cites 0.0.2

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 7981c7021e09b78536ea2da88b1babc9e6d93f4e
+  data.tar.gz: 57d1535b97db170b66f20581fa20ce5f0fade62b
+SHA512:
+  metadata.gz: 52d393ca56353d91ee08a4967063813e4982dd4a5ccdd18ee400014be19f09ca3df574ac2e14044465bb601ada03aae7fc2972f1042b430afc6320925cc2f0a3
+  data.tar.gz: 74a13bd74953774843af9be7d4a30baeacf5d55c2391201ba02ad3c6800978615f2a1213c2f3cabeefd76d67e10da922f45e542d645f45be9e947030cc12953b

data/bin/crref

@@ -0,0 +1,9 @@
+#!/usr/bin/env ruby
+
+require 'doiref'
+
+# if ARGV[1].length == 0
+	
+# end
+
+puts DOIref.doi2cit(doi=ARGV[0].to_s, format=ARGV[1].to_s, style=ARGV[2].to_s, locale=ARGV[3].to_s)

data/bin/crsearch

@@ -0,0 +1,4 @@
+#!/usr/bin/env ruby
+
+require 'doiref'
+puts DOIref.search(ARGV[0])

data/lib/cites.rb

@@ -0,0 +1,346 @@
+require 'api_cache'
+require 'bibtex'
+require 'digest/sha1'
+require 'httparty'
+require 'json'
+require 'moneta'
+
+def response_ok(code)
+	# See CrossCite documentation http://crosscite.org/cn/
+	case code
+	  when 200
+	    return true
+	  when 204
+	  	raise "The request was OK but there was no metadata available (response code: #{code})"
+	  when 404
+	    raise "The DOI requested doesn't exist (response code: #{code})"
+	  when 406
+	  	raise "Can't serve any requested content type (response code: #{code})"
+	  when 500...600
+	    raise "ZOMG ERROR #{code}"
+  	end
+end
+
+# Cites: The single class (for now) in cites
+
+class Cites
+
+	class << self; attr_accessor :cache_location end
+  	@cache_location =  ENV['HOME'] + '/.cites/cache'
+
+ 	##
+	# Get a single citation in various formats from a DOI
+	#
+	# Args: 
+	# * doi: A DOI
+	# * format: one of rdf-xml, turtle, citeproc-json, text, ris, bibtex, crossref-xml, 
+	# * style: Only used if format='text', e.g., apa, harvard3
+	# * locale: A locale, e.g., en-US
+	# * cache: Should cache be used
+	# 	* true: Try fetcing from cache and store to cache (default)
+	#   * false: Do use cache at all
+	#   * 'flush': Get a fresh response and cache it
+	#
+	def self.getcite(doi, format='text', style='apa', locale='en-US', 
+					 cache=true)
+		formats = {"rdf-xml" => "application/rdf+xml",
+				   "turtle" => "text/turtle",
+				   "citeproc-json" => "application/vnd.citationstyles.csl+json",
+				   "text" => "text/x-bibliography",
+				   "ris" => "application/x-research-info-systems",
+			       "bibtex" => "application/x-bibtex",
+				   "crossref-xml" => "application/vnd.crossref.unixref+xml",
+				   "datacite-xml" => "application/vnd.datacite.datacite+xml"
+		}
+		formatuse = formats[format]
+		if format == 'text'
+			type = "#{formatuse}; style=#{style}; locale=#{locale}"
+		else
+			type = formatuse
+		end
+		doi = 'http://dx.doi.org/' + doi
+
+		if cache == true or cache == 'flush'
+			if cache == true
+				cache_time = 6000
+				msg = "Requested DOI not in cache or is stale, requesting..."
+			elsif cache == 'flush'
+				cache_time = 1
+				msg = "Flushing cache, requesting..."
+			end
+			# Keep cache data valid forever
+			# [todo] - should using cache be reported?
+
+			# Create a cache key based on the DOI requested + the type on
+			# content
+			cache_key = Digest::SHA1.hexdigest("#{doi}-#{type}")
+
+			content = APICache.get(cache_key, :cache => cache_time, 
+								   :valid => :forever, :period => 0,
+								   :timeout => 30) do
+			    puts msg
+			    response = HTTParty.get(doi, :headers => {"Accept" => type})
+			   
+			    # If response code is ok (200) get response body and return
+			    # that from this block. Otherwise an error will be raised.
+			   	begin
+				    if response_ok(response.code)
+				    	content = response.body
+				    end
+					content
+				rescue Exception => e
+					puts e.message
+					puts "Format requested: #{formatuse}"
+					exit
+				end
+			end
+		elsif cache == false
+			puts "Not using cache, requesting..."
+			response = HTTParty.get(doi, :headers => {"Accept" => type})
+			
+			if response_ok(response.code)
+			    content = response.body
+			end
+		else
+			fail "Invalid cache value #{cache}"
+		end
+		# response = HTTParty.get(doi, :headers => {"Accept" => type})
+		if format == 'bibtex'
+			output = BibTeX.parse(content).to_s
