Class: ChemScanner::Docx

Inherits:
Doc
  • Object
show all
Defined in:
lib/chem_scanner/docx.rb

Overview

Read and Parse DOCX

Instance Attribute Summary

Attributes inherited from Doc

#cdx_map, #molecules, #reactions

Instance Method Summary collapse

Methods inherited from Doc

#extract_cdx_data, #to_cml

Constructor Details

#initialize ⇒ Docx

Returns a new instance of Docx.



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# File 'lib/chem_scanner/docx.rb', line 13

def initialize
  super
end

Instance Method Details

#read(file) ⇒ Object 



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# File 'lib/chem_scanner/docx.rb', line 17

def read(file)
  dir = Dir.mktmpdir
  unzip_docx(file, dir)

  cdx_infos = retrieve_cdx_info(dir)

  cdx_infos.each do |cdx_info|
    ole_path = cdx_info[:ole_path]
    ole_contents = Ole::Storage.open(ole_path).root["CONTENTS"]
    next if ole_contents.nil?

    cdx_content = ole_contents.read
    next unless cdx_content[0, 8] == "VjCD0100"

    cdx = Cdx.new
    cdx