paper_metadata 0.0.1

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+*.sublime-project
+*.sublime-workspace
+

data/Gemfile

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

data/LICENSE.txt

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+Copyright (c) 2013 Jure Triglav
+
+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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+# PaperMetadata
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'paper_metadata'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install paper_metadata
+
+## Usage
+
+TODO: Write usage instructions here
+
+## 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

data/Rakefile

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+require "bundler/gem_tasks"
+
+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+  t.libs << 'test'
+end
+
+desc "Run tests"
+task :default => :test

data/lib/paper_metadata.rb

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+require 'paper_metadata/version'
+require 'nokogiri'
+require 'net/http'
+require 'open-uri'
+require 'pry'
+
+module PaperMetadata
+  class << self
+    attr_accessor :doi_username
+
+    def doi_username
+      raise "PaperMetadata needs the DOI username to work with CrossRef API" unless @doi_username
+      @doi_username
+    end
+
+    def metadata_for(identifier)
+      if identifier =~ /^arxiv\:/i
+        metadata_for_arxiv(identifier)
+      elsif identifier =~ /^doi\:/i
+        metadata_for_doi(identifier)
+      end
+    end
+
+    def metadata_for_doi(doi)
+      doc = Nokogiri::XML(open("http://www.crossref.org/openurl/?id=doi:#{doi}&noredirect=true&pid=#{PaperMetadata.doi_username}&format=unixref"))
+      paper = Hash.new
+
+      if doc.xpath("//titles/title").first
+        paper[:volume] = doc.xpath("//journal_issue/journal_volume/volume").inner_html.to_s
+        paper[:isssue] = doc.xpath("//journal_issue/issue").inner_html.to_s
+        paper[:first_page] = doc.xpath("//pages/first_page").inner_html.to_s
+        paper[:last_page] = doc.xpath("//pages/last_page").inner_html.to_s
+        paper[:title] = doc.xpath("//titles/title").inner_html.to_s
+        paper[:authors] = doc.xpath("//contributors/person_name").
+          map{ |author| author.content.strip}
+
+        paper[:authors] = paper[:authors].map do |author|
+          author.gsub(/\s+/, ' ')
+        end.join(', ')
+
+        paper[:journal] = doc.xpath("//abbrev_title").inner_html + " " +
+          doc.xpath("//journal_issue/publication_date/year").first.inner_html
+        paper[:resource] = doc.xpath("//journal_article/doi_data/resource").inner_html
+      else
+        paper[:status] = :NODOI
+      end
+      paper
+    end
+
+    def metadata_for_arxiv(identifier)
+      identifier.gsub!(/^arXiv\:/i, '')
+      url = URI.parse("http://export.arxiv.org/api/query?search_query=#{identifier}&start=0&max_results=1")
+      res = Net::HTTP.get_response(url)
+      doc = Nokogiri::XML(res.body)
+      doc.remove_namespaces!
+      paper = Hash.new
+      if entry = doc.xpath("//entry").first
+        paper[:title] = entry.xpath('title').text
+        paper[:author] = entry.xpath('author').text.strip
+        paper[:id] = entry.xpath('id').text
+        paper[:updated] = entry.xpath('updated').text
+        paper[:summary] = entry.xpath('summary').text
+        paper[:published] = entry.xpath('published').text
+      end
+      paper
+    end
+  end
+end

data/lib/paper_metadata/version.rb

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+module PaperMetadata
+  VERSION = "0.0.1"
+end

data/paper_metadata.gemspec

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+# -*- encoding: utf-8 -*-
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'paper_metadata/version'
+
+Gem::Specification.new do |gem|
+  gem.name          = "paper_metadata"
+  gem.version       = PaperMetadata::VERSION
+  gem.authors       = ["Jure Triglav"]
+  gem.email         = ["juretriglav@gmail.com"]
+  gem.summary   = %q{Paper_metadata gem gets the metadata for papers with a DOI or an arXiv identifier}
+  gem.description       = %q{Metadata getter for scientific papers}
+  gem.homepage      = "http://github.com/jure/paper_metadata"
+
+  gem.files         = `git ls-files`.split($/)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.require_paths = ["lib"]
+
+  gem.add_development_dependency "pry"
+  gem.add_development_dependency "rake"
+  gem.add_development_dependency "webmock"
+  gem.add_runtime_dependency "nokogiri", ["= 1.5.6"]
+
+end

