biburi 0.0.1

checksums.yaml

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data/.gitignore

@@ -0,0 +1,17 @@
+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/.travis.yml

@@ -0,0 +1,6 @@
+language: ruby
+rvm:
+  - 2.0.0
+  - 1.9.3
+notifications:
+  email: false

data/CHANGELOG.mediawiki

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+= BibURI Changelog =
+
+* 0.0.1 (October 2, 2013)
+** First release, with basic support for DOIs using the CrossRef API.

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in biburi.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2013 Gaurav Vaidya
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# BibURI
+
+[![Gem Version](https://badge.fury.io/rb/biburi.png)](http://badge.fury.io/rb/biburi)
+[![Continuous Integration Status][1]][2]
+[![Coverage Status][3]][4]
+[![Dependency Status][5]][6]
+
+This is a gem to extract BibTeX information for URIs which refer to bibliographic
+resources, such as DOIs, Biodiversity Heritage Library links, and others.
+
+Currently, BibURI supports the following types of data:
+
+ - DOIs (via CrossRef)
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'biburi'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install biburi
+
+## Usage
+
+BibURI mainly works out of a single method:
+
+    require 'biburi'
+
+    results = BibURI::lookup('doi:10.1038/171737a0')
+
+Full documentation is [available online at RubyDoc.org](http://rubydoc.org/github/gaurav/biburi/master/frames).
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new pull request
+
+[1]: https://secure.travis-ci.org/gaurav/biburi.png
+[2]: http://travis-ci.org/gaurav/biburi
+[3]: https://coveralls.io/repos/gaurav/biburi/badge.png?branch=master
+[4]: https://coveralls.io/r/gaurav/biburi?branch=master
+[5]: https://gemnasium.com/gaurav/biburi.png
+[6]: https://gemnasium.com/gaurav/biburi

data/Rakefile

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+require 'bundler/gem_tasks'
+
+require 'rake'
+
+# Set up Rspec
+require 'rspec/core/rake_task'
+
+# Allow testing using spec
+RSpec::Core::RakeTask.new(:spec)
+task :default => :spec
+task :test => :spec

data/biburi.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'biburi/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "biburi"
+  spec.version       = BibURI::VERSION
+  spec.authors       = ["Gaurav Vaidya"]
+  spec.email         = ["gaurav@ggvaidya.com"]
+  spec.description   = %q{Find the BibTeX information when your citation has an identifier}
+  spec.summary       = %q{URI to BibTeX lookup gem}
+  spec.homepage      = "http://github.com/gaurav/biburi"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "rake"
+  spec.add_development_dependency "rspec"
+  spec.add_development_dependency "rspec-core"
+  spec.add_development_dependency "coveralls"
+
+  spec.add_runtime_dependency 'bibtex-ruby', '~> 2.0'
+end

