Class: Whedon::Paper

Inherits:
Object
  • Object
show all
Includes:
GitHub
Defined in:
lib/whedon.rb

Constant Summary collapse

EXPECTED_MARKDOWN_FIELDS = 
%w{
  title
  tags
  authors
  affiliations
  date
  bibliography
}
EXPECTED_LATEX_FIELDS = 
%w{
  title
  keywords
  authors
  affiliations
  date
  bibliography
}

Constants included from GitHub

GitHub::MEDIA_TYPE

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from GitHub

#client

Constructor Details

#initialize(review_issue_id, custom_path = nil, paper_path = nil) ⇒ Paper

Initialized with JOSS paper including YAML header e.g. joss.theoj.org/about#paper_structure Optionally return early if no paper_path is set



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# File 'lib/whedon.rb', line 85

def initialize(review_issue_id, custom_path=nil, paper_path=nil)
  @review_issue_id = review_issue_id
  @review_repository = ENV['REVIEW_REPOSITORY']
  @custom_path = custom_path

  return if paper_path.nil?

  parsed = load_yaml(paper_path)

  check_fields(parsed, paper_path)
  check_orcids(parsed)

  @paper_path = paper_path
  @authors = parse_authors(parsed)
  @title = parsed['title']
  @languages = detect_languages
  @tags = parsed['tags']
  @date = parsed['date']
  @bibliography_path = parsed['bibliography']
  # Probably a much nicer way to do this...
  @current_year = ENV["CURRENT_YEAR"].nil? ? Time.new.year : ENV["CURRENT_YEAR"]
  @current_volume = ENV["CURRENT_VOLUME"].nil? ? Time.new.year - (Time.parse(ENV['JOURNAL_LAUNCH_DATE']).year - 1) : ENV["CURRENT_VOLUME"]
  @current_issue = ENV["CURRENT_ISSUE"].nil? ? 1 + ((Time.new.year * 12 + Time.new.month) - (Time.parse(ENV['JOURNAL_LAUNCH_DATE']).year * 12 + Time.parse(ENV['JOURNAL_LAUNCH_DATE']).month)) : ENV["CURRENT_ISSUE"]
end

Instance Attribute Details

#authors ⇒ Object

Returns the value of attribute authors.



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# File 'lib/whedon.rb', line 48

def authors
  @authors
end

#bibliography_path ⇒ Object

Returns the value of attribute bibliography_path.



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# File 'lib/whedon.rb', line 48

def bibliography_path
  @bibliography_path
end

#current_issue ⇒ Object

Returns the value of attribute current_issue.



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# File 'lib/whedon.rb', line 52

def current_issue
  @current_issue
end

#current_volume ⇒ Object

TODO: work out how to resolve this code duplication with lib/processor.rb



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# File 'lib/whedon.rb', line 51

def current_volume
  @current_volume
end

#current_year ⇒ Object

Returns the value of attribute current_year.



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

def current_year
  @current_year
end

#custom_path ⇒ Object

Returns the value of attribute custom_path.



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# File 'lib/whedon.rb', line 48

def custom_path
  @custom_path
end

#date ⇒ Object

Returns the value of attribute date.



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# File 'lib/whedon.rb', line 48

def date
  @date
end

#editor ⇒ Object

Returns the value of attribute editor.



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# File 'lib/whedon.rb', line 48

def editor
  @editor
end

#languages ⇒ Object

Returns the value of attribute languages.



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# File 'lib/whedon.rb', line 48

def languages
  @languages
end

#paper_path ⇒ Object

Returns the value of attribute paper_path.



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# File 'lib/whedon.rb', line 48

def paper_path
  @paper_path
end

#review_issue_body ⇒ Object

Returns the value of attribute review_issue_body.



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# File 'lib/whedon.rb', line 47

def review_issue_body
  @review_issue_body
end

#review_issue_id ⇒ Object

Returns the value of attribute review_issue_id.



