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zotero.R
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# parse rdf zotero files
# zotero.rdf <- zotero(x)
#zotero2[[2]]
#zotero2 <- zotero_rdf(x)
#length(zotero2)
#zotero2[[1]]
#zoteropdf <- extractPdfZotero(zotero2)
#zoteropdf[[5]][1]
#zot_data <- zoteropdf#[[5]]
#length(zoteropdf)
#k=3
# query="europ"
# query1="cyberspace"
# query2="policy"
# query2="operations"
# condition = "and"
# between = 5
# len = 10
# i=5
# path_to_rdf = x
# k=1
#
# mydata <- extractZotero(dir.list,query,query2,len, path_to_rdf)
# mydata$titles
#extract <- mydata
#save(zoteropdf, file="zoteropdf.rda")
#load("zoteropdf.rda")
#zot_data <- zoteropdf
# mydata <- extractZoteroTxt(zot_data,query1,query2,condition, len, between)
#length(mydata[[2]])
zotero_rdf <- function(x) {
require(XML)
xml = xmlTreeParse(x,useInternalNodes=TRUE)
k=1
articles <- list()
title <- ""
abstract <- ""
date <- ""
surname <- ""
firstname <- ""
link <- ""
type <- ""
path <- ""
nodes = getNodeSet(xml, "//bib:Article")
#nodes = xpathSApply(xml, "//bib:[contains(Article) or contains(Report)]",xmlValue)
#bib:BookSection
#bib:Thesis
attachments <- getNodeSet(xml, "//z:Attachment")
print(length(nodes))
print(length(attachments))
#i=4
for (i in 1:length(nodes)) {
# print("NEW")
node <- nodes[[i]]
doc <- xmlToList(node)
title <- doc$title
abstract <- doc$abstract
date <- doc$date
surname <- doc$authors$Seq$li$Person$surname
firstname <- doc$authors$Seq$li$Person$givenname
link <- [email protected]
# print(link)
# attachments <- getNodeSet(xml, "//z:Attachment")
attachment <- attachments[[i]]
doc2 <- xmlToList(attachment)
# print(doc2$.attrs[[1]])
## Test for file item # between article and attachement
if (link %in% doc2$.attrs[[1]]==TRUE) {
# print(link)
# print(doc2$.attrs[[1]])
type <- doc2$type # test pdf
path <- [email protected] # file path
# if (type %in% "application/pdf"==TRUE) {
if (is.null(title)) {title=""}
if (is.null(date)) {date=""}
if (is.null(abstract)) {abstract=""}
if (is.null(surname)) {surname=""}
if (is.null(firstname)) {firstname=""}
if (is.null(link)) {link=""}
if (is.null(type)) {type=""}
if (is.null(path)) {path=""}
article <- c(title, abstract,date,surname, firstname,link,type,path)
articles[[k]] <- article
k=k+1
# print(type)
# print(path)
}
else { print("none")
# print("NEW")
# print(link)
# print(doc2$.attrs[[1]])
# print(path)
}
}#}
return(articles)
}
zotero <- function(x) {
uris.name <- x
# #Get all the lines of interest in the file
zot.lines <- readLines(uris.name)#zot.file)
zot.lines <- zot.lines[grep("<rdf:resource",zot.lines)]
#zot.lines <- zot.lines[grepl(".pdf\"", zot.lines)]
zot.line.parser <- function(z){
#This takes one of our rdfresource lines and returns the pdf title
#This relies on the rdf:resource tag having exactly two double quotes
#Seems safe enough, but just to be safe we take the first and last quote mark
#This avoids issues with quotes in a title/file name.