data/test/arxiv.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<feed xmlns="http://www.w3.org/2005/Atom">
+  <link href="http://arxiv.org/api/query?search_query%3D1301.7746%26id_list%3D%26start%3D0%26max_results%3D1" rel="self" type="application/atom+xml"/>
+  <title type="html">ArXiv Query: search_query=1301.7746&amp;id_list=&amp;start=0&amp;max_results=1</title>
+  <id>http://arxiv.org/api/NIaVv86zj4leHWkr6xTS1LwRjlw</id>
+  <updated>2013-02-02T00:00:00-05:00</updated>
+  <opensearch:totalResults xmlns:opensearch="http://a9.com/-/spec/opensearch/1.1/">1</opensearch:totalResults>
+  <opensearch:startIndex xmlns:opensearch="http://a9.com/-/spec/opensearch/1.1/">0</opensearch:startIndex>
+  <opensearch:itemsPerPage xmlns:opensearch="http://a9.com/-/spec/opensearch/1.1/">1</opensearch:itemsPerPage>
+  <entry>
+    <id>http://arxiv.org/abs/1301.7746v1</id>
+    <updated>2013-01-31T20:46:12Z</updated>
+    <published>2013-01-31T20:46:12Z</published>
+    <title>Phases and phase transitions in disordered quantum systems</title>
+    <summary>  These lecture notes give a pedagogical introduction to phase transitions in
+disordered quantum systems and to the exotic Griffiths phases induced in their
+vicinity. We first review some fundamental concepts in the physics of phase
+transitions. We then derive criteria governing under what conditions spatial
+disorder or randomness can change the properties of a phase transition. After
+introducing the strong-disorder renormalization group method, we discuss in
+detail some of the exotic phenomena arising at phase transitions in disordered
+quantum systems. These include infinite-randomness criticality, rare regions
+and quantum Griffiths singularities, as well as the smearing of phase
+transitions. We also present a number of experimental examples.
+</summary>
+    <author>
+      <name>Thomas Vojta</name>
+    </author>
+    <arxiv:comment xmlns:arxiv="http://arxiv.org/schemas/atom">Pedagogical introduction to strong disorder physics at quantum phase
+  transitions. Based on lectures given at the XVII Training Course in the
+  Physics of Strongly Correlated Systems in Vietri sul Mare, Italy in October
+  2012. Submitted to the proceedings of this school. 60 pages and 23 figures.
+  Builds on material reviewed in arXiv:cond-mat/0602312 and arXiv:1005.2707</arxiv:comment>
+    <link href="http://arxiv.org/abs/1301.7746v1" rel="alternate" type="text/html"/>
+    <link title="pdf" href="http://arxiv.org/pdf/1301.7746v1" rel="related" type="application/pdf"/>
+    <arxiv:primary_category xmlns:arxiv="http://arxiv.org/schemas/atom" term="cond-mat.dis-nn" scheme="http://arxiv.org/schemas/atom"/>
+    <category term="cond-mat.dis-nn" scheme="http://arxiv.org/schemas/atom"/>
+    <category term="cond-mat.str-el" scheme="http://arxiv.org/schemas/atom"/>
+  </entry>
+</feed>

