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I have nearly one thousand pdf journal articles in a folder. I need to text mine on all article's abstracts from the whole folder. Now I am doing the following:

dest <- "~/A1.pdf"

# set path to pdftotxt.exe and convert pdf to text
exe <- "C:/Program Files (x86)/xpdfbin-win-3.03/bin32/pdftotext.exe"
system(paste("\"", exe, "\" \"", dest, "\"", sep = ""), wait = F)

# get txt-file name and open it
filetxt <- sub(".pdf", ".txt", dest)
shell.exec(filetxt)

By this, I am converting one pdf file to one .txt file and then copying the abstract in another .txt file and compile it manually. This work is troublesome.

How can I read all individual articles from the folder and convert them into .txt file which contain only the abstract from each article. It can be done by limiting the content between ABSTRACT and INTRODUCTION in each article; but I am not able to do so. Any help is appreciated.

Elin
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S Das
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  • This is not really an R question. You need a utility to extract text from pdf documents and that is NOT a design goal of R. My vote to close is based on the fact that this is an implicit call for such a tool. – IRTFM Jan 30 '14 at 02:33
  • Not totally a R question; but Ben's reply worked a lot for me. Thanks. – S Das Jan 30 '14 at 06:08
  • possible duplicate of [How to export pdf form fields to xml automatically](http://stackoverflow.com/questions/21009608/how-to-export-pdf-form-fields-to-xml-automatically) – James Kingsbery Jan 30 '14 at 17:44

2 Answers2

22

Yes, not really an R question as IShouldBuyABoat notes, but something that R can do with only minor contortions...

Use R to convert PDF files to txt files...

# folder with 1000s of PDFs
dest <- "C:\\Users\\Desktop"

# make a vector of PDF file names
myfiles <- list.files(path = dest, pattern = "pdf",  full.names = TRUE)

# convert each PDF file that is named in the vector into a text file 
# text file is created in the same directory as the PDFs
# note that my pdftotext.exe is in a different location to yours
lapply(myfiles, function(i) system(paste('"C:/Program Files/xpdf/bin64/pdftotext.exe"', 
             paste0('"', i, '"')), wait = FALSE) )

Extract only abstracts from txt files...

# if you just want the abstracts, we can use regex to extract that part of
# each txt file, Assumes that the abstract is always between the words 'Abstract'
# and 'Introduction'
mytxtfiles <- list.files(path = dest, pattern = "txt",  full.names = TRUE)
abstracts <- lapply(mytxtfiles, function(i) {
  j <- paste0(scan(i, what = character()), collapse = " ")
  regmatches(j, gregexpr("(?<=Abstract).*?(?=Introduction)", j, perl=TRUE))
})

Write abstracts into separate txt files...

# write abstracts as txt files 
# (or use them in the list for whatever you want to do next)
lapply(1:length(abstracts),  function(i) write.table(abstracts[i], file=paste(mytxtfiles[i], "abstract", "txt", sep="."), quote = FALSE, row.names = FALSE, col.names = FALSE, eol = " " ))

And now you're ready to do some text mining on the abstracts.

Ben
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8

We can use library pdftools

library(pdftools)
# you can use an url or a path
pdf_url <- "https://cran.r-project.org/web/packages/pdftools/pdftools.pdf"

# `pdf_text` converts it to a list
list_output <- pdftools::pdf_text('https://cran.r-project.org/web/packages/pdftools/pdftools.pdf')

# you get an element by page
length(list_output) # 5 elements for a 5 page pdf

# let's print the 5th
cat(list_output[[5]])
# Index
# pdf_attachments (pdf_info), 2
# pdf_convert (pdf_render_page), 3
# pdf_fonts (pdf_info), 2
# pdf_info, 2, 3
# pdf_render_page, 2, 3
# pdf_text, 2
# pdf_text (pdf_info), 2
# pdf_toc (pdf_info), 2
# pdftools (pdf_info), 2
# poppler_config (pdf_render_page), 3
# render (pdf_render_page), 3
# suppressMessages, 2
# 5

To extract abstracts from articles, OP chooses to extract content between Abstract and Introduction.

We'll take a list of CRAN pdfs and extract the author(s) as the text between Author and Maintainer (I handpicked a few that had a compatible format).

For this we loop on our url list then extract the content, collapse all texts into one for each pdf, and then extract the relevant info with regex.

urls <- c(pdftools = "https://cran.r-project.org/web/packages/pdftools/pdftools.pdf",
          Rcpp     = "https://cran.r-project.org/web/packages/Rcpp/Rcpp.pdf",
          jpeg     = "https://cran.r-project.org/web/packages/jpeg/jpeg.pdf")

lapply(urls,function(url){
  list_output <- pdftools::pdf_text(url)
  text_output <- gsub('(\\s|\r|\n)+',' ',paste(unlist(list_output),collapse=" "))
  trimws(regmatches(text_output, gregexpr("(?<=Author).*?(?=Maintainer)", text_output, perl=TRUE))[[1]][1])
})

# $pdftools
# [1] "Jeroen Ooms"
# 
# $Rcpp
# [1] "Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou, Nathan Russell, Douglas Bates and John Chambers"
# 
# $jpeg
# [1] "Simon Urbanek <Simon.Urbanek@r-project.org>"
moodymudskipper
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