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# File 'lib/whedon.rb', line 45

def review_issue_id
  @review_issue_id
end

#review_repository ⇒ Object

Returns the value of attribute review_repository.



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# File 'lib/whedon.rb', line 46

def review_repository
  @review_repository
end

#reviewers ⇒ Object

Returns the value of attribute reviewers.



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# File 'lib/whedon.rb', line 48

def reviewers
  @reviewers
end

#tags ⇒ Object

Returns the value of attribute tags.



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# File 'lib/whedon.rb', line 48

def tags
  @tags
end

#title ⇒ Object

Returns the value of attribute title.



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# File 'lib/whedon.rb', line 48

def title
  @title
end

Class Method Details

.list ⇒ Object 



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# File 'lib/whedon.rb', line 73

def self.list
  reviews = Whedon::Reviews.new(ENV['REVIEW_REPOSITORY']).list_current
  return "No open reviews" if reviews.nil?

  reviews.each do |issue_id, vals|
    puts "#{issue_id}: #{vals[:url]} (#{vals[:opened_at]})"
  end
end

Instance Method Details

#audit ⇒ Object 



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# File 'lib/whedon.rb', line 381

def audit
  review_issue if review_issue_body.nil?
  Whedon::Auditor.new(review_issue_body).audit
end

#authors_string ⇒ Object 



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# File 'lib/whedon.rb', line 279

def authors_string
  authors_array = []

  authors.each_with_index do |author, index|
    authors_array << "#{author.name}"
  end

  return authors_array.join(', ')
end

#bibtex_path ⇒ Object 



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# File 'lib/whedon.rb', line 257

def bibtex_path
  "#{directory}/#{bibliography_path}"
end

#check_fields(parsed, paper_path) ⇒ Object

Check that the paper has the expected YAML header. Raise if missing fields



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# File 'lib/whedon.rb', line 145

def check_fields(parsed, paper_path)
  if paper_path.include?('.tex')
    expected_fields = EXPECTED_LATEX_FIELDS
  else
    expected_fields = EXPECTED_MARKDOWN_FIELDS
  end
  fields = expected_fields - parsed.keys
  raise "Paper YAML header is missing expected fields: #{fields.join(', ')}" if !fields.empty?
end

#check_orcids(parsed) ⇒ Object

Check that the user-defined ORCIDs look valid



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# File 'lib/whedon.rb', line 156

def check_orcids(parsed)
  authors = parsed['authors']
  authors.each do |author|
    next unless author.has_key?('orcid')
    raise "Problem with ORCID (#{author['orcid']}) for #{author['name']}" unless OrcidValidator.new(author['orcid']).validate
  end
end

#citation_author ⇒ Object

User when generating the citation snipped, returns either: ‘Smith et al’ for multiple authors or ‘Smith’ for a single author



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# File 'lib/whedon.rb', line 268

def citation_author
  surname = authors.first.last_name
  initials = authors.first.initials

  if authors.size > 1
    return "#{surname} et al."
  else
    return "#{surname}, #{initials}"
  end
end

#compile ⇒ Object 



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# File 'lib/whedon.rb', line 391

def compile
  review_issue if review_issue_body.nil?
  processor = Whedon::Processor.new(review_issue_id, review_issue_body)
end

#crossref_authors ⇒ Object

Returns an XML snippet to be included in the Crossref XML



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# File 'lib/whedon.rb', line 321

def crossref_authors
  builder = Nokogiri::XML::Builder.new do |xml|
    xml.contributors {
      authors.each_with_index do |author, index|
        given_name = author.given_name
        surname = author.last_name
        orcid = author.orcid
        if index == 0
          sequence = "first"
        else
          sequence = "additional"
        end
        xml.person_name(:sequence => sequence, :contributor_role => "author") {
        xml.given_name given_name.encode(:xml => :text)
        if surname.nil?
          xml.surname "No Last Name".encode(:xml => :text)
        else
          xml.surname surname.encode(:xml => :text)
        end
        xml.ORCID "http://orcid.org/#{author.orcid}" if !orcid.nil?
        }
      end
    }
  end

  return builder.doc.xpath('//contributors').to_xml
end

#deposit_payload ⇒ Object

Create the payload that we’re going to use to post back to JOSS/JOSE



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# File 'lib/whedon.rb', line 175

def deposit_payload
  review_issue if review_issue_body.nil?
  payload = {
    'paper' => {}
  }

