Module: Compilers

Included in:
Whedon::Processor
Defined in:
lib/whedon/compilers.rb

Overview

This module has methods to compile PDFs and Crossref XML depending upon the content type of the paper (Markdown or LaTeX)

Instance Method Summary collapse

Instance Method Details

#crossref_from_latex(paper_issue = nil, paper_volume = nil, paper_year = nil, paper_month = nil, paper_day = nil) ⇒ Object 



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# File 'lib/whedon/compilers.rb', line 197

def crossref_from_latex(paper_issue=nil, paper_volume=nil, paper_year=nil, paper_month=nil, paper_day=nil)
  cross_ref_template_path = "#{Whedon.resources}/crossref.template"
  bibtex = Whedon::BibtexParser.new(paper.bibtex_path)

  # Pass the citations that are actually in the paper to the CrossRef
  # citations generator.

  citations_in_paper = File.read(paper.paper_path).scan(/(?<=\\cite\{)\w+/)
  # FIXME
  # Because of the way citations are handled in Pandoc, we need to prepend and @
  # to the front of each of the citation strings.
  citations_in_paper = citations_in_paper.map {|c| c.prepend("@")}

  citations = bibtex.generate_citations(citations_in_paper)
  authors = paper.crossref_authors
  # TODO fix this when we update the DOI URLs
  # crossref_doi = archive_doi.gsub("http://dx.doi.org/", '')

  paper_day ||= Time.now.strftime('%d')
  paper_month ||= Time.now.strftime('%m')
  paper_year ||= @current_year
  paper_issue ||= @current_issue
  paper_volume ||= @current_volume

  `cd #{paper.directory} && pandoc \
  -V timestamp=#{Time.now.strftime('%Y%m%d%H%M%S')} \
  -V doi_batch_id=#{generate_doi_batch_id} \
  -V formatted_doi=#{paper.formatted_doi} \
  -V archive_doi=#{archive_doi} \
  -V review_issue_url=#{paper.review_issue_url} \
  -V paper_url=#{paper.pdf_url} \
  -V joss_resource_url=#{paper.joss_resource_url} \
  -V journal_alias=#{ENV['JOURNAL_ALIAS']} \
  -V journal_abbrev_title=#{ENV['JOURNAL_ABBRV_TITLE']} \
  -V journal_url=#{ENV['JOURNAL_URL']} \
  -V journal_name='#{ENV['JOURNAL_NAME']}' \
  -V journal_issn=#{ENV['JOURNAL_ISSN']} \
  -V citations='#{citations}' \
  -V authors='#{authors}' \
  -V month=#{paper_month} \
  -V day=#{paper_day} \
  -V year=#{paper_year} \
  -V issue=#{paper_issue} \
  -V volume=#{paper_volume} \
  -V page=#{paper.review_issue_id} \
  -V title='#{paper.plain_title}' \
  -f markdown #{File.basename(paper.paper_path)} -o #{paper.filename_doi}.crossref.xml \
  --template #{cross_ref_template_path}`

  if File.exists?("#{paper.directory}/#{paper.filename_doi}.crossref.xml")
    "#{paper.directory}/#{paper.filename_doi}.crossref.xml"
  else
    abort("Looks like we failed to compile the Crossref XML")
  end
end

#crossref_from_markdown(paper_issue = nil, paper_volume = nil, paper_year = nil, paper_month = nil, paper_day = nil) ⇒ Object 



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

def crossref_from_markdown(paper_issue=nil, paper_volume=nil, paper_year=nil, paper_month=nil, paper_day=nil)
  cross_ref_template_path = "#{Whedon.resources}/crossref.template"
  bibtex = Whedon::BibtexParser.new(paper.bibtex_path)

