information Markup Language Chromatograms" jsonSettings="{&quot;Filename&quot;:&quot;{chromatogram_name}{extension}&quot;,&quot;Export Folder&quot;:&quot;path_out&quot;}" symbolicName="" className="" dataTypes=""'
+  wsd_csv_converter <- 'ProcessEntry id="wsd.export.org.eclipse.chemclipse.csd.converter.supplier.csv" name="CSV Chromatogram (*.csv)" description="Reads and Writes Chromatograms to CSV." jsonSettings="{&quot;Filename&quot;:&quot;{chromatogram_name}{extension}&quot;,&quot;Export Folder&quot;:&quot;path_out&quot;}" symbolicName="" className="" dataTypes=""'
+  if (format_in == "msd"){
+  parser <- switch(export_format,
+                   "mzml" = msd_mzml_converter,
+                   "cdf" = msd_netcdf_converter,
+                   "animl" = msd_animl_converter,
+                    "csv" = msd_csv_converter)
+  } else if (format_in == "csd"){
+    parser <- switch(export_format,
+                     "csv" = csd_csv_converter,
+                     "animl" = csd_animl_converter)
+  } else if (format_in == "wsd"){
+    parser <- switch(export_format,
+                     "csv" = wsd_csv_converter,
+                     "animl" = wsd_animl_converter)
+  }
+  x %>% xml_children %>% .[[4]] %>% xml_add_child(.value=gsub("path_out", path_out, parser))
+  path_xml <- paste0(path_out, "batchfile_", strftime(Sys.time(),format = "%Y-%m-%d_%H-%M-%S"), ".xml")
+  write_xml(x, file = path_xml)
+  openchrom_path <- "/Applications/OpenChrom_CL.app/Contents/MacOS/openchrom"
+  system(paste0(openchrom_path, " -nosplash -cli -batchfile ", path_xml))
+  new_files <- paste0(path_out, sapply(strsplit(basename(files), "\\."), function(x) x[1]), ".", export_format)
+  if (export_paths){
+    new_files
+  } else{
+    if (export_format == "csv"){
+      lapply(new_files, read.csv)
+    }
+  }
+}
+
+#' Configure OpenChrom parser
+#'
+#' @name configure_openchrom_parser
+#' @param cli Defaults to NULL. If "true", R will rewrite openchrom ini file to enable CLI.
+#' If "false", R will disable CLI. If NULL, R will not modify the ini file.
+#' @return No return value.
+#' @author Ethan Bass
+#' @noRd
+configure_openchrom_parser <- function(cli = c(NULL, "true", "false")){
+  cli <- match.arg(cli, c(NULL, "true", "false"))
+  path_parser <- readLines(system.file("shell/path_to_openchrom_commandline.txt", package = 'chromConverter'))
+  if (!file.exists(path_parser)){
+    warning("OpenChrom not found!", immediate. = TRUE)
+    path_parser <- readline(prompt="Please provide path to `OpenChrom` command line):")
+    writeLines(path_parser, con = system.file('shell/path_to_openchrom_commandline.txt', package='chromConverter'))
+  }
+  path_ini <- switch(.Platform$OS.type,
+                     "unix" = paste0(gsub("MacOS/openchrom", "", path_parser), "Eclipse/openchrom.ini"),
+                     "linux" = paste0(path_parser, ".uni"),
+                     "windows" = paste0(gsub(".exe", "", path_parser), ".ini"))
+  ini <- readLines(path_ini)
+  cli_index <- grep("-Denable.cli.support",ini)
+  ini_split <- strsplit(ini[cli_index],"=")[[1]]
+  cli_tf <- ini_split[2]
+  if(cli_tf == "false"){
+    message("    The OpenChrom command-line interface is turned off!
+    Update `openchrom.ini` to activate the command-line interface (y/n)?
+    (Warning: This will deactivate the GUI on your OpenChrom installation!)")
+    ans <- readline()
+    if (ans %in% c("y","Y", "yes", "Yes", "YES")){
+      cli <- "true"
+    } else{
+      stop("-Denable.cli.support must be enabled to use the OpenChrom parsers from R.")
+    }
+  }
+  if (cli %in% c("true", "false")){
+    ini_split[2] <- cli
+    ini[cli_index] <- paste(ini_split, collapse="=")
+    writeLines(ini, path_ini)
+  }
+  path_parser[1]
+}
+
+utils::globalVariables(names = c('.'))
+