data/test/doi.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<doi_records>
+  <doi_record owner="10.1021" timestamp="2011-05-21 00:52:16">
+    <crossref>
+      <journal>
+        <journal_metadata language="en">
+          <full_title>Analytical Chemistry</full_title>
+          <abbrev_title>Anal. Chem.</abbrev_title>
+          <issn media_type="print">0003-2700</issn>
+          <issn media_type="electronic">1520-6882</issn>
+        </journal_metadata>
+        <journal_issue>
+          <publication_date media_type="print">
+            <month>10</month>
+            <year>2010</year>
+          </publication_date>
+          <journal_volume>
+            <volume>82</volume>
+          </journal_volume>
+          <issue>19</issue>
+        </journal_issue>
+        <journal_article publication_type="full_text">
+          <titles>
+            <title>Basic Modeling Approach To Optimize Elemental Imaging by Laser Ablation ICPMS</title>
+          </titles>
+          <contributors>
+            <person_name sequence="first" contributor_role="author">
+              <given_name>Jure</given_name>
+              <surname>Triglav</surname>
+            </person_name>
+            <person_name sequence="additional" contributor_role="author">
+              <given_name>Johannes T.</given_name>
+              <surname>van Elteren</surname>
+            </person_name>
+            <person_name sequence="additional" contributor_role="author">
+              <given_name>Vid S.</given_name>
+              <surname>Šelih</surname>
+            </person_name>
+          </contributors>
+          <publication_date media_type="print">
+            <month>10</month>
+            <year>2010</year>
+          </publication_date>
+          <pages>
+            <first_page>8153</first_page>
+            <last_page>8160</last_page>
+          </pages>
+          <publisher_item>
+            <identifier id_type="doi">10.1021/ac1014832</identifier>
+          </publisher_item>
+          <doi_data>
+            <doi>10.1021/ac1014832</doi>
+            <resource>http://pubs.acs.org/doi/abs/10.1021/ac1014832</resource>
+          </doi_data>
+        </journal_article>
+      </journal>
+    </crossref>
+  </doi_record>
+</doi_records>

data/test/test_helper.rb

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+require 'webmock/test_unit'

data/test/test_paper_metadata.rb

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+require 'test/unit'
+require 'paper_metadata'
+require 'test_helper'
+
+class PaperMetadataTest < Test::Unit::TestCase
+  def test_doi_parsing
+
+    doi_response = File.read(File.join(File.dirname(__FILE__), 'doi.xml'))
+    stub_request(:any, /www.crossref.org\/.*/).
+      to_return(:body => doi_response, :status => 200,  :headers => { 'Content-Length' => doi_response.length } )
+
+    PaperMetadata.doi_username = 'test@example.com'
+    assert_equal "Basic Modeling Approach To Optimize Elemental Imaging by Laser Ablation ICPMS",
+      PaperMetadata.metadata_for('doi:10.1021/ac1014832')[:title]
+  end
+
+  def test_fail_doi_if_no_username
+    doi_response = File.read(File.join(File.dirname(__FILE__), 'doi.xml'))
+    stub_request(:any, /www.crossref.org\/.*/).
+      to_return(:body => doi_response, :status => 200,  :headers => { 'Content-Length' => doi_response.length } )
+    PaperMetadata.doi_username = nil
+    assert_raise RuntimeError do
+      PaperMetadata.metadata_for('doi:10.1021/ac1014832')
+    end
+  end
+
+  def test_arxiv_parsing
+    arxiv_response = File.read(File.join(File.dirname(__FILE__), 'arxiv.xml'))
+    stub_request(:any, /.*arxiv.org\/.*/).
+      to_return(:body => arxiv_response, :status => 200,  :headers => { 'Content-Length' => arxiv_response.length } )
+    assert_equal "Thomas Vojta",
+      PaperMetadata.metadata_for('arXiv:1301.7746')[:author]
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: paper_metadata
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Jure Triglav
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-02-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: webmock
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: nokogiri
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.5.6
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.5.6
+description: Metadata getter for scientific papers
+email:
+- juretriglav@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .DS_Store
+- .gitignore
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/paper_metadata.rb
+- lib/paper_metadata/version.rb
+- paper_metadata.gemspec
+- test/arxiv.xml
+- test/doi.xml
+- test/test_helper.rb
+- test/test_paper_metadata.rb
+homepage: http://github.com/jure/paper_metadata
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: Paper_metadata gem gets the metadata for papers with a DOI or an arXiv identifier
+test_files:
+- test/arxiv.xml
+- test/doi.xml
+- test/test_helper.rb
+- test/test_paper_metadata.rb
+has_rdoc: