searchTerm2pdf.rb

#!/usr/bin/env ruby 

# == Synopsis 
#   This program tries to download a PDF file for the given search term
#
# == Required GEMS
#     mechanize (0.9.3)
#     bio (1.3.0)
#     socksify (1.1.0) (if you plan on using SOCKS)
#
# == Examples
#     searchTerm2pdf.rb 'Torarinsson E[Author]' > list
#     NB! The output list is just like a .csv file except that we use '|' and not ',' as a separator
#
#   Other examples:
#    This example downloads through SOCKS, here we are using a localhost connection through port 9999
#    Meaning that you can ssh to your some server you have access to that can access some PDFs that you cannot, f.ex. your University
#    This is done with this command: ssh -D 9999 username@server in another terminal
#    To use SOCKS call the program with the server and the port, in this case 127.0.0.1 and 9999
#     searchTerm2pdf.rb 'Torarinsson E[Author]' 127.0.0.1 9999
#
# == Usage 
#    searchTerm2pdf.rb search-term [server] [port] > list
#
# == Author
#   Bio-geeks (adapted a script by Edoardo "Dado" Marcora, Ph.D.)
#   <http://bio-geeks.com>
#
# == Copyright
#   Copyright (c) 2009 Bio-geeks. Licensed under the MIT License:
#   http://www.opensource.org/licenses/mit-license.php

require 'rubygems'
require 'bio'
require 'date'
require 'pdfetch.rb'
require 'rdoc/usage'

#query = '(Lindow M[Author] OR Torarinsson E[Author] OR Lindgreen S[Author] OR Marstrand T[Author]) AND (1998/01/01[PDAT]:3000[PDAT])'
#query = "Torarinsson"
query = ARGV[0]

if (query.nil?)
  RDoc::usage() #exits app
end

ids = Bio::PubMed.esearch(query, {'retmax' => 5000})
warn "Found #{ids.length} articles matching your search term: #{query}"

if ids.length > 0
  puts "pubmedid|first_author|last_author|journal|publication_type,title|affiliations|doi|mesh|year|abstract"
else
  warn "Couldn't find any articles matching your search term"  
end

fetcher = Fetch.new()
server = ARGV[1]
port = ARGV[2]
if (!server.nil? && !port.nil?)
  fetcher.useSocks(server,port)
end

ids.reverse.each do |pubmedid|
  manuscript = Bio::PubMed.efetch(pubmedid)
  m = Bio::MEDLINE.new(manuscript.first)
  
  pt = "Original research"
  allpt=m.publication_type.join("")
  pt = "Review" if allpt =~ /review/i
  pt = "Comment" if allpt =~ /comment/i
  pt = "News" if allpt =~ /news/i
    
  pubmedid = m.pmid
  first_author = m.authors.first
  last_author = m.authors.last
  journal = m.journal
  publication_type = pt
  title = m.title
  affiliations = m.affiliations.join(';').gsub(/\-/, "")
  doi = m.doi
  mesh = m.mesh.join(", ")
  year = m.year
  abstract = m.abstract
  
  puts "#{pubmedid}|#{first_author}|#{last_author}|#{journal}|#{publication_type}|#{title}|#{affiliations}|#{doi}|#{mesh}|#{year}|#{abstract}"
  
  warn "Attempting to fetch the PDF file for the following article:
        Title: #{title}
        First author: #{first_author}
        Last author: #{last_author}
        Journal: #{journal}"
        
  fetcher.get(pubmedid)
  
end