R/elife_paper.r

In ropensci/elife: R interface to the eLife API.

#' Get full text eLife papers via XML. 
#' 
#' @import httr XML
#' @export
#' @param doi DOI to get full text for. 
#' @param what Specify what you want returned. One of xml, all, abstract, introduction,
#'    methods, results, discussion, figtabcaps, references.
#' @details Returns what you like with the what parameter.
#' @examples \dontrun{
#' elife_paper(doi="10.7554/eLife.00160", 'xml')
#' elife_paper(doi="10.7554/eLife.00160", 'abstract')
#' elife_paper(doi="10.7554/eLife.00160", 'exec_summary')
#' }

elife_paper <- function(doi = NULL, what='xml')
{
	url <- sprintf("http://elife.elifesciences.org/elife-source-xml/%s", doi)
	tt <- content(GET(url), as="text")
  
  what <- match.arg(what, c('text','xml','all','abstract','exec_summary','introduction','methods','results','discussion'))
  
	if(what=='text'){ tt } else {
	  out <- xmlParse(tt)
	  
	  if(what=='xml') { 
	    out 
	  } else if(what=='all') { 
	    message("to be fixed")
	    #     tmp <- xpathApply(out, "//p", fun=xmlValue)
	    #     tmp[!vapply(tmp, function(z) grepl("DOI", z), TRUE)]
	  } else if(what=='abstract'){  
	    abstract <- xpathApply(out, "//abstract[@hwp:id='abstract-1']/p", fun=xmlValue)
	    extract_section(abstract)
	  } else if(what=='exec_summary'){
	    exec_summary <- xpathApply(out, "//abstract[@hwp:id='abstract-2']/p", fun=xmlValue)
	    extract_section(exec_summary)
	  } else if(what=='introduction'){
	    intro <- xpathApply(out, "//body/sec[@sec-type='intro']/p", fun=xmlValue)
	    extract_section(intro)
	  } else if(what=='results'){
	    ## FIX ME
	    message("to be fixed")
	    # 	xpathApply(out, "//body/sec[@sec-type='results']//p", fun=xmlValue)
	    #     resultsnodes_title <- getNodeSet(out, "//body/sec[@sec-type='results']/sec/title")
	    #     resultsnodes_p <- getNodeSet(out, "//body/sec[@sec-type='results']/sec/p")
	    #     res_titles <- sapply(resultsnodes_title, xmlValue)
	    #     res_p <- sapply(resultsnodes_p, xmlValue)
	    #     names(res_p) <- res_titles
	  } else if(what=='methods'){
	    ## FIX ME
	    message("to be fixed")
	    #     disc <- 
	    #       xpathApply(out, "//body/sec[@sec-type='methods']//p", fun=xmlValue)
	    #     res <- list()
	    #     res$doi <- disc[grepl("DOI", disc)][[1]]
	    #     res$text <- disc[!grepl("DOI", disc)]
	    #     res
	  } else if(what=='discussion'){
	    disc <- xpathApply(out, "//body/sec[@sec-type='discussion']//p", fun=xmlValue)
	    extract_section(disc)
	  } 
	}
}

extract_section <- function(x){
  res <- list()
  res$doi <- gsub("DOI:", "", x[grepl("DOI", x)][[1]])
  res$text <- x[!grepl("DOI", x)]
  res
}