  # Pass the citations that are actually in the paper to the CrossRef
  # citations generator.

  citations_in_paper = File.read(paper.paper_path).scan(/@[\w|\-|:|_|\/|\+]+/)
  citations = bibtex.generate_citations(citations_in_paper)
  authors = paper.crossref_authors
  # TODO fix this when we update the DOI URLs
  # crossref_doi = archive_doi.gsub("http://dx.doi.org/", '')

  url = "#{ENV['JOURNAL_URL']}/papers/lookup/#{@review_issue_id}"
  response = RestClient.get(url)
  parsed = JSON.parse(response)
  submitted = parsed['submitted']
  published = parsed['accepted']

  # If we have already published the paper then overwrite the year, volume, issue
  if published
    paper_day = generate_day(published)
    paper_month = generate_month(published)
    paper_year = generate_year(published)
    paper_issue = generate_issue(published)
    paper_volume = generate_volume(published)
  else
    paper_issue ||= @current_issue
    paper_volume ||= @current_volume
    paper_day ||= Time.now.strftime('%d')
    paper_month ||= Time.now.strftime('%m')
    paper_year ||= Time.now.strftime('%Y')
  end

  metadata = {
    "timestamp" => Time.now.strftime('%Y%m%d%H%M%S'),
    "doi_batch_id" => generate_doi_batch_id,
    "formatted_doi" => paper.formatted_doi,
    "repository_doi" => repository_doi,
    "data_doi" => data_doi,
    "book_doi" => book_doi,
    "docker_doi" => docker_doi,
    "book_exec_url" => book_exec_url,
    "review_issue_url" => paper.review_issue_url,
    "paper_url" => paper.pdf_url,
    "joss_resource_url" => paper.joss_resource_url,
    "journal_alias" => ENV['JOURNAL_ALIAS'],
    "journal_abbrev_title" => ENV['JOURNAL_ABBRV_TITLE'],
    "journal_url" => ENV['JOURNAL_URL'],
    "journal_name" => ENV['JOURNAL_NAME'],
    "journal_issn"=> ENV['JOURNAL_ISSN'],
    "month" => paper_month,
    "day" => paper_day,
    "year" => paper_year,
    "issue" => paper_issue,
    "volume" => paper_volume,
    "page" => paper.review_issue_id,
    "title" => paper.plain_title,
    "crossref_authors" => authors,
    "citations" => citations
  }

  File.open("#{paper.directory}/crossref-metadata.yaml", 'w') { |file| file.write(metadata.to_yaml) }

  `cd #{paper.directory} && pandoc \
  -V title="#{paper.plain_title}" \
  -f markdown #{File.basename(paper.paper_path)} -o #{paper.filename_doi}.crossref.xml \
  --template #{cross_ref_template_path} \
  --metadata-file=crossref-metadata.yaml`

  if File.exists?("#{paper.directory}/#{paper.filename_doi}.crossref.xml")
    doc = Nokogiri::XML(File.open("#{paper.directory}/#{paper.filename_doi}.crossref.xml", "r"), &:noblanks)
    File.open("#{paper.directory}/#{paper.filename_doi}.crossref.xml", 'w') {|f| f.write(doc.to_xml(:indent => 2))}
    "#{paper.directory}/#{paper.filename_doi}.crossref.xml"
  else
    abort("Looks like we failed to compile the Crossref XML")
  end
end

#generate_crossref(paper_issue = nil, paper_volume = nil, paper_year = nil, paper_month = nil, paper_day = nil) ⇒ Object 



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# File 'lib/whedon/compilers.rb', line 17

def generate_crossref(paper_issue=nil, paper_volume=nil, paper_year=nil, paper_month=nil, paper_day=nil)
  if paper.latex_source?
    crossref_from_latex(paper_issue=nil, paper_volume=nil, paper_year=nil, paper_month=nil, paper_day=nil)
  elsif paper.markdown_source?
    crossref_from_markdown(paper_issue=nil, paper_volume=nil, paper_year=nil, paper_month=nil, paper_day=nil)
  end
end

