ProcessRequest.R

#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)

source ("basicFunctions.R")
source ("auth.R")

library(mailR)


# code <- list.files(file.path("output"))

code <- args[1]  

#Process ----------
request <- readRDS(file.path("output", code, "request.rds"))
email <- request$email
dirname <- request$dirname
term <- request$term
retmax <- 10000
year <- request$year
force <- request$force



nAuthors <- 100

#Extract forced authors ------

if(force[1] != ""){  
  force <- strsplit(force, ",")[[1]]
  for(i in 1:length(force)){
    force[i] <- trimws(force[i])
  }
}

#Get PUBMED results ------
search_results <- makeQuery(term, year, retmax)
if(length(search_results)==0){
  filename <- paste(dirname, "/results.rds", sep="")
  
  toSave <- list(ter = term)
  saveRDS(toSave, file = filename)
  
  myCodeErrorMail(term, code, email)
  stop("Could not get results from query")
}

if(force[1] != ""){
  for(i in 1:length(force)){
    termp <- paste(term, "AND", force[i], sep=" ")
    search_results <- c(search_results, makeQuery(termp, year, retmax))
  }
}
search_results <- unique(search_results)
files <- fetchSearchResults(search_results)

#Process PUBMED files --------
if(file.exists(file.path("output", code, "df.rds"))){
  df <- readRDS(file.path("output", code, "df.rds"))
} else {
  df <- extractInfo(files)
  saveRDS(df, file.path("output", code, "df.rds"))
}
dataFrame <- df[["df"]]

#Get authors to display --------
freqAuthors <- data.frame(table(c(dataFrame[,"FirstAuthor"], dataFrame[, "LastAuthor"])))
freqAuthors <- freqAuthors[order(freqAuthors[,"Freq"], decreasing = T),]

if(!(is.na(force[1]) || force[1]=="")){
  forcedAuthors <- NULL
  for(i in 1:length(force)){
    forceEntry <- strsplit(force[i], " ")[[1]]
    forcedAuthorsFirst <- grep(forceEntry[1], freqAuthors[,"Var1"])
    forcedAuthorsLast <- grep(forceEntry[length(forceEntry)], freqAuthors[,"Var1"])  
    forcedAuthors <- c(forcedAuthors, intersect(forcedAuthorsFirst, forcedAuthorsLast))
  }
  
  toKeep <- c(1:(nAuthors-length(forcedAuthors)))
  toKeep <- toKeep[-forcedAuthors]
  toKeep <- c(forcedAuthors, toKeep)
} else {
  toKeep <- 1:nAuthors
}

mainAuthors <- as.character(freqAuthors[toKeep, "Var1"])


# Make workdclouds ------
figs <- createWordClouds(df[["df"]], mainAuthors, nkeys=30)

#Get faces and make wordcloud images-------
imgs <- list()
library(rvest)

dirname <- file.path("www", code)
if(!dir.exists(dirname)){
  dir.create(dirname)
}

for (i in 1:length(figs)){
  #Make a google search and extract the first image
  sterm <- paste(term, names(figs[i]), "profile")
  sterm <- gsub(" ", "+", sterm)
  url <- paste("https://www.google.com/search?q=", sterm, "&tbm=isch", sep="")
  page <- read_html(url)
  img <- page %>% html_nodes("img") %>% html_attr("src")
  #img <- "" #THIS SHOULD BE REMOVED IF img IS RUN
  imgs <- c(imgs, list(img[[2]]))
  names(imgs)[i] <- make.names(names(figs[i]))
  
  # saveWidget(figs[[i]], paste(dirname, "/tmp.html", sep=""), selfcontained = F)
  # webshot(paste(dirname, "/tmp.html", sep=""),
  #         paste(dirname,"/", names(imgs)[i], ".jpg", sep=""),
  #         delay = 3, vwidth = 300, vheight=300) # changed to png.
}



#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#Network -----------------
Authors <- as.character(freqAuthors[, "Var1"])


if(!(is.na(force[1]) || force[1]=="")){
  net <- MakeNetwork(df[["df"]], Authors = Authors, 
                     mainAuthors = mainAuthors,
                     forcedAuthors = freqAuthors[forcedAuthors, "Var1"], 
                     collaborators = df[["collaborators"]])
} else {
  net <- MakeNetwork(df[["df"]], Authors = Authors, 
                     mainAuthors = mainAuthors,
                     collaborators = df[["collaborators"]])
  
}

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#Save Results -----------------
dirname <- file.path(getwd(), "output", code)

filename <- paste(dirname, "/results.rds", sep="")

toSave <- list(ter = term, df = df, figs = figs, imgs = imgs, net = net)
saveRDS(toSave, file = filename)

myCodeMail(term, code, email)

#}