R/AnnotationData.io.R

In qutang/mhealth-visualizer-r: Interactive visualizer for annotated mhealth data

#' @name AnnotationData.io.write
#' @title Write annotation data into mhealth folder structure and with mhealth filename convention.
#' @export
#' @import lubridate stringr
#' @param folder the output folder
#' @param annotationData the input dataframe that matches mhealth specification.
#' @param ontologyId the ontology ID for this set of annotations
#' @param annotatorId the annotator's ID for this set of annotations
#' @param tz the time zone string (P/MHHMM) used in filename.
#' @param gzip whether to gzip the output csv file.
#' @param flatDir whether to use mhealth folder structure or just use flat directory.
#' @param splitHour whether to split input dataframe into hourly csv files.
#' @param custom_name if provided, the file name will be custom_name and all other file name preset parameters such as sensorType will be discarded.
#' @param append whether to append to a file if the file exists
#' @param header whether to add column header or not
AnnotationData.io.write = function(folder, annotationData, ontologyId = NA, annotatorId = NA, tz, gzip = TRUE, flatDir = FALSE, splitHour = TRUE, custom_name, append = FALSE, header = TRUE){
  if(missing(custom_name)){
    # TODO: support split hour
    if(missing(tz)){
      warning("Use local time zone in the file name")
      startTime = annotationData[1,1]
      utcTime = ymd_hms(startTime)
      localTime = startTime
      hourDiff = round(utcTime - localTime, digits = 2)
      tzStr = .SensorData.io.formatTimezone(hourDiff)
    }else{
      tzStr = tz
    }
    timeStamp = strftime(startTime, format = MHEALTH_FILE_TIMESTAMP_FORMAT, origin = origin)
    timeStamp = str_replace(timeStamp, pattern = "\\.", replacement = "-")
    timeStampStr = paste(timeStamp, tzStr, sep="-")
    section1 = ontologyId
    section2 = annotatorId
    annotationFilename = paste(section1, section2, timeStampStr, "annotation", "csv", sep = ".")
  }else{
    annotationFilename = custom_name;
  }
  if(!flatDir){
    containFolder = file.path(folder, year(startTime), month(startTime), day(startTime), hour(startTime))
  }else{
    containFolder = folder
  }
  dir.create(containFolder, showWarnings = FALSE, recursive = TRUE)
  fullPath = file.path(containFolder, annotationFilename)
  options(digits.secs = 3)
  if(gzip){
    gzFile = gzfile(description = paste(fullPath, "gz", sep = "."), open = "w", compression = 6, encoding = "UTF-8")
    write.table(x = annotationData, file = gzFile, append = append, quote = FALSE, sep = ",", na = "", row.names = FALSE, col.names = header)
    close(gzFile)
  }else{
    write.table(x = annotationData, file = fullPath, append = append, quote = FALSE, sep = ",", na = "", row.names = FALSE, col.names = header)
  }
}

#' @name AnnotationData.io.getAnnotatorId
#' @title Get annotator Id from annotation file name
#' @import stringr
#' @export
AnnotationData.io.getAnnotatorId = function(filename){
  tokens = str_split(filename, "\\.")
  tokens = str_split(tokens[[1]][2], "-")
  return(tokens[[1]][1])
}

#' @name AnnotationData.io.getOntologyId
#' @title Get ontology Id from annotation file name
#' @import stringr
#' @export
AnnotationData.io.getOntologyId = function(filename){
  tokens = str_split(filename, "\\.")
  return(tokens[[1]][1])
}