require(stringr)
require(tools)
first <- 1
last <- dim(str_locate_all(z,'"')[[1]])[1]
start <- str_locate_all(z,'"')[[1]][first] + 1
stop <- str_locate_all(z[1],'"')[[1]][last] -1
substr(z, start, stop)
}
zot.pdf <- unlist(lapply(zot.lines, zot.line.parser))
}
zoteroMeta <- function(x) {
uris.name <- x
# #Get all the lines of interest in the file
zot.lines <- readLines(uris.name)#zot.file)
date.lines <- zot.lines[grep("<dc:date",zot.lines)]
author.lines <- zot.lines[grep("<foaf:surname",zot.lines)]
abstract.lines <- zot.lines[grep("<dcterms:abstract",zot.lines)]
date.lines <- gsub("<dc:date>","",date.lines)
date.lines <- gsub("</dc:date>","",date.lines)
date.lines <- gsub("[a-zA-Z\\s]*","",date.lines)
date.lines <- as.integer(date.lines)
author.lines <- gsub("<foaf:surname>","",author.lines)
author.lines <- gsub("</foaf:surname>","",author.lines)
author.lines <-gsub("\\s+","",author.lines)
abstract.lines <- gsub("<dcterms:abstract>","",abstract.lines)
abstract.lines <- gsub("</dcterms:abstract>","",abstract.lines)
abstract.lines <-gsub("\\s+"," ",abstract.lines)
info <- list(date.lines,abstract.lines,author.lines,zot.pdf)
return(info)
}
#extractPdfZotero <- function(list.rdf,zot.pdf){
#### extract pdf files from a list of rdf articles
extractPdfZotero <- function(zot.rdf) {
# list.rdf <- list.rdf
# num <- length(list.rdf)
# zot.rdf <- zot.pdf
removeURL <- function(x) gsub("http[^[:space:]]*", "", x)
removeWWW <- function(x) gsub("www[^[:space:]]*", "", x)
require(tm)
substrRight <- function(x, n){
substr(x, nchar(x)-n+1, nchar(x))
}
num <- length(zot.rdf) # list of rdf articles with sublist of 5 title, abstract,date,surname, firstname,link,type,path
titles <-vector()
authors <-vector()
datetimes <- vector()
abstracts <- vector()
names <- vector()
# cont <- rep("",num)
text.extract <- list()
# pdf.str <- ".pdf"
for (i in 1:num) {
lists <- zot.rdf[[i]]
# uris.name <- as.character(paste0(list.rdf[i]))
uris.name <- lists[8]
# print(uris.name)
# uris.name <- zotero.rdf[5]
# if (uris.name %in% ".pdf") {
# if (substrRight(uris.name,3)=="pdf") {
# uris.name <- "/Users/olgascrivner/Documents/ITMS/TextMiningZotero/HCSS-Rizzoma/files/3422/Adamsky_2018_From Moscow with coercion.pdf"
# if (nchar(uris.name)<100) {
# print(substrRight(uris.name,3))
tempPDF <- readPDF(control = list(info="-f",text = "-layout"))(elem = list(uri = uris.name),
language="en",id="id1")
read.file <- tempPDF$content
# print(read.file)
# id <- tempPDF$meta$id
# title <- tempPDF$meta$id
texts <- enc2utf8(read.file)
text.collapse <- paste(texts,collapse=" ")
text.url <- removeURL(text.collapse)
text.url <- removeWWW(text.url)
text.hyphen <- gsub("-\\s+","",text.url)
text.space <- gsub("\\s\\s+"," ",text.hyphen)
# split_title <- unlist(strsplit(id," - "))
# if (!is.null(tempPDF$meta$datetimestamp)) {
# title <- tempPDF$meta$heading
# author <- tempPDF$meta$author # Alan Ritter ; Colin Cherry ; Bill Dolan
#id <-tempPDF$meta$id