#generate_day(date) ⇒ Object 



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# File 'lib/whedon/compilers.rb', line 101

def generate_day(date)
  parsed = Date.parse(date)
  return parsed.day
end

#generate_issue(date) ⇒ Object 



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# File 'lib/whedon/compilers.rb', line 81

def generate_issue(date)
  parsed = Date.parse(date)
  return 1 + ((parsed.year * 12 + parsed.month) - (Time.parse(ENV['JOURNAL_LAUNCH_DATE']).year * 12 + Time.parse(ENV['JOURNAL_LAUNCH_DATE']).month))
end

#generate_jats(paper_issue = nil, paper_volume = nil, paper_year = nil, paper_month = nil, paper_day = nil) ⇒ Object 



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# File 'lib/whedon/compilers.rb', line 25

def generate_jats(paper_issue=nil, paper_volume=nil, paper_year=nil, paper_month=nil, paper_day=nil)
  if paper.latex_source?
    jats_from_latex(paper_issue=nil, paper_volume=nil, paper_year=nil, paper_month=nil, paper_day=nil)
  elsif paper.markdown_source?
    jats_from_markdown(paper_issue=nil, paper_volume=nil, paper_year=nil, paper_month=nil, paper_day=nil)
  end
end

#generate_month(date) ⇒ Object 



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# File 'lib/whedon/compilers.rb', line 96

def generate_month(date)
  parsed = Date.parse(date)
  return parsed.month
end

#generate_pdf(custom_branch = nil, draft = true, paper_issue = nil, paper_volume = nil, paper_year = nil) ⇒ Object

Generate the paper PDF Optionally pass in a custom branch name as first param



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# File 'lib/whedon/compilers.rb', line 9

def generate_pdf(custom_branch=nil, draft=true, paper_issue=nil, paper_volume=nil, paper_year=nil)
  if paper.latex_source?
    pdf_from_latex(custom_branch, draft, paper_issue, paper_volume, paper_year)
  elsif paper.markdown_source?
    pdf_from_markdown(custom_branch, draft, paper_issue, paper_volume, paper_year)
  end
end

#generate_volume(date) ⇒ Object 



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# File 'lib/whedon/compilers.rb', line 86

def generate_volume(date)
  parsed = Date.parse(date)
  return parsed.year - (Date.parse(ENV['JOURNAL_LAUNCH_DATE']).year - 1)
end

#generate_year(date) ⇒ Object 



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# File 'lib/whedon/compilers.rb', line 91

def generate_year(date)
  parsed = Date.parse(date)
  return parsed.year
end

#jats_from_latex(paper_issue = nil, paper_volume = nil, paper_year = nil, paper_month = nil, paper_day = nil) ⇒ Object 



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# File 'lib/whedon/compilers.rb', line 332

def jats_from_latex(paper_issue=nil, paper_volume=nil, paper_year=nil, paper_month=nil, paper_day=nil)
  "JATS from LaTeX"
end

#jats_from_markdown(paper_issue = nil, paper_volume = nil, paper_year = nil, paper_month = nil, paper_day = nil) ⇒ Object 



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# File 'lib/whedon/compilers.rb', line 336

def jats_from_markdown(paper_issue=nil, paper_volume=nil, paper_year=nil, paper_month=nil, paper_day=nil)
  latex_template_path = "#{Whedon.resources}/latex.template"
  jats_template_path = "#{Whedon.resources}/jats.template"
  csl_file = "#{Whedon.resources}/jats.csl"


  url = "#{ENV['JOURNAL_URL']}/papers/lookup/#{@review_issue_id}"
  response = RestClient.get(url)
  parsed = JSON.parse(response)
  submitted = parsed['submitted']
  published = parsed['accepted']

  # If we have already published the paper then overwrite the year, volume, issue
  if published
    paper_day = Date.parse(published).strftime('%d')
    paper_year = generate_year(published)
    paper_issue = generate_issue(published)
    paper_volume = generate_volume(published)
  else
    paper_day ||= Time.now.strftime('%d')
    paper_month ||= Time.now.strftime('%m')
    paper_year ||= Time.now.strftime('%Y')
  end

  # TODO: may eventually want to swap out the latex template
  `cd #{paper.directory} && pandoc \
  -V repository="#{repository_address}" \
  -V archive_doi="#{archive_doi}" \
  -V paper_url="#{paper.pdf_url}" \
  -V journal_name='#{ENV['JOURNAL_NAME']}' \
  -V journal_issn=#{ENV['JOURNAL_ISSN']} \
  -V journal_abbrev_title=#{ENV['JOURNAL_ALIAS']} \
  -V graphics="true" \
  -V issue="#{paper_issue}" \
  -V volume="#{paper_volume}" \
  -V page="#{paper.review_issue_id}" \
  -V logo_path="#{Whedon.resources}/#{ENV['JOURNAL_ALIAS']}-logo.png" \
  -V month=#{paper_month} \
  -V day=#{paper_day} \
  -V year="#{paper_year}" \
  -V jats_authors='#{paper.jats_authors}' \
  -V jats_affiliations='#{paper.jats_affiliations}' \
  -t jats \
  -s \
  --citeproc \
  -o #{paper.filename_doi}.jats.xml  \
  #{File.basename(paper.paper_path)} \
  --template #{jats_template_path}`

  if File.exists?("#{paper.directory}/#{paper.filename_doi}.jats.xml")
    "#{paper.directory}/#{paper.filename_doi}.jats.xml"
  else
    abort("Looks like we failed to compile the JATS XML")
  end
end

#pdf_from_latex(custom_branch = nil, draft = true, paper_issue = nil, paper_volume = nil, paper_year = nil) ⇒ Object 



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# File 'lib/whedon/compilers.rb', line 33

def pdf_from_latex(custom_branch=nil, draft=true, paper_issue=nil, paper_volume=nil, paper_year=nil)
  # Optionally pass a custom branch name
  `cd #{paper.directory} && git checkout #{custom_branch} --quiet` if custom_branch

  metadata = YAML.load_file("#{paper.directory}/paper.yml")

  for k in ["title", "authors", "affiliations", "keywords"]
    raise "Key #{k} not present in metadata" unless metadata.keys().include?(k)
  end

  # Remove everything that shouldn't be there before processing

  `cd #{paper.directory} && rm -f *.aux \
  && rm -f *.blg && rm -f *.fls && rm -f *.log\
  && rm -f *.fdb_latexmk`

  open("#{paper.directory}/header.tex", 'w') do |f|
    f << "% **************GENERATED FILE, DO NOT EDIT**************\n\n"
    f << "\\title{#{metadata["title"]}}\n\n"
    for auth in metadata["authors"]
      f << "\\author[#{auth["affiliation"]}]{#{auth["name"]}}\n"
    end
    for aff in metadata["affiliations"]
      f << "\\affil[#{aff["index"]}]{#{aff["name"]}}\n"
    end
    f << "\n\\keywords{"
    for i in 0...metadata["keywords"].length-1
      f << "#{metadata["keywords"][i]}, "
    end
    f << metadata["keywords"].last
    f << "}\n"
    
    # draft mode by default.
    if draft
      f << "\\usepackage{draftwatermark}\n\n"
    end
  end

  `cd #{paper.directory} && latexmk -f -bibtex -pdf paper.tex`

  if File.exists?("#{paper.directory}/paper.pdf")
    `mv #{paper.directory}/paper.pdf #{paper.directory}/#{paper.filename_doi}.pdf`
    puts "#{paper.directory}/#{paper.filename_doi}.pdf"
  else
    abort("Looks like we failed to compile the PDF")
  end
end

#pdf_from_markdown(custom_branch = nil, draft = true, paper_issue = nil, paper_volume = nil, paper_year = nil) ⇒ Object 