+		else
+			output = content
+		end
+		# output.display
+		return output
+	end
+
+	##
+	# Get a citation in various formats from a DOI
+	#
+	# Args: 
+	# * doi: A DOI
+	# * format: one of rdf-xml, turtle, citeproc-json, text, ris, bibtex, crossref-xml, 
+	# * style: Only used if format='text', e.g., apa, harvard3
+	# * locale: A locale, e.g., en-US
+	# * cache: Should cache be used
+	# 	* true: Try fetcing from cache and store to cache (default)
+	#   * false: Do use cache at all
+	#   * 'flush': Get a fresh response and cache it
+	# 
+	# Examples:
+	#     require 'cites'
+	#     Cites.doi2cit('10.1371/journal.pone.0000308')
+	#     Cites.doi2cit('10.1371/journal.pbio.0030427')
+	#     Cites.doi2cit('10.1371/journal.pbio.0030427', 'crossref-xml')
+	#     Cites.doi2cit('10.1371/journal.pbio.0030427', 'bibtex')
+	#     Cites.doi2cit('10.1371/journal.pbio.0030427', 'ris')
+	#
+	#     out = Cites.doi2cit(['10.1371/journal.pone.0000308','10.1371/journal.pbio.0030427','10.1371/journal.pone.0084549'], 'bibtex')
+	# 	  Cites.show(out)
+	#
+	# Returns an array of citation content. The structure of the content will 
+	# depend on the format requested.
+	#
+	def self.doi2cit(doi, format='text', style='apa', locale='en-US', 
+					 cache=true)
+		if doi.class == String
+			doi = [doi]
+		elsif doi.class == Array
+			doi = doi
+		else
+			fail 'doi must be one of String or Array class'
+		end		
+
+		cc = []
+		doi.each do |iter|
+			# if iter.include?('http://')
+			# 	iter = iter.sub('http://dx.doi.org/', '')
+			# else
+			# 	nil
+			# end
+			# cc << Cites.getcite(doi=iter, format=format, style=style, locale=locale)
+			content = Cites.getcite(iter, format, style, locale, cache)
+			if format == 'citeproc-json'
+				content = JSON.parse(content)
+			end
+			cc << content
+		end
+
+		return cc
+	end
+
+	def self.show(input)
+		input.each do |iter|
+			puts iter.display,"\n"
+		end
+	end
+
+	##
+	# match: Look for matches to free-form citations to DOIs for an object (article, book, etc). in CrossRef
+	#
+	# Args: 
+	# * query: A free form string of terms.
+	#
+	# Examples:
+	#     require 'cites'
+	#     Cites.match('Piwowar sharing data increases citation PLOS')
+	#     Cites.match('boettiger Modeling stabilizing selection')
+	# 	  Cites.match(['Piwowar sharing data increases citation PLOS', 'boettiger Modeling stabilizing selection'])
+	# 	  out = Cites.match(['piwowar sharing data increases citation PLOS', 
+	# 	  				'boettiger Modeling stabilizing selection',
+	# 					'priem Using social media to explore scholarly impact',
+	#					'fenner Peroxisome ligands for the treatment of breast cancer'])
+	# 	  out.map {|i| i['doi']}
+	#     
+	#     # Feed into the doi2cit method
+	#     Cites.doi2cit(out.map {|i| i['doi']})
+	def self.match(query)
+		if query.class == String
+			query = [query]
+		elsif query.class == Array
+			query = query
+		else
+			fail 'query must be one of String or Array class'
+		end
+		url = "http://search.labs.crossref.org/links"
+		out = 
+			HTTParty.post(url, 
+				:body => query.to_json, 
+				:headers => { "Content-Type" => "application/json"}
+			)
+		if out.code == 200
+			nil
+		else
+			puts "ERROR #{out.code}"
+		end
+		tt = out['results']
+		coll = []
+		tt.each do |item|
+			gg = item['doi']
+			if gg!=nil
+				gg = gg.sub('http://dx.doi.org/', '')
+			end
+			coll << 
+			{
+				'match'=>item['match'], 
+				'doi'=>gg,
+				'text'=>item['text']
+			}
+		end
+        # coll.display
+        return coll
+	end
+
+	##
+	# search: Search for scholary objects in CrossRef
+	#
+	# Args: 
+	# * query: A single or many terms (in an array). This function performs 
+	#          a single search if multiple terms are supplied. If this is 
+	#          supplied, the doi arg is ignored. 
+	# * doi: A DOI to search for. If this is supplied, query is ignored.
+	# * page: Page number to return.
+	# * rows: Number of records to return
+	# * sort: Sort (logical)
+	# * year: Year to restrict search to.
+	#
+	# Examples:
+	#     require 'cites'
+	#     Cites.search(query='renear')
+	#     Cites.search('palmer')
+	# 	  Cites.search(['ecology', 'microbiology'])
+	# 	  out = Cites.search(['renear', 'science', 'smith birds'])
+	# 	  out.map {|i| i['doi']}