  %w(title tags languages).each { |var| payload['paper'][var] = self.send(var) }
  payload['paper']['authors'] = authors.collect { |a| a.to_h }
  payload['paper']['doi'] = formatted_doi
  payload['paper']['repository_doi'] = review_issue_body[ARCHIVE_REPOSITORY_REGEX].gsub('"', '')
  payload['paper']['data_doi'] = review_issue_body[ARCHIVE_DATA_REGEX].gsub('"', '')
  payload['paper']['book_doi'] = review_issue_body[ARCHIVE_BOOK_REGEX].gsub('"', '')
  payload['paper']['docker_doi'] = review_issue_body[ARCHIVE_DOCKER_REGEX].gsub('"', '')
  payload['paper']['book_exec_url'] = review_issue_body[BOOK_EXEC_REGEX].gsub('"', '')
  payload['paper']['repository_address'] = review_issue_body[REPO_REGEX].gsub('"', '')
  payload['paper']['editor'] = "@#{editor}"
  payload['paper']['reviewers'] = reviewers.collect(&:strip)
  payload['paper']['volume'] = current_volume
  payload['paper']['issue'] = current_issue
  payload['paper']['year'] = current_year
  payload['paper']['page'] = review_issue_id

  return payload
end

#detect_languages ⇒ Object 



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# File 'lib/whedon.rb', line 164

def detect_languages
  path = custom_path ? custom_path : "tmp/#{review_issue_id}"

  repo = Rugged::Repository.new("#{path}")
  project = Linguist::Repository.new(repo, repo.head.target_id)

  # Take top five languages from Linguist
  project.languages.keys.take(5)
end

#directory ⇒ Object 



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# File 'lib/whedon.rb', line 253

def directory
  File.dirname(paper_path)
end

#download ⇒ Object 



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# File 'lib/whedon.rb', line 386

def download
  review_issue if review_issue_body.nil?
  Whedon::Processor.new(review_issue_id, review_issue_body, custom_path).clone
end

#filename_doi ⇒ Object

A slightly modified DOI string for writing out files 10.21105/00001 -> 10.21105.00001



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# File 'lib/whedon.rb', line 364

def filename_doi
  formatted_doi.gsub('/', '.')
end

#formatted_doi ⇒ Object

The full DOI e.g. 10.21105/00001



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# File 'lib/whedon.rb', line 262

def formatted_doi
  "#{ENV['DOI_PREFIX']}/#{joss_id}"
end

#google_scholar_authors ⇒ Object 



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# File 'lib/whedon.rb', line 349

def google_scholar_authors
  authors_string = ""

  authors.each_with_index do |author, index|
    given_name = author.given_name
    surname = author.last_name

    authors_string << "<meta name=\"citation_author\" content=\"#{surname}, #{given_name}\">"
  end

  return authors_string
end

#jats_affiliations ⇒ Object 



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# File 'lib/whedon.rb', line 311

def jats_affiliations
  affiliations = ""
  authors.each_with_index do |author, index|
    affiliations << "<aff id=\"aff-#{index+1}\">#{author.affiliation}</aff>\n"
  end

  return affiliations
end

#jats_authors ⇒ Object 



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# File 'lib/whedon.rb', line 289

def jats_authors
  builder = Nokogiri::XML::Builder.new do |xml|
    xml.send(:'contrib-group', "content-type" => "authors") {
      authors.each_with_index do |author, index|
        given_name = author.given_name
        surname = author.last_name
        orcid = author.orcid
        xml.contrib("contrib-type" => "author", "id" => "author-#{index+1}") {
          xml.send(:'contrib-id', orcid, "contrib-id-type" => "orcid")
          xml.name {
            xml.surname surname.encode(:xml => :text)
            xml.send(:'given-names', given_name.encode(:xml => :text))
          }
          xml.xref("ref-type" => "aff", "rid" => "aff-#{index+1}")
        }
      end
    }
  end

  return builder.doc.xpath('//contrib-group').to_xml
end

#joss_id ⇒ Object

A 5-figure integer used to produce the JOSS DOI Note, this doesn’t actually include the string ‘joss’ in the DOI any longer (it’s now generalized) but the method name remains



