Module: Cites

Defined in:
lib/cites.rb

Constant Summary collapse

@@cache_location = 
ENV['HOME'] + '/.cites/cache'

Class Method Summary collapse

Class Method Details

.doi2cit(doi, format = 'text', style = 'apa', locale = 'en-US', cache = true) ⇒ Object

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.



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# File 'lib/cites.rb', line 153

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

.getcache ⇒ Object 



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# File 'lib/cites.rb', line 28

def self.getcache()
	return @@cache_location
end

.getcite(doi, format = 'text', style = 'apa', locale = 'en-US', cache = true) ⇒ Object

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



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# File 'lib/cites.rb', line 53

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

.match(query) ⇒ Object

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}

# Feed into the doi2cit method
Cites.doi2cit(out.map {|i| i['doi']})



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# File 'lib/cites.rb', line 206

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(query, options = {}) ⇒ Object

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}

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)



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# File 'lib/cites.rb', line 271

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(directory) ⇒ Object 



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# File 'lib/cites.rb', line 32

def self.setcache(directory)
	if File.directory?(directory)
		@@cache_location = directory
	else
		puts "Directory path #{directory} does not exist"
	end
end

.show(input) ⇒ Object 



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# File 'lib/cites.rb', line 181

def self.show(input)
	input.each do |iter|
		puts iter.display,"\n"
	end
end