data/lib/biburi/driver/doi.rb

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+# A driver to read BibTeX for DOI via CrossRef's
+# public API: http://search.crossref.org/help/api
+#
+# Author:: Gaurav Vaidya
+# Copyright:: Copyright (c) 2013 Gaurav Vaidya
+# License:: MIT
+
+require 'biburi'
+require 'biburi/driver'
+require 'net/http'
+require 'json'
+require 'bibtex'
+ 
+# For CGI::parse to make sense of COinS
+require 'cgi'
+
+# This driver provides information in BibTeX on a DOI by
+# querying CrossRef's metadata search API. 
+
+module BibURI::Driver::DOI
+  include BibURI::Driver
+
+  # We support an identifier if we can make them look
+  # canonical.
+  def self.supported?(id)
+    canonical = BibURI::Driver::DOI::canonical(id)
+    return !(canonical.nil?)
+  end
+
+  # The canonical form of a DOI can be one of
+  # - http://dx.doi.org/10.1234/abcd-5678
+  # - doi:10.1234/abcd-5678
+  def self.canonical(id)
+    # doi:10.1234/abcd-5678
+    match = id.match(/^doi:(.*)$/i)
+    if match
+        return "http://dx.doi.org/" + match[1]
+    end
+
+    # http://dx.doi.org/10.1234/abcd-5678
+    match = id.match(/^http:\/\/dx\.doi\.org\/(.*)$/i)
+    if match
+        return "http://dx.doi.org/" + match[1]
+    end
+
+    # If no match, return nil.
+    nil
+  end
+
+  # Returns a list of parsed values with
+  # BibTeX names by looking up the provided id.
+  def self.lookup(id)
+    # Calculate the canonical identifier.
+    canonical_id = canonical(id)
+    if canonical_id.nil? then
+        return nil
+    end
+
+    # Search for the DOI on CrossRef.
+    crossref_url = "http://search.crossref.org/dois?" + 
+        URI.encode_www_form([["q", canonical_id]])
+
+    content = Net::HTTP.get(URI(crossref_url))
+    as_json = JSON.parse(content)
+
+    # No values returned? Returned nil so that the search
+    # can continue.
+    if as_json.length == 0 then
+        return nil
+    end
+
+    # Go through results and format them as BibTeX::Entry.
+    # We support both 
+    results = [] unless block_given?
+    as_json.each do |match|
+        # Skip non-identical DOI matches.
+        next unless match['doi'].downcase == canonical_id.downcase
+
+        # Create a BibTeX entry to store these values.
+        bibentry = BibTeX::Entry.new
+
+        # Set identifiers so we know where this came from.
+        bibentry[:url] = canonical_id
+        bibentry[:doi] = canonical_id.match(/^http:\/\/dx\.doi\.org\/(.*)$/)[1]
+
+        # CrossRef itself provides a full citation and year.
+        if match.key?('fullCitation') then
+            bibentry[:title] = match['fullCitation']
+        end
+
+        if match.key?('year') then
+            bibentry[:year] = match['year'] 
+        end
+        
+        # If we have COinS data, we have a lot more data.
+        if match.key?('coins') then
+            coins_kv = CGI::parse(match['coins'])
+            metadata = {}
+            coins_kv.each do |key, val|
+                if val.length == 1 then
+                    metadata[key] = val[0]
+                else
+                    metadata[key] = val
+                end
+            end
+
+            # COinS values are explained at http://ocoins.info/cobg.html
+            # Some values need to be handled separately.
+            
+            # Journal title: title, jtitle
+            journal_title = metadata['rft.title']       # The old-style journal title.
+            journal_title ||= metadata['rft.stitle']    # An abbreviated title.
+            journal_title ||= metadata['rft.jtitle']    # Complete title.
+            bibentry[:journal] = journal_title
+
+            # Pages: spage, epage
+            pages = metadata['rft.pages']       # If only pages are provided
+            pages ||= metadata['rft.spage'] + "-" + metadata['rft.epage']
+                                            # If we have start and end pages
+            bibentry[:pages] = pages
+
+            # Authors are all in 'rft.au'
+            authors = BibTeX::Names.new
+            metadata['rft.au'].each do |author|
+                authors.add(BibTeX::Name.parse(author))
+            end
+            bibentry[:author] = authors
+
+            # COinS supports some types
+            genre = metadata['rft.genre']
+            if genre == 'article' then
+                bibentry.type = "article"
+            elsif genre == 'proceeding' || genre == 'conference' then
+                bibentry.type = "inproceeding"
+            end 
+
+            # Map remaining fields to BibTeX.
+            standard_mappings = {
+                "rft.atitle" =>     "title",
+                "rft.date" =>       "date",
+                "rft.volume" =>     "volume",
+                "rft.issue" =>      "number",
+                "rft.artnum" =>     "article_number",
+                "rft.issn" =>       "issn",
+                "rft.eissn" =>      "eissn",
+                "rft.isbn" =>       "isbn",
+                "rft.coden" =>      "CODEN",
+                "rft.sici" =>       "SICI",
+                "rft.chron" =>      "chronology",
+                "rft.ssn" =>        "season",
+                "rft.quarter" =>    "quarter",
+                "rft.part" =>       "part",
+            }
+            standard_mappings.keys.each do |field|
+                if metadata.key?(field) then
+                    bibentry[standard_mappings[field]] = metadata[field]
+                end
+            end
+        end
+
+        # Yield values or return array.
+        if block_given? then
+            yield(bibentry)
+        else
+            results.push(bibentry)
+        end 
+    end
+
+    # If we built an array, return it.
+    unless block_given? then
+        return results
+    end
+  end
+end