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# File 'lib/whedon.rb', line 232

def joss_id
  id = "%05d" % review_issue_id
  "#{ENV['JOURNAL_ALIAS']}.#{id}"
end

#joss_resource_url ⇒ Object

The JOSS site url for a paper e.g. joss.theoj.org/papers/10.21105/00001



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# File 'lib/whedon.rb', line 370

def joss_resource_url
  "#{ENV['JOURNAL_URL']}/papers/#{formatted_doi}"
end

#latex_source? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/whedon.rb', line 136

def latex_source?
  paper_path.end_with?('.tex')
end

#load_yaml(paper_path) ⇒ Object 



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# File 'lib/whedon.rb', line 128

def load_yaml(paper_path)
  if paper_path.include?('.tex')
    return YAML.load_file(paper_path.gsub('.tex', '.yml'))
  else
    return YAML.load_file(paper_path)
  end
end

#markdown_source? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/whedon.rb', line 140

def markdown_source?
  paper_path.end_with?('.md')
end

#paper_org ⇒ Object 



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# File 'lib/whedon.rb', line 241

def paper_org
  ENV['PAPER_REPOSITORY'].split('/').first
end

#paper_repo ⇒ Object 



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# File 'lib/whedon.rb', line 245

def paper_repo
  ENV['PAPER_REPOSITORY'].split('/').last
end

#parse_affiliations(affliations_yaml) ⇒ Object 



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# File 'lib/whedon.rb', line 220

def parse_affiliations(affliations_yaml)
  returned = {}
  affliations_yaml.each do |affiliation|
    returned[affiliation['index']] = affiliation['name']
  end

  returned
end

#parse_authors(yaml) ⇒ Object 



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# File 'lib/whedon.rb', line 205

def parse_authors(yaml)
  returned = []
  authors_yaml = yaml['authors']
  affiliations = parse_affiliations(yaml['affiliations'])

  # Loop through the authors block and build up the affiliation
  authors_yaml.each do |author|
    affiliation_index = author['affiliation']
    raise "Author (#{author['name']}) is missing affiliation" if affiliation_index.nil?
    returned << Author.new(author['name'], author['orcid'], affiliation_index, affiliations)
  end

  returned
end

#pdf_url ⇒ Object 



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# File 'lib/whedon.rb', line 237

def pdf_url
  "http://neurolibre.org/#{paper_repo}/#{joss_id}/#{ENV['DOI_PREFIX']}.#{joss_id}.pdf"
end

#plain_title ⇒ Object 



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# File 'lib/whedon.rb', line 200

def plain_title
  renderer = Redcarpet::Markdown.new(Redcarpet::Render::StripDown)
  return renderer.render(self.title).strip
end

#review_issue ⇒ Object

Return the Review object associated with the Paper



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# File 'lib/whedon.rb', line 375

def review_issue
  review = Whedon::Review.new(review_issue_id, review_repository)
  @review_issue_body = review.issue_body
  return review
end

#review_issue_url ⇒ Object 



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# File 'lib/whedon.rb', line 249

def review_issue_url
  "https://github.com/#{ENV['REVIEW_REPOSITORY']}/issues/#{review_issue_id}"
end

#reviewers_without_handles ⇒ Object 



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# File 'lib/whedon.rb', line 115

def reviewers_without_handles
  reviewers.map { |reviewer_name| reviewer_name.sub(/^@/, "") }
end