# des <- tempPDF$meta$datetimestamp
# y <- strsplit(as.character(des), "-")
# datetime <- y[[1]][1]
# name <- tempPDF$meta$id
# }
# if (!is.null(tempPDF$meta$author)) {
# title <- tempPDF$meta$id
# name <- tempPDF$meta$id
# author <- tempPDF$meta$author
# }
# des <- tempPDF$meta$datetimestamp
# y <- strsplit(as.character(des), "-")
# datetime <- des#y[[1]][1]
# }
# if (is.null(tempPDF$meta$datetimestamp)) {
# datetime <- split_title[2]#strsplit(id," - ")[[1]]
# zoteroData()$texts[[1]]
# title <- "NA"
# }
# if (is.null(tempPDF$meta$author)) {
# author <- split_title[1] #strsplit(id," - ")[[1]]
# author <- "NA"
# }
# if (length(datetime)<1) {
# datetime <- strsplit(id," - ")[[2]]
# }
# if (length(name)<1) {
# name <-x$name[i]
# }
title <- lists[1]
n <- length(strsplit(lists[3], " ")[[1]])
if (n==1) {
datetime <- lists[3]
}
else if (n>1) {
datetime <- strsplit(lists[3], " ")[[1]][n]
}
else {
datetime <- ""# tempPDF$meta$datetimestamp
}
abstract <- lists[2]
name <- paste0(lists[5]," ",lists[4])
titles[i] <- title
authors[i] <- name
datetimes[i] <- datetime
names[i] <- name
abstracts[i] <- abstract
text.extract[[i]] <- text.space
# text.extract <- unlist(text.extract)
# }
# else {print("none")}
# print("extractpdfzotero")
# print(i)
# }
}
info <- list(titles=titles, abstracts=abstracts, authors=authors,datetimes=datetimes, text.extract=text.extract)
return(info)
}
extractAllPdfZotero <- function(zot.rdf) {
# list.rdf <- list.rdf
# num <- length(list.rdf)
# zot.rdf <- zot.pdf
removeURL <- function(x) gsub("http[^[:space:]]*", "", x)
# removeWWW <- function(x) gsub("www[^[:space:]]*", "", x)
require(tm)
substrRight <- function(x, n){
substr(x, nchar(x)-n+1, nchar(x))
}
num <- length(zot.rdf) # list of rdf articles with sublist of 5 title, abstract,date,surname, firstname,link,type,path
titles <-vector()
authors <-vector()
datetimes <- vector()
abstracts <- vector()
names <- vector()
# cont <- rep("",num)
text.extract <- list()
# pdf.str <- ".pdf"
for (i in 1:num) {
lists <- zot.rdf[[i]]
# uris.name <- as.character(paste0(list.rdf[i]))
uris.name <- lists[8]
# print(uris.name)
# uris.name <- zotero.rdf[5]
# if (uris.name %in% ".pdf") {
# if (substrRight(uris.name,3)=="pdf") {
# uris.name <- "/Users/olgascrivner/Documents/ITMS/TextMiningZotero/HCSS-Rizzoma/files/3422/Adamsky_2018_From Moscow with coercion.pdf"
# if (nchar(uris.name)<100) {
# print(substrRight(uris.name,3))
tempPDF <- readPDF(control = list(info="-f",text = "-layout"))(elem = list(uri = uris.name),
language="en",id="id1")
read.file <- tempPDF$content
# print(read.file)
# id <- tempPDF$meta$id
# title <- tempPDF$meta$id
texts <- enc2utf8(read.file)
text.collapse <- paste(texts,collapse=" ")
text.url <- removeURL(text.collapse)
text.hyphen <- gsub("-\\s+","",text.url)
text.space <- gsub("\\s\\s+"," ",text.hyphen)
# split_title <- unlist(strsplit(id," - "))
# if (!is.null(tempPDF$meta$datetimestamp)) {
# title <- tempPDF$meta$heading
# author <- tempPDF$meta$author # Alan Ritter ; Colin Cherry ; Bill Dolan
#id <-tempPDF$meta$id