data/lib/biburi/driver.rb

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+# All lookup types implement this mixin, which
+# defines the interface lookups use to talk to 
+# the main controller.
+# 
+# Author:: Gaurav Vaidya
+# Copyright:: Copyright (c) 2013 Gaurav Vaidya
+# License:: MIT
+
+require 'biburi'
+
+module BibURI::Driver
+  # An array of drivers in order of preference. The
+  # first driver which supports the ID and which
+  # provides a valid lookup will stop processing.
+  @@drivers = Array.new
+
+  # Return a list of drivers.
+  def self.drivers
+    return @@drivers
+  end
+
+  # Returns true if this Lookup supports this id.
+  def self.supported?(id)
+    raise NotImplementedError
+  end
+
+  # Returns a canonical form of the identifier,
+  # preferably as a URL.
+  def self.canonical(id)
+    raise NotImplementedError
+  end
+
+  # Returns a dictionary of parsed values with
+  # BibTeX names by looking up the provided id.
+  def self.lookup(id)
+    raise NotImplementedError
+  end
+ 
+end
+
+# Load all the drivers, and add them to BibURI::Driver
+# in order of preference.
+require "biburi/driver/doi"
+
+module BibURI::Driver
+  @@drivers = [
+    BibURI::Driver::DOI
+  ]
+end
+

data/lib/biburi/version.rb

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+module BibURI
+  VERSION = "0.0.1"
+end

data/lib/biburi.rb

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+# BibURI looks up URIs refering to citations (such as DOIs,
+# Mendeley or Zotero URLs, and so on) and extracts the BibTeX
+# data associated with them.
+#
+# Author:: Gaurav Vaidya
+# Copyright:: Copyright (c) 2013 Gaurav Vaidya
+
+require 'biburi/version'
+
+module BibURI
+  # Returns a list of all drivers.
+  def self.drivers
+    return BibURI::Driver::drivers
+  end
+
+  # Query all the drivers in the order
+  # they are recorded in; return the results
+  # for the first driver.
+  def self.lookup(id)
+    self.drivers.each do |driver|
+      if driver.supported?(id) then
+        results = driver.lookup(id)  
+        if !results.nil? then
+          return results
+        end
+      end
+    end
+
+    return nil
+  end
+end
+
+require 'biburi/driver'

data/spec/biburi_spec.rb

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+require_relative 'spec_helper'
+
+describe BibURI do
+    describe "VERSION" do
+        it "should exist" do
+            version = BibURI::VERSION
+        end
+    end
+
+    describe "drivers" do
+        it "should have multiple drivers" do
+            drivers = BibURI::drivers
+
+            expect(drivers).to be_an_instance_of(Array)
+            expect(drivers.length).to be > 0
+        end
+    end
+
+    describe "lookup" do
+        it "should be able to do simple lookups" do
+            queries = {
+                "doi:10.1038/171737a0" => [
+                    BibTeX::Entry.new(
+                        :url => "http://dx.doi.org/10.1038/171737a0", 
+                        :doi => "10.1038/171737a0",
+                        :title => "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid, year = 1953, journal = Nature, pages = 737-738", 
+                        :author => "WATSON, J. D. and CRICK, F. H. C.", 
+                        :date => "1953",
+                        :volume => "171", 
+                        :number => "4356"
+                    )
+                ],
+                "http://dx.doi.org/10.1111/j.1096-0031.2010.00329.x" => [
+                    BibTeX::Entry.new({
+                        "url" => "http://dx.doi.org/10.1111/j.1096-0031.2010.00329.x",
+                        "doi" => "10.1111/j.1096-0031.2010.00329.x",
+                        "title" => "SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information",
+                        "year" => "2011",
+                        "journal" => "Cladistics", 
+                        "pages" => "171-180",
+                        "author" => "Vaidya, Gaurav and Lohman, David J. and Meier, Rudolf",
+                        "date" => "2011",
+                        "volume" => "27", 
+                        "number" => "2"
+                    })
+                ]
+            }
+
+            queries.keys.each do |query|
+                result = BibURI::lookup(query)
+
+                expect(result.to_s).to eq(queries[query].to_s)
+            end 
+        end
+    end
+end
+
+describe BibURI::Driver do
+    it "should return NotImplementedError for all methods" do
+        expect { BibURI::Driver::supported?("doi:10.1038/171737a0") }.to raise_error(NotImplementedError)
+        expect { BibURI::Driver::canonical("doi:10.1038/171737a0") }.to raise_error(NotImplementedError)
+        expect { BibURI::Driver::lookup("doi:10.1038/171737a0") }.to raise_error(NotImplementedError)
+    end
+end

