R/read_ris_internal.R

In seabbs/trendsinpapers: Loads, Cleans and Analyses .RES Files of Academic Publications

#' @title An Internal Function to Read in .RIS Files
#' @description A function to read in generic .RIS  files, this function was originally
#' part of the [ris r package](https://github.com/cran/ris) written by Stephanie Kovalchik.
#' @param file A character string of the path to the .ris file to read in.
#' @param ... Additional arguements to pass to readLines.
#'
#' @return A nested list for each reference in the .ris file.
#' @export
#'
#' @examples
#'
read_ris_internal <- function(file, ...){

  ###DEPENDENT FUNCTIONS

  get.entry <- function(ty){
    #TAKE RIS TY CHARACTER/VECTOR TYPE AND RETURN BIBTEX TYPE
    #IF MULTIPLE ENTRIES TAKE THE ONE THAT FOLLOWS RIS FORM

    if(length(ty)>1){
      ty <- ty[grep("[A-Z]{2,}",ty)]
    }

    if(ty%in%c("ABST","INPR","JFULL","JOUR","MGZN","NEWS")){
      return("article")
    }
    else if(ty%in%c("SER","BOOK")){
      return("book")
    }
    else if(ty%in%c("CONF","CHAP")){
      return("incollection")
    }
    else if(ty=="THES"){
      return("phdthesis")
    }
    else{
      #RPRT, UNPB AS MISC
      return("misc")
    }
  }

  make.reference <- function(lines){

    get.date.info <- function(date){
      #PROCESS RIS CHARACTER DATE INTO LIST WITH YEAR,MONTH,DAY,INFO
      if(length(grep("/",date)!=0)){
        i <- grep("/",date)
        date.list <- as.list(strsplit(date[i],"/")[[1]])
        if(length(date.list)==3){
          names(date.list) <- c("year","month","day")
          date.list$info <- ""
        }
        else{
          names(date.list) <- c("year","month","day","info")
        }
      }
      else{
        #TAKE YEAR IF DOES NOT FOLLOW RIS CONVENTION
        date <- sub(".*([0-9]{4,4}).*","\\1",date[1])
        date.list <- list(year=date,month="",day="",info="")
      }
      return(date.list)
    }

    get.content <- function(index){
      #GENERAL FUNCTION TO EXTRACT CONTENT OF A GIVEN FIELD LINE
      content <- strsplit(lines[index],"[A-Z]([A-Z]|[0-9])  - ")
      content <- unlist(content)
      content[content!=""]
    }

    field.names <-  c(
      "ris.type",
      "type",
      "id",
      "title.primary",
      "title.secondary",
      "author.primary",
      "author.secondary",
      "keyword",
      "date",
      "abstract",
      "journal",
      "journal.abbrev",
      "volume",
      "number",
      "city",
      "publisher",
      "isbn",
      "address",
      "pages",
      "url"
    )

    #RIS CORRESPONDING FIELD PATTERNS
    ris.type <- "^TY"
    ris.id <- "^ID"
    ris.title.primary <- "(^T[1I])|(^BT)|(^CT)"
    ris.title.secondary <- "^T[23]"
    ris.author.primary <- "^A[1U]"
    ris.author.secondary <- "(^A[23])|(^ED)"
    ris.keyword <- "^KW"
    ris.date <- "(^Y1)|(^PY)"
    ris.abstract <- "(^N1)|(^N2)|(^AB)"
    ris.journal <- "^J[FO]"
    ris.journal.abbrev <- "JA"
    ris.volume <- "^VL"
    ris.number <- "(^IP)|(^CP)"
    ris.city <- "CY"
    ris.publisher <- "PB"
    ris.isbn <- "^SN"
    ris.address <- "^AD"
    ris.pages <- "(^[ES]P)|(^PG)"
    ris.url <- "^UR"

    fields <- c(
      ris.type,
      ris.type,
      ris.id,
      ris.title.primary,
      ris.title.secondary,
      ris.author.primary,
      ris.author.secondary,
      ris.keyword,
      ris.date,
      ris.abstract,
      ris.journal,
      ris.journal.abbrev,
      ris.volume,
      ris.number,
      ris.city,
      ris.publisher,
      ris.isbn,
      ris.address,
      ris.pages,
      ris.url
    )

    field.index <- sapply(fields,function(pattern){grep(pattern,lines)})

    i <- sapply(field.index,function(x){length(x)!=0})

    if(any(i)){
      ref <- lapply(field.index[i],get.content)
      names(ref) <- field.names[i]
      ref[2] <- get.entry(ref[2])

      if("date"%in%names(ref)){
        ref$date <- get.date.info(ref$date)
        ref$year <- as.numeric(ref$date$year)
      }
      else{
        ref$year <- NA
      }
    }
    else{
      ref <- list()
    }
    return(ref)
  }

  ###
  lines <- readLines(con=file,...)

  #REMOVE SPACE
  lines <- lines[lines!=""]

  #INDEX OF BEGINNING AND END OF EACH CITATION
  stops <- grep("^ER",lines)-1

  starts <- c(1,stops[-length(stops)]+1)

  citations <- lapply(1:length(starts),function(index){
    ref.list <- make.reference(lines[starts[index]:stops[index]])
    return(ref.list)
  })

  return(citations)
}