jats 0.1.0

data/spec/fixtures/text.xml

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+<p>Many seasonal breeders undergo seasonal cycles of gonadal growth and regression, accompanied by changes in sex steroid production and gamete maturation. (<xref ref-type="bibr" rid="ref-20">Dawson et al., 2001</xref>).</p>

data/spec/jats/affiliation_spec.rb

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+require 'spec_helper'
+
+module Jats
+  describe Affiliation do 
+    def aff
+      Jats::Affiliation.from_xml(fixture('affiliation.xml'))
+    end
+
+    it "should cast to hash correctly" do
+      aff.to_hash.should == {
+        label: '1',
+        department: 'Laboratory of Reproductive Neuroendocrinology, Department of Integrative Biology',
+        address: 'University of California at Berkeley',
+        country: 'USA'
+      }
+    end
+  end
+end

data/spec/jats/annotation_spec.rb

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+require 'spec_helper'
+
+module Jats
+  describe Annotation do
+    def annotation
+      Jats::Annotation.from_xml(fixture('annotation.xml').at('xref'))
+    end
+
+    it "should have the correct attributes" do
+      ann = annotation
+
+      ann.source = 'source'
+
+      ann.attributes.should == {
+        source:  'source',
+        content: 'Dawson et al., 2001',
+        target:  'article:bib20'
+      }
+    end
+  end
+end
+

data/spec/jats/article_spec.rb

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+require 'spec_helper'
+
+module Jats
+  describe Article do
+    it "should parse a xml" do
+      article = double("Article")
+      Article.should_receive(:new).with('xml').and_return article
+      article.should_receive(:parse).and_return 'parsed'
+      Article.from_xml('xml').should == 'parsed'
+    end
+
+    it "add a node to the outline" do
+      article = Article.new
+
+      node = double("Node", name: 'name')
+      article.add_to_outline node
+
+      article.doc[:views][:content].should include('name')
+    end
+
+    it "should add a node to the nodes" do
+      article = Article.new
+
+      node = double("Node", to_hash: { name: 'name' })
+      article.add_node node
+
+      article.doc[:nodes].should include(name: 'name')
+    end
+
+    it "should parse the front, body and back" do
+      article = Article.new
+
+      article.should_receive(:parse_front)
+      article.should_receive(:parse_body)
+      article.should_receive(:parse_back)
+
+      article.parse
+    end
+  end
+end
+

data/spec/jats/body_spec.rb

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+require 'spec_helper'
+
+describe Jats::Body do
+  def body
+    xml = fixture('peerj.xml')
+    Jats::Article.from_xml(xml)
+  end
+
+  it "should map the headings" do
+    nodes = body[:nodes]
+
+    nodes['heading:1'].should == {
+      type:    'heading',
+      id:      'heading:1',
+      content: 'Introduction',
+      level:    1
+    }
+
+    nodes['heading:2'].should == {
+      type:    'heading',
+      id:      'heading:2',
+      content: 'Materials and Methods',
+      level:    1
+    }
+
+    nodes['heading:3'].should == {
+      type:    'heading',
+      id:      'heading:3',
+      content: 'Gonad culture',
+      level:   2
+    }
+  end
+
+  it "should map the paragraphs" do
+    nodes = body[:nodes]
+
+    nodes['text:27'].should == {
+      type: 'text',
+      id:   'text:27',
+      content: 'In sum, the evidence provided by our model shows that the testes and ovaries of European starlings respond directly to chronically elevated corticosterone and metabolic stress independently of the brain by modulating testosterone and estradiol secretion. This modulation is season- and sex-specific: it occurs only while birds are deciding to breed, and it appears to involve the gonadal GnIH system. It is likely that this direct modulation of gonadal function in response to stress is most important prior to the onset of breeding because the gonads are not already maximally stimulated by components of the HPG axis and fully recrudesced. Taken together, our data indicate that photosensitive temperate songbird testes and ovaries are capable of responding directly to corticosterone and metabolic stress, in addition to GnRH-induced gonadotropin release, by increasing GnIH expression and decreasing testosterone and estradiol secretion. Thus, we suggest that the GnRH system is not the only pathway for integration of cues into a gonadal response.'
+    }
+  end
+
+  it "should map the figures" do
+    nodes = body[:nodes]
+    
+    nodes['figure:fig-1'].should == {
+      doi:   '10.7717/peerj.139/fig-1',
+      id:    'figure:fig-1',
+      label: 'Figure 1',
+      type:  'figure',
+      url:   'https://peerj.com/articles/139/fig-1.png',
+      caption: {
+        title: 'Seasonal differences in response to corticosterone and metabolic stress in European starling (Sturnus vulgaris) testes.',
+        content: '(A) In testes collected from photostimulated male starlings, testosterone secretion is significantly increased in culture by incubation with LH/FSH compared to media alone. Corticosterone and the metabolic inhibitors 2DG/MA do not attenuate LH/FSH-stimulated testosterone levels in photostimulated starlings. (B) In testes collected from photosensitive male starlings, testosterone secretion is significantly increased in culture by incubation with LH/FSH compared to media alone. Corticosterone and the metabolic inhibitors 2DG/MA significantly attenuate LH/FSH-stimulated testosterone levels. Bars are mean testosterone secreted +-  S.E.M. Different letters above columns indicate statistically significant differences.'
+      }
+    }
+  end
+
+  it "should map the annotation" do
+    nodes = body[:nodes]
+    nodes['annotation:1'].should == {
+      type:     'annotation',
+      content:  'Dawson et al., 2001',
+      id:       'annotation:1',
+      target:   'article:bib20',
+      source:   'text:1',
+    }
+
+    nodes['annotation:15'].should == {
+      type:     'annotation',
+      content:  'Calisi, Perfito & Bentley, 2010',
+      id:       'annotation:15',
+      target:   'article:bib16',
+      source:   'text:2',
+    }
+  end
+end

