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corresponding.R
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corresponding.R
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#rm(list = ls(all = TRUE))
#install if not installed
list.of.packages <- c("rscopus", "statcheck", "dplyr", "XML", "RPostgreSQL", "pdftools", "stringr", "pryr")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)
#load
lapply(list.of.packages, require, character.only = TRUE)
id<-''
api_key = get_api_key(id, error = FALSE)
options(elsevier_api_key_filename = id)
options(elsevier_api_key = id)
options(warn = -1)
#create list of ScienceDirect Psychology articles via CopyPaste on the web search interface
#scopusJournalList20171005 <-read.csv("C:\\Users\\User\\Documents\\Projects\\correspondingAuthor\\ScienceDirectJournalList.csv", header = FALSE, sep= ";")
scopusJournalList20171005 <-read.csv("ScienceDirectJournalList.csv",
header = FALSE, sep= ";", fileEncoding = "LATIN2")
#dbSetup
pg = dbDriver("PostgreSQL")
# Local Postgres.app database; no password by default
# Of course, you fill in your own database information here.
con = dbConnect(pg, user="postgres", password="",
host="localhost", port=5432, dbname="miningDB")
###code
## import extraction method
source("extractMetadata.R")
#months <- c("January", "February", "March", "April", "May", "June", "July", "August", "September", "October", "November", "December")
years <- c("2010","2011","2012","2013","2014","2015","2016")
#dates <- expand.grid(months, years)
#dates <- paste(dates$Var1,dates$Var2)
dates<- years
journalIndex <- 1
#memory handling
maxMemory <- mem_used()+(6*1e8)
#helperfuncionr
getResultSet <- function(journalIndex, dateIndex, resultOffset=0)
{
res <- generic_elsevier_api(
query = paste(
"SRCTITLE (",scopusJournalList20171005$V1[journalIndex],")",
"AND PUBYR(", dates[dateIndex],")"
),
type = "search",
search_type = "scidir",
api_key = api_key,
start = resultOffset,
count = 25
)
print(paste(journalIndex,dateIndex))
return(res)
}
#res$content$`search-results`$entry[[1]]$`prism:doi`
extractMeta<-function(i,j=1){
while(j<=length(dates)){
while (i < nrow(scopusJournalList20171005))
{
res <- getResultSet(i,j)
#handle empty resultSet condition
while (is.null(res$content$`search-results`$`opensearch:totalResults`)
|| as.numeric(res$content$`search-results`$`opensearch:totalResults`) >= 5000
|| as.numeric(res$content$`search-results`$`opensearch:totalResults`) == 0
|| res$get_statement$status_code!=200)
{
i<-i+1
res <-getResultSet(i,j)
if(i == nrow(scopusJournalList20171005))
{
return()
}
if(!is.null(res$content$`search-results`$`opensearch:totalResults`) ){
if(as.numeric(res$content$`search-results`$`opensearch:totalResults`) >= 5000){
dbWriteTable(con,'repeatquery',data.frame(cbind(i,j)), row.names=FALSE, append=TRUE)
}
}
}
totalResCount <-
as.numeric(res$content$`search-results`$`opensearch:totalResults`)
### MAIN - examine all abstracts in resultsSet in 25 length batches
for (k in seq(0, as.numeric(totalResCount), by = 25))
{
if (k == 0)
{
res <- res #do nothing
} else{
res <- getResultSet(i, j, k)
}
mem <- system('systeminfo', intern=TRUE)
available<-str_extract_all(mem[26],"\\(?[0-9˙]+\\)?")
available<-strtoi(gsub("˙","",available))
total<-str_extract_all(mem[25],"\\(?[0-9˙]+\\)?")
total<-strtoi(gsub("˙","",total))
mem<-available/total*100
###MEMORY POLICE
if(mem>85){
stop("Memory limit reached")
}else{
dbWriteTable(con,'memoryuse',data.frame("memoryused"=as.numeric(mem_used()/1048576), projectid), row.names=FALSE, append=TRUE)
}
idSet <- NULL
message(paste("Current page index is:", "date",j, "journal", i, 'offset ', k))
message(paste(res$get_statement$headers$`x-els-status`))
if(res$get_statement$headers$`x-els-status`!="OK"){
dbWriteTable(con,'repeatquery',data.frame(cbind(i,j)), row.names=FALSE, append=TRUE)
}
if(!is.null(res$content$`search-results`$entry))
{
entryCount <- length(res$content$`search-results`$entry)
#Total number of results examined in a given batch
for (l in 1:entryCount){
#scopusId
message("batchIndex:","date ",j," ", i, " ", k, " ", l)
if (is.null(res$content$`search-results`$entry[[l]]$`prism:doi`))
{
idSet[l] <- NA
} else{
idSet[l] <- res$content$`search-results`$entry[[l]]$`prism:doi`
}
##################################
#Return Abstract of given article
#lapply(res$content$`search-results`$entry,function(l) l$`dc:identifier`)
if (is.na(idSet[l]))
{
s <- NA
}
else{
link<-paste("http://api.elsevier.com/content/article/doi/",idSet[l],"?apiKey=",id,"&httpAccept=text%2Fxml", sep = "")
resultList<-NULL
tryCatch({resultList <- extractMetadata(link, con, idSet[l])},error=function(e){resultList<-NULL})
if(!is.null(resultList)){
result <- tryCatch({
dbWriteTable(con,'articles',resultList[[1]], row.names=FALSE,append=TRUE)
},error = function(err) {
# error handler picks up where error was generated
print(paste("MY_ERROR: ","ID:",idSet[l], "index: ", l , err))
dbWriteTable(con,'duplicates',resultList[[1]], row.names=FALSE, append=TRUE)
}) # END tryCatch
#if article with given doi does not exist then insert
if(result==TRUE){
#authors always have to be present in result
dbWriteTable(con,'authors',resultList[[2]], row.names=FALSE,append=TRUE)
#keywords dont always have to be present in result
if(!is.null(resultList[[3]])){
dbWriteTable(con,'keywords',resultList[[3]], row.names=FALSE,append=TRUE)
}
if(!is.null(resultList[[4]])){
dbWriteTable(con,'statcheck',resultList[[4]], row.names=FALSE,append=TRUE)
}
if(!is.null(resultList[[5]])){
dbWriteTable(con,'statcheck',resultList[[5]], row.names=FALSE,append=TRUE)
}
if(!is.null(resultList[[6]])){
dbWriteTable(con,'emails',resultList[[6]], row.names=FALSE,append=TRUE)
}
}else{
if(grepl("Key(.+)already exists", result))
{
message("Article already in db...")
}else{
stop(result)
}
}
}
}
}
}
}
i<- i+1
do.call(file.remove, list(list.files("pdfs", full.names = TRUE)))
cat("\014")
.rs.restartR()
}
j<-j+1
i<-1
cat("\014")
.rs.restartR()
print("nextdate")
}
}
#extractMeta(i)
lastInsert<- dbGetQuery(con, "SELECT to_number(s.row, '99'), to_number(y.row, '99')
FROM articles a
LEFT JOIN scidirjournal s
ON a.publicationname = s.publicationname
LEFT JOIN years y
ON to_char(EXTRACT(YEAR FROM coverdate), '9999') LIKE '%'|| y.years || '%'
ORDER BY createdon DESC
LIMIT 1")
extractMeta(lastInsert[[1]],lastInsert[[2]])