parsePub: Parse publication details (provided in JSON format) returned by sortPubsToHTML: sorts pubs by year and parse with parsePub, optionally sending output to a text file. Here, pubs refers to a list of publications in JSON format, each of which is returned by the Mendeley Group Document Details method - http://apidocs.mendeley.com/home/user…

parsePub.R

parsePub <- function(x, emphasize=NULL) {  
  if (!is.null(emphasize)) {
    lname <- sapply(strsplit(sapply(x$authors, '[[', 2), '\\s+'), tail, 1)
    finit <- substr(sapply(x$authors, '[[', 1), 1, 1)
    em.lname <- sapply(strsplit(emphasize, '\\s+'), tail, 1)
    em.finit <- substr(emphasize, 1, 1)
    em <- !is.na(match(paste(finit, lname), paste(em.finit, em.lname)))  
  }
  
  authsToVec <- function(y, emphasize=emphasize) {
    initials <- paste0(substring(strsplit(x$authors[[y]]['forename'], 
                                          '\\s+')[[1]], 1, 1), '.', collapse='')
    sprintf('%s%s, %s%s', 
            ifelse(!is.null(emphasize) && em[y], '<strong>', ''), 
            x$authors[[y]]['surname'], 
            initials, 
            ifelse(!is.null(emphasize) && em[y], '</strong>', ''))
  }
  
  authvec <- sapply(seq_along(x$authors), authsToVec, emphasize=emphasize)
  
  authstring <- gsub(',([^,]*,[^,]*)$', ' &\\1', paste(authvec, collapse=', '))
  if (is.null(x$volume)) {
    sprintf("<p>%s (%s), <a href='%s'>%s.</a> <em>%s</em>.</p>", 
            authstring, x$year, x$url, x$title, x$published_in)    
  } else {
    sprintf("<p>%s (%s), <a href='%s'>%s.</a> <em>%s</em>, %s: %s.</p>", 
            authstring, x$year, x$url, x$title, x$published_in, 
            x$volume, x$pages)    
  }
}

# See https://gist.github.com/johnbaums/7000303#file-publist-r for example usage.

pubList.R

library(devtools)
library(RMendeley)
library(ROAuth)

mkey <- 'mendeley consumer key' # see http://apidocs.mendeley.com/
msecret <- 'mendeley consumer secret'
#mc <- mendeley_auth(mkey, msecret)
#save(mc, file="~/../Dropbox/credentials/mendeley_credential.rdata")
load("~/../Dropbox/credentials/mendeley_credential.rdata")


# grab function to scrape QAECO member names from website
source_url('https://gist.github.com/johnbaums/32d902b7ecac0dac9ec4/raw/qaecoMembers.R')
qmem <- qaecoMembers()


# grab functions to parse pubs
source_url('https://gist.github.com/johnbaums/7000303/raw/sortPubsToHTML.R')
source_url('https://gist.github.com/johnbaums/7000303/raw/parsePub.R')
 

# grab Mendeley publication IDs
pubID <- function(group_id, maxresults=500, mkey) {
  fromJSON(sprintf(
    'http://api.mendeley.com/oapi/documents/groups/%s/docs/?consumer_key=%s&items=%s',
    group_id, mkey, maxresults))$document_ids
}
pub_ids <- pubID(group_id='3762151', mkey=mkey)


h <- getCurlHandle()
# grab publication details for pub ids
pubs <- lapply(pub_ids, function(x) {
  fromJSON(OAuthRequest(mc, sprintf("http://api.mendeley.com/oapi/library/groups/3762151/%s/", x), 
                        method="GET", curl=h))  
})
 

# parse a single publication to hmtl
parsePub(pubs[[1]], qmem)
 

# split pubs by year and parse all to html
sortPubsToHTML(pubs, qmem)
sortPubsToHTML(pubs, qmem, 'pubs.txt') # to a text file

sortPubsToHTML.R

sortPubsToHTML <- function(pubList, emphasize, file, overwrite=FALSE) {
  require(devtools)
  if(!missing(file)) {
    if(!isTRUE(overwrite) && file.exists(file)) 
      stop('File exists. Use overwrite=TRUE.', call.=FALSE)
  }
  if (!exists('parsePub') || !is.function(parsePub)) {
    source_url('https://gist.github.com/johnbaums/7000303/raw/parsePub.R')
  }
  years <- sapply(pubList, '[[', 'year')
  pubList <- split(pubList, factor(as.numeric(years), 
                                   levels=sort(unique(years), dec=TRUE)))  
  Y <- names(pubList)
  out <- sapply(seq_along(pubList), function(i) {
    c(sprintf("<h2 style='text-align:center;'><strong><em>%s</em></strong></h2>", Y[i]),
      sapply(pubList[[i]], function(x) {
        parsePub(x, emphasize=emphasize)
      }))
  })
  if(!missing(file)) {
    cat(unlist(out), sep='\n\n', file=file)
  } else return(out)
}
 
# See https://gist.github.com/johnbaums/7000303#file-publist-r for example usage.