data/spec/jats/figure_spec.rb

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+require 'spec_helper'
+
+module Jats
+  describe Figure do
+    def figure
+      Jats::Figure.from_xml(fixture('figure.xml'))
+    end
+
+    it "should have the correct doi" do
+      figure.doi.should == '10.7717/peerj.139/fig-1'
+    end
+
+    it "should have the correct label" do
+      figure.label.should == 'Figure 1'
+    end
+
+    it "should have the correct url" do
+      figure.url.should == 'https://peerj.com/articles/139/fig-1.png'
+    end
+
+    it "should have the correct caption" do
+      figure.caption.should == {
+        title: 'Seasonal differences',
+        content: 'In testes collected from photostimulated male starlings.'
+      }
+    end
+
+    it "should return the correct attributes" do
+      figure.attributes.should == {
+        doi: '10.7717/peerj.139/fig-1',
+        label: 'Figure 1',
+        url: 'https://peerj.com/articles/139/fig-1.png',
+        caption: {
+          title: 'Seasonal differences',
+          content: 'In testes collected from photostimulated male starlings.'
+        }
+      }
+    end
+  end
+end
+

data/spec/jats/front_spec.rb

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+require 'spec_helper'
+
+describe Jats::Front do
+  def article
+    xml = fixture('peerj.xml')
+    Jats::Article.from_xml(xml)
+  end
+
+  describe "properties" do
+    def props
+      article[:properties]
+    end
+
+    it "should set the correct title" do
+      props[:title].should == 'The direct response of the gonads to cues of stress in a temperate songbird species is season-dependent'
+    end
+
+    it "should set the correct doi" do
+      props[:doi].should == '10.7717/peerj.139'
+    end
+
+    it "should set the correct history" do
+      props[:received_on].should == '2012-11-29'
+      props[:accepted_on].should == '2013-07-31'
+      props[:published_on].should == '2013-08-15'
+    end
+
+    it "should set the correct categories" do
+      props[:categories].should == [
+        'Ecology', 'Zoology', 'Diabetes and Endocrinology'
+      ]
+    end
+
+    it "should set the authors" do
+      props[:authors].should == [
+        "person:author-1",
+        "person:author-2",
+        "person:author-3",
+        "person:editor-1"
+      ]
+    end
+
+    it "should set the authors affiliations" do
+      person = article[:nodes]['person:author-1'].to_hash
+      person[:affiliations].should == [
+        {
+          label: '1',
+          department: 'Laboratory of Reproductive Neuroendocrinology, Department of Integrative Biology',
+          address: 'University of California at Berkeley',
+          country: 'USA'
+        }
+      ]
+    end
+
+    it "should set the keywords" do
+      props[:keywords].should == [
+        'Stress', 'Gonadotropin inhibitory hormone (GnIH)', 'Corticosterone',
+        'Gonadotropin releasing hormone (GnRH)', 'Testes', 'Estradiol',
+        'Testosterone', 'Avian', 'Supplementary cues', 'Photoperiod', 'Ovary'
+      ]
+    end
+  end
+
+end
+