# des <- tempPDF$meta$datetimestamp
# y <- strsplit(as.character(des), "-")
# datetime <- y[[1]][1]
# name <- tempPDF$meta$id
# }
# if (!is.null(tempPDF$meta$author)) {
# title <- tempPDF$meta$id
# name <- tempPDF$meta$id
# author <- tempPDF$meta$author
# }
# des <- tempPDF$meta$datetimestamp
# y <- strsplit(as.character(des), "-")
# datetime <- des#y[[1]][1]
# }
# if (is.null(tempPDF$meta$datetimestamp)) {
# datetime <- split_title[2]#strsplit(id," - ")[[1]]
# zoteroData()$texts[[1]]
# title <- "NA"
# }
# if (is.null(tempPDF$meta$author)) {
# author <- split_title[1] #strsplit(id," - ")[[1]]
# author <- "NA"
# }
# if (length(datetime)<1) {
# datetime <- strsplit(id," - ")[[2]]
# }
# if (length(name)<1) {
# name <-x$name[i]
# }
title <- lists[1]
n <- length(strsplit(lists[3], " ")[[1]])
if (n==1) {
datetime <- lists[3]
}
else if (n>1) {
datetime <- strsplit(lists[3], " ")[[1]][n]
}
else {
datetime <- ""# tempPDF$meta$datetimestamp
}
abstract <- lists[2]
name <- paste0(lists[5]," ",lists[4])
titles[i] <- title
authors[i] <- name
datetimes[i] <- datetime
names[i] <- name
abstracts[i] <- abstract
text.extract[[i]] <- text.space
# text.extract <- unlist(text.extract)
# }
# else {print("none")}
# print("extractpdfzotero")
# print(i)
# }
}
info <- list(titles=titles, abstracts=abstracts, authors=authors,datetimes=datetimes, text.extract=text.extract)
return(info)
}
#extract <- extractZotero(uris.name,query,query2,len, x)
#extract
extractZotero <- function(links_pdf,query,query2,len, path_to_rdf){#, words){#p1,p2) {
path = links_pdf
# path <- dir.list
query = query
query2 = query2
len <- len
context <- 5
num <- length(path)
text.extract <- list()
#text.full <- vector()
titles <- vector()
authors <- vector()
datetimes <- vector()
z = 1
# uris.name = zotero.rdf[3]
for (i in 1:num) {
uris.name <- paste0(path[i])
#uris.name <- "/Users/olgascrivner/Documents/ITMS/TextMiningZotero/HCSS-Rizzoma/English - first spiral corpus.rdf"
# uris.name <-"/Users/olgascrivner/Documents/MCS/TextMiningClass/Project/TestingFiles/files/137482/Giliker - 2015 - The Influence of Eu and European Human Rights Law .pdf"
tempPDF <- readPDF(control = list(info="-f",text = "-layout"))(elem = list(uri = uris.name),language="en",id="id1")
read.file <- tempPDF$content
read.meta <-tempPDF$meta$id
# year <- tempPDF$meta$datetimestamp
author <- tempPDF$meta$author
texts <- enc2utf8(read.file)
# pat1 <- grep(pattern1, texts, ignore.case = TRUE)
# pat2 <- grepl(pattern2, texts, ignore.case = TRUE)
text.collapse <- paste(texts,collapse=" ")
text.hyphen <- gsub("-\\s+","",text.collapse)
text.space <- gsub("\\s\\s+"," ",text.hyphen)
# pat1 <- grepl(pattern1, text.space, ignore.case = TRUE)#,perl=TRUE)
#if ((patern1 %in% texts) && (pattern2 %in% texts)) {
# if (!is.null(tempPDF$meta$heading)) {
# title <- tempPDF$meta$heading
# author <- tempPDF$meta$author # Alan Ritter ; Colin Cherry ; Bill Dolan
id <- tempPDF$meta$id
# name <- tempPDF$meta$id
# }
# if (is.null(tempPDF$meta$heading)) {
# title <- tempPDF$meta$id
# name <- tempPDF$meta$id
# author <- tempPDF$meta$author
# des <- tempPDF$meta$datetimestamp
# y <- strsplit(as.character(des), "-")
# datetime <- des#y[[1]][1]
des <- tempPDF$meta$datetimestamp
# y <- strsplit(as.character(des), "-")
datetime <-des# y[[1]][1]
# }
# if (length(title)<1) {
# zoteroData()$texts[[1]]
# title <- "NA"
# }
if (length(author)<1) {
author <- strsplit(id," - ")[1]
# author <- "NA"
}
if (length(datetime) < 1) {
datetime <- strsplit(id," - ")[2]
}
# else {
# des <- tempPDF$meta$datetimestamp
# y <- strsplit(as.character(des), "-")
# datetime <- y[[1]][1]
# }
# if (length(name)<1) {
# name <-x$name[i]
# }
# if (sum(pat1)>0) {#&& (sum(pat2)>0)) {
# text.full[z] <-text.space
# text.split <-unlist(strsplit(text.space," "))
# k <- kwic(text.space, query,len,valuetype = "regex")
# z=1
k <- kwic(text.space, query,context,valuetype = "regex")
kpaste <- paste(k$contextPre,k$keyword,k$contextPost,collapse=" ")
if (grepl(query2,kpaste)) {
if (length(k) == 5) {
#
zot <- paste(k$contextPre,k$keyword,k$contextPost,collapse=" ")
zot <- gsub("\\s\\s+"," ",zot)
text.extract[[z]] <- zot
# k <- kwic(text.space, query,len)
# if (!is.na(k)) {
# if (length(k) == 5) {
# zot <- paste(k$contextPre,k$keyword,k$contextPost,collapse=" ")
# zot <- gsub("\\s\\s+"," ",zot)
# titles[z] <- read.meta
text.extract[[z]] <- zot
# text.full[z] <- text.space
z = z+1
titles[i] <- read.meta
authors[i] <- author
datetimes[i] <- datetime
# names[i] <- name
# text.extract[[1]] <-text.space
}
}
}
text.extract <- unlist(text.extract)
info <- list(text.extract=text.extract,titles=titles,datetimes=datetimes, authors=authors)
return(info)
}
# extractZotero <- function(extracts,query,query2,len,words,author,title,date){#p1,p2) {
# extract = extracts
# # wordnum=as.numeric(words)
# author.extract <- author
# title.extract <-title
# date.extract <- date
# query=query
# query2=query2
# # query<- unlist(strsplit(query1," "))[1]
# len <-len
# num <- length(extract)
# text.extract <- list()
# # text.extract[[1]] <-text.space
# # text.full <- vector()
# titles <- vector()
# authors <- vector()
# datetimes <- vector()
# # abstracts <- vector()
# # uris.name <- x
# # #Get all the lines of interest in the file
# # zot.lines <- readLines(uris.name)#zot.file)
# # date.lines <- zot.lines[grep("<dc:date",zot.lines)]
# # author.lines <- zot.lines[grep("<foaf:surname",zot.lines)]
# # abstract.lines <- zot.lines[grep("<dcterms:abstract",zot.lines)]
# # title.lines <- zot.lines[grep("<dc:title>",zot.lines)]
# # date.lines <- gsub("<dc:date>","",date.lines)
# # date.lines <- gsub("</dc:date>","",date.lines)
# # date.lines <- gsub("[a-zA-Z\\s]*","",date.lines)
# # data.lines <- as.integer(date.lines)
# # author.lines <- gsub("<foaf:surname>","",author.lines)
# # author.lines <- gsub("</foaf:surname>","",author.lines)
# # author.lines <- gsub("\\s+","",author.lines)
# # abstract.lines <- gsub("<dcterms:abstract>","",abstract.lines)
# # abstract.lines <- gsub("</dcterms:abstract>","",abstract.lines)
# # abstract.lines <- gsub("\\s+"," ",abstract.lines)
# # title.lines <- gsub("<dc:title>","",title.lines)
# # title.lines <- gsub("</dc:title>","",title.lines)
# # title.lines <- gsub("\\s+"," ",title.lines)
#
# n <- 1
# for (i in 1:num) {
# data <- extract[i]
# # data<- text.extract[1]
# text <- paste(data, collapse = " ")
# text.hyphen <- gsub("-\\s+","",text)
# text.space<- gsub("\\s\\s+"," ",text.hyphen)
# #kwiclist<-vector()
# # if (paths[i]!