+	# 	  
+	# 	  Cites.search('science', :rows => 5)
+	# 	  
+	#     
+	#     # Feed into the doi2cit method
+	#     out = Cites.search('palmer')
+	#     g = Cites.doi2cit(out[1]['doi'], format='bibtex')
+	#     Cites.show(g)
+	def self.search(query, options = {})
+		defaults = {:doi => nil, :page => nil, :rows => 10, 
+			:sort => nil, :year => nil, :header => true, 
+			:fields => ["doi","normalizedScore","title","year"]}
+		# defaults = {"query" => 'ecology', "doi" => nil, "page" => nil, "rows" => 10, 
+		# 	"sort" => nil, "year" => nil, "header" => true, 
+		# 	"fields" => ["doi","normalizedScore","title","year"]}
+		options = defaults.merge(options)
+		fields = options[:fields]
+		options.delete(:fields)
+
+		if query.class == String
+			nil
+		elsif query.class == Array
+			query = query.join('+')
+		else
+			fail 'query must be one of String or Array class'
+		end
+
+		url = "http://search.labs.crossref.org/dois"
+		
+		if options[:doi] == nil
+			# [fimxe] - looks like "rows" option isn't working like it's supposed to
+	        args = {"q" => query, "page" => options[:page], "rows" => options[:rows],
+	        	"sort" => options[:sort], "year" => options[:year], "header" => options[:header]}
+	        args = args.delete_if { |k, v| v.nil? }
+	        out = HTTParty.get(url, :query => args)
+	        if out.code == 200
+				nil
+			else
+				puts "ERROR #{out.code}"
+			end
+
+			items = out['items']
+	        coll = []
+			items.each do |item|
+				gg = item.reject { |key,_| !fields.include? key }
+				coll << gg
+			end
+			
+			if options[:header] == true
+				out = out.to_hash
+	        	meta = out.except('items')
+	        	coll = {'meta' => meta, 'items' => coll}
+	        else
+	        	nil
+	        end
+		else
+			nil
+		end
+		return coll
+	end
+	
+	##
+	# setcache: Search for scholary objects in CrossRef
+	#
+	# Args: 
+	# * query: A free form string of terms.
+	#
+	# Examples:
+	#     require 'cites'
+	#     Cites.search(query='renear')
+	#     Cites.search('palmer')
+	# 	  Cites.search(['ecology', 'microbiology'])
+	# 	  out = Cites.search(['renear', 'science', 'smith birds'])
+	# 	  out.map {|i| i['doi']}
+	#     
+	#     # Feed into the doi2cit method
+	#     out = Cites.search('palmer')
+	#     g = Cites.doi2cit(out[1]['doi'], format='bibtex')
+	#     Cites.show(g)	
+end
+
+class Hash
+	def except(which)
+		self.tap{ |h| h.delete(which) }
+	end
+end
+
+# [fixme] - Setting the cache_location should really be handled by a method
+# but since all the methods in class Cites are static setting the cache
+# has to done manually in each static method (because we don't know which
+# is called first) or then we would need a propers initializer.
+
+APICache.store = Moneta.new(:File, dir: Cites::cache_location)

metadata

@@ -0,0 +1,133 @@
+--- !ruby/object:Gem::Specification
+name: cites
+version: !ruby/object:Gem::Version
+  version: 0.0.2
+platform: ruby
+authors:
+- Scott Chamberlain
+- Joona Lehtomäki
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-02-22 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bibtex-ruby
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: httparty
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.12'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.12'
+- !ruby/object:Gem::Dependency
+  name: thor
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.18'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.18'
+- !ruby/object:Gem::Dependency
+  name: json
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
+- !ruby/object:Gem::Dependency
+  name: api_cache
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.2'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.2'
+- !ruby/object:Gem::Dependency
+  name: moneta
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
+description: Search for articles, and get citations from DOIs
+email: myrmecocystus@gmail.com
+executables:
+- crsearch
+- crref
+extensions: []
+extra_rdoc_files: []
+files:
+- bin/crref
+- bin/crsearch
+- lib/cites.rb
+homepage: http://github.com/sckott/cites
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.0
+signing_key: 
+specification_version: 4
+summary: Gets citations from DOIs
+test_files: []