data/spec/doi_spec.rb

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+require_relative 'spec_helper'
+
+describe BibURI::Driver::DOI do
+    describe "supported" do
+        it "should support real DOIs" do
+            real_dois = [
+                "doi:10.1111/j.1529-8817.2010.00939.x",
+                "doi:10.1038/171737a0",
+                "DOI:10.1038/171737A0",
+                "http://dx.doi.org/doi:10.1038/171737a0"
+            ]
+
+            real_dois.each do |doi|
+                expect(BibURI::Driver::DOI::supported?(doi)).to be_true;
+            end
+        end
+
+        it "should not support incorrect DOIs" do
+            incorrect_dois = [
+                "10.1111/j.1529-8817.2010.00939.x",
+                "dxoi:10.1038/171737a0",
+                "https://dx.doi.org/doi:10.1038/171737a0"
+            ]
+
+            incorrect_dois.each do |doi|
+                expect(BibURI::Driver::DOI::supported?(doi)).to be_false;
+            end
+
+        end
+    end
+
+    describe "canonical" do
+        it "should canonicalize DOIs correctly" do
+            canonicalize = {
+                "doi:10.1038/171737a0" => "http://dx.doi.org/10.1038/171737a0",
+                "http://dx.doi.org/10.1038/171737a0" => "http://dx.doi.org/10.1038/171737a0"
+            }
+
+            canonicalize.keys.each do |value|
+                expected = canonicalize[value]
+                expect(BibURI::Driver::DOI::canonical(value)).to eq(expected)
+            end
+        end
+    end
+
+    describe "lookup" do
+        it "should be able to download information on some DOIs" do
+            queries = {
+                "doi:10.1038/171737a0" => [
+                    BibTeX::Entry.new(
+                        :url => "http://dx.doi.org/10.1038/171737a0", 
+                        :doi => "10.1038/171737a0",
+                        :title => "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid, year = 1953, journal = Nature, pages = 737-738", 
+                        :author => "WATSON, J. D. and CRICK, F. H. C.", 
+                        :date => "1953",
+                        :volume => "171", 
+                        :number => "4356"
+                    )
+                ],
+                "http://dx.doi.org/10.1111/j.1096-0031.2010.00329.x" => [
+                    BibTeX::Entry.new({
+                        "url" => "http://dx.doi.org/10.1111/j.1096-0031.2010.00329.x",
+                        "doi" => "10.1111/j.1096-0031.2010.00329.x",
+                        "title" => "SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information",
+                        "year" => "2011",
+                        "journal" => "Cladistics", 
+                        "pages" => "171-180",
+                        "author" => "Vaidya, Gaurav and Lohman, David J. and Meier, Rudolf",
+                        "date" => "2011",
+                        "volume" => "27", 
+                        "number" => "2"
+                    })
+                ]
+            }
+
+            queries.keys.each do |query|
+                result = BibURI::Driver::DOI::lookup(query)
+
+                expect(result.to_s).to eq(queries[query].to_s)
+            end 
+        end
+    end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,5 @@
+# Start coverage tracking.
+require 'coveralls'
+Coveralls.wear!
+
+require_relative '../lib/biburi'

metadata

@@ -0,0 +1,146 @@
+--- !ruby/object:Gem::Specification
+name: biburi
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Gaurav Vaidya
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-10-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec-core
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bibtex-ruby
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.0'
+description: Find the BibTeX information when your citation has an identifier
+email:
+- gaurav@ggvaidya.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- .travis.yml
+- CHANGELOG.mediawiki
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- biburi.gemspec
+- lib/biburi.rb
+- lib/biburi/driver.rb
+- lib/biburi/driver/doi.rb
+- lib/biburi/version.rb
+- spec/biburi_spec.rb
+- spec/doi_spec.rb
+- spec/spec_helper.rb
+homepage: http://github.com/gaurav/biburi
+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: 2.0.0
+signing_key: 
+specification_version: 4
+summary: URI to BibTeX lookup gem
+test_files:
+- spec/biburi_spec.rb
+- spec/doi_spec.rb
+- spec/spec_helper.rb