data/spec/jats/heading_spec.rb

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+require 'spec_helper'
+
+module Jats
+  describe Heading do
+    def heading
+      Jats::Heading.from_xml(fixture('heading.xml').at_css('sec[id="this-one"]'))
+    end
+
+    it "should have the correct content" do
+      heading.content.should == 'Materials and methods'
+    end
+
+    it "should have the correct level" do
+      heading.level.should == 2
+    end
+
+    it "should have the correct attributes" do
+      { 
+        content: 'Materials and methods',
+        level: 2
+      }
+    end
+  end
+end
+

data/spec/jats/node_spec.rb

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+require 'spec_helper'
+
+module Jats
+  describe Node do
+    def node
+      Jats::Node.from_xml(fixture('text.xml'))
+    end
+
+    describe "indices" do
+      it "should return the correct index for a type" do
+        Node.index_for('moo').should == 1
+        Node.index_for('moo').should == 2
+        Node.index_for('zar').should == 1
+      end
+
+      it "should reset the indices correctly" do
+        Node.index_for('moo').should == 1
+        Node.index_for('moo').should == 2
+        Node.reset_indices
+        Node.index_for('moo').should == 1
+      end
+    end
+
+    it "should return the correct type" do
+      Node.new.type.should == 'node'
+    end
+
+    it "should have the correct name" do
+      node.name.should == 'node:1'
+    end
+
+    it "should have the correct attributes" do
+      node.attributes.should == {}
+    end
+
+    it "should cast to hash correctly" do
+      nod = node
+      nod.stub(:attributes).and_return({'attr' => 'value'})
+
+      nod.to_hash.should == {
+        'node:1' => {
+          type: 'node',
+          id: 'node:1',
+          'attr' => 'value'
+        }
+      }
+    end
+  end
+end
+

data/spec/jats/person_spec.rb

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+require 'spec_helper'
+
+module Jats
+  describe Person do
+    def person
+      Jats::Person.from_xml(fixture('person.xml').at('contrib'))
+    end
+
+    it "should set the correct given_names" do
+      person.given_names.should == 'Nicolette L.'
+    end
+
+    it "should set the correct last_name" do
+      person.last_name.should == 'McGuire'
+    end
+
+    it "should set the correct role" do
+      person.role.should == 'author'
+    end
+
+    it "should set the correct aff_rids" do
+      person.affiliation_ids.should == ['aff-1']
+    end
+
+    it "should set the correct attributes" do
+      person.attributes.should == {
+        affiliations: [],
+        given_names: 'Nicolette L.',
+        last_name: 'McGuire',
+        role: 'author'
+      }
+    end
+  end
+end

data/spec/jats/text_spec.rb

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+require 'spec_helper'
+
+module Jats
+  describe Text do
+    def text
+      Jats::Text.from_xml(fixture('text.xml'))
+    end
+
+    it "should return the correct content" do
+      text.content.should == 'Many seasonal breeders undergo seasonal cycles of gonadal growth and regression, accompanied by changes in sex steroid production and gamete maturation. (Dawson et al., 2001).'
+    end
+
+    it "should generate the correct annotations" do
+      text.annotations.size.should == 1
+      text.annotations.first.source.should == "text:2"
+    end
+
+    it "should return the correct attributes" do
+      text.attributes.should == {
+        content: 'Many seasonal breeders undergo seasonal cycles of gonadal growth and regression, accompanied by changes in sex steroid production and gamete maturation. (Dawson et al., 2001).'
+      }
+    end
+  end
+end

data/spec/jats_spec.rb

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+require 'spec_helper'
+
+require 'jats'
+
+describe Jats do
+end
+

data/spec/spec_helper.rb

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+# encoding: UTF-8
+#
+require 'jats'
+
+require 'nokogiri'
+require 'json'
+
+def fixture(file)
+  doc = Nokogiri::XML(open("spec/fixtures/#{file}").read) do |config|
+    config.noblanks
+  end
+end
+
+RSpec.configure do |config|
+  config.treat_symbols_as_metadata_keys_with_true_values = true
+  config.run_all_when_everything_filtered = true
+  config.filter_run :focus
+
+  config.order = 'random'
+
+  config.before do
+    Jats::Node::reset_indices
+  end
+end