="") {
# # p <- unlist(strsplit(paths[i],"\\\\|/"))
# #pjoin <- paste0("./",p[1],"/",p[2])
# # if (length(list.files(path=pjoin))>1) {
# # uris <- gsub(".pdf","",paths[i])
# # uris.name <- paste0(uris,".txt")
#
# # if (is.na(file.size(uris.name))==FALSE) {
# # if (file.size(uris.name)>0) {
# # if (length(uris.name)>0) {
# # if (file.exists(uris.name)) {
# #uris.name <- paste0(paths[i])
# # uris.name <- paths[i]
# # text.scan <- scan(uris.name, what="character", sep="\n",blank.lines.skip = TRUE)
# # if (length(text.scan)>0) {
# # data=enc2utf8(text.scan)
# # if (length(data)>0){
# # texts <- paste(data, collapse = " ")
# # uris.name <-"/Users/olgascrivner/Documents/MCS/TextMiningClass/Project/TestingFiles/files/137482/Giliker - 2015 - The Influence of Eu and European Human Rights Law .pdf"
# # tempPDF <- readPDF(control = list(info = "-f",text = "-layout"))(elem = list(uri = uris.name),language = "en",id = "id1")
# # tempPDF <- readPDF(control = list(text = "-layout"))(elem = list(uri = uris.name),language = "en",id = "id1")
# # read.file <- tempPDF$content
# # datetime <- data.lines[i]
# # abstract <- abstract.lines[i]
# # author <- author.lines[i]
# # title <- title.lines[i]#tempPDF$meta$id
# # texts <- enc2utf8(read.file)
# # pat1 <- grep(pattern1, texts, ignore.case = TRUE)
# # pat2 <- grepl(pattern2, texts, ignore.case = TRUE)
# # text.collapse <- paste(texts,collapse=" ")
# # text.collapse <- paste(data,collapse=" ")
# # text.collapse <- paste(texts,collapse=" ")
# # text.hyphen <- gsub("-\\s+","",text.collapse)
# # text.space<- gsub("\\s\\s+"," ",text.hyphen)
# # sent <- segment(text.space,what='sentences')
# #tok<-tokenize(text.space)
# # k <- kwic(text.space, query,len,valuetype="regex")
# # if (length(text.space)>0) {
# # k <- kwic(text.space, query,wordnum,valuetype = "regex")
# k <- kwic(text.space, query,len,valuetype = "regex")
# # k[,3]
# # kpaste <- paste(k$contextPre,k$keyword,k$contextPost,collapse=" ")
# # kpaste <- paste(k[,3],k[,4],k[,5])
# # kpaste[1]
# # query2="Union"
# if (length(k)==5) {
# kpaste <- paste(k[,3],k[,4],k[,5])
# kpaste <- gsub("\\s+"," ",kpaste)
# #for (n in 1:length(kpaste)) {
# # grepl(query2,kpaste[n])
# pat <- grep(query2,kpaste)
# if (length(pat>0)) {
# zots <- kpaste[pat]
# zot <-paste(zots, collapse=" ")
# #q<- grep("european", unlist(strsplit(kpaste[1]," ")),ignore.case = TRUE)
# # zot <-kpaste[n] #paste(k[1,3],k[1,4],k[1,5])
# # paste(k$contextPre,k$keyword,k$contextPost,collapse=" ")
# # zot <- gsub("\\s\\s+"," ",zot)
# # kwiclist[n] <- zot
# # }
# # kwicpaste <- paste(kwiclist,collapse=" ")
# author <- author.extract[i]
# title <- title.extract[i]
# datetime <- date.extract[i]
# # datetime <- data.lines[i]
# # abstract <- abstract.lines[i]
# # author <- author.lines[i]
# # title <- title.lines[i]#tempPDF$meta$id
# text.extract[[n]] <- zot
# # text.full[i] <-text.space
# titles[n] <- title
# authors[n] <-author
# datetimes[n] <- datetime
# # abstracts[i] <- abstract
# text.extract <- unlist(text.extract)
# n=n+1
# # z=z+1
# # }
# # }#else {z=z+1}
# # text.extract <- unlist(text.extract)
# }
# }
# }
# # text.extract <- unlist(text.extract)
# # return(text.extract)
# info <- list(text.extract=text.extract,titles=titles,datetimes=datetimes, authors=authors)#, text.full=text.full,abstracts=abstracts)
# return(info)
# }
# extractZotero <- function(y,query,query2,len,x,words){#p1,p2) {
# path = y
# wordnum=as.numeric(words)
# query=query
# query2=query2
# # query<- unlist(strsplit(query1," "))[1]
# len <-len
# num <-length(path)
# text.extract <- list()
# # text.extract[[1]] <-text.space
# text.full <- vector()
# titles <-vector()
# authors <- vector()
# datetimes <- vector()
# abstracts <- vector()
# uris.name <- x
# # #Get all the lines of interest in the file
# zot.lines <- readLines(uris.name)#zot.file)
# date.lines <- zot.lines[grep("<dc:date",zot.lines)]
# author.lines <- zot.lines[grep("<foaf:surname",zot.lines)]
# abstract.lines <- zot.lines[grep("<dcterms:abstract",zot.lines)]
# date.lines <- gsub("<dc:date>","",date.lines)
# date.lines <- gsub("</dc:date>","",date.lines)
# date.lines <- gsub("[a-zA-Z\\s]*","",date.lines)
# data.lines <- as.integer(date.lines)
# author.lines <- gsub("<foaf:surname>","",author.lines)
# author.lines <- gsub("</foaf:surname>","",author.lines)
# author.lines <-gsub("\\s+","",author.lines)
# abstract.lines <- gsub("<dcterms:abstract>","",abstract.lines)
# abstract.lines <- gsub("</dcterms:abstract>","",abstract.lines)
# abstract.lines <-gsub("\\s+"," ",abstract.lines)
# z=1
# for (i in 1:num) {
# uris.name <- paste0(path[i])
# tempPDF <- readPDF(control = list(info="-f",text = "-layout"))(elem = list(uri = uris.name),language="en",id="id1")
# read.file <- tempPDF$content
# datetime <- data.lines[i]
# abstract <-abstract.lines[i]
# author <- author.lines[i]
# title <- tempPDF$meta$id
# texts <- enc2utf8(read.file)
# # pat1 <- grep(pattern1, texts, ignore.case = TRUE)
# # pat2 <- grepl(pattern2, texts, ignore.case = TRUE)
# text.collapse<-paste(texts,collapse=" ")
# text.hyphen <- gsub("-\\s+","",text.collapse)
# text.space<- gsub("\\s\\s+"," ",text.hyphen)
# # sent <- segment(text.space,what='sentences')
# #tok<-tokenize(text.space)
# # k <- kwic(text.space, query,len,valuetype="regex")
# k <- kwic(text.space, query,wordnum,valuetype="regex")
# kpaste <- paste(k$contextPre,k$keyword,k$contextPost,collapse=" ")
# if (grepl(query2,kpaste)) {
# if (length(k)==5) {
#
# zot <- paste(k$contextPre,k$keyword,k$contextPost,collapse=" ")
# zot <- gsub("\\s\\s+"," ",zot)
# text.extract[[z]] <- zot
# text.full[z] <-text.space
# titles[z] <- title
# authors[z] <-author
# datetimes[z] <- datetime
# abstracts[z] <-abstract
# z=z+1
# }
# }
# }
#
# text.extract <- unlist(text.extract)
# info <- list(text.extract=text.extract,titles=titles,datetimes=datetimes, authors=authors, text.full=text.full,abstracts=abstracts)
# return(info)
# }