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# File 'lib/whedon/compilers.rb', line 106

def pdf_from_markdown(custom_branch=nil, draft=true, paper_issue=nil, paper_volume=nil, paper_year=nil)
  latex_template_path = "#{Whedon.resources}/#{ENV['JOURNAL_ALIAS']}/latex.template"
  csl_file = "#{Whedon.resources}/#{ENV['JOURNAL_ALIAS']}/apa.csl"

  url = "#{ENV['JOURNAL_URL']}/papers/lookup/#{@review_issue_id}"
  response = RestClient.get(url)
  parsed = JSON.parse(response)
  submitted = parsed['submitted']
  published = parsed['accepted']

  # TODO - remove this once JOSE has their editors hooked up in the system
  if ENV['JOURNAL_ALIAS'] == "neurolibre" && !paper.editor.nil?
    editor_lookup_url = "#{ENV['JOURNAL_URL']}/editors/lookup/#{paper.editor}"
    response = RestClient.get(editor_lookup_url)
    parsed = JSON.parse(response)
    editor_name = parsed['name']
    editor_url = parsed['url']
  else
    editor_name = "Pending Editor"
    editor_url = "http://example.com"
  end

  # If we have already published the paper then overwrite the year, volume, issue
  if published
    paper_year = generate_year(published)
    paper_issue = generate_issue(published)
    paper_volume = generate_volume(published)
  else
    published = Time.now.strftime('%d %B %Y')
    paper_year ||= @current_year
    paper_issue ||= @current_issue
    paper_volume ||= @current_volume
  end

  # Optionally pass a custom branch name
  `cd #{paper.directory} && git checkout #{custom_branch} --quiet` if custom_branch

  metadata = {
    "repository" => repository_address,
    "repository_doi" => repository_doi,
    "data_doi" => data_doi,
    "book_doi" => book_doi,
    "docker_doi" => docker_doi,
    "book_exec_url" => book_exec_url,
    "paper_url" => paper.pdf_url,
    "journal_name" => ENV['JOURNAL_NAME'],
    "review_issue_url" => paper.review_issue_url,
    "issue" => paper_issue,
    "volume" => paper_volume,
    "page" => paper.review_issue_id,
    "logo_path" => "#{Whedon.resources}/#{ENV['JOURNAL_ALIAS']}/logo.png",
    "aas_logo_path" => "#{Whedon.resources}/#{ENV['JOURNAL_ALIAS']}/aas-logo.png",
    "year" => paper_year,
    "submitted" => submitted,
    "published" => published,
    "formatted_doi" => paper.formatted_doi,
    "citation_author" => paper.citation_author,
    "editor_name" => editor_name,
    "reviewers" => paper.reviewers_without_handles,
    "link-citations" => true
  }

  metadata.merge!({"draft" => true}) if draft

  File.open("#{paper.directory}/markdown-metadata.yaml", 'w') { |file| file.write(metadata.to_yaml) }

  `cd #{paper.directory} && pandoc \
  -V repository="#{repository_address}" \
  -V repository_doi="#{repository_doi}" \
  -V data_doi="#{data_doi}" \
  -V book_doi="#{book_doi}" \
  -V docker_doi="#{docker_doi}" \
  -V book_exec_url="#{book_exec_url}" \
  -V review_issue_url="#{paper.review_issue_url}" \
  -V editor_url="#{editor_url}" \
  -V graphics="true" \
  -o #{paper.filename_doi}.pdf -V geometry:margin=1in \
  --pdf-engine=xelatex \
  --citeproc #{File.basename(paper.paper_path)} \
  --from markdown+autolink_bare_uris \
  --csl=#{csl_file} \
  --template #{latex_template_path} \
  --metadata-file=markdown-metadata.yaml`

  if File.exists?("#{paper.directory}/#{paper.filename_doi}.pdf")
    puts "#{paper.directory}/#{paper.filename_doi}.pdf"
  else
    abort("Looks like we failed to compile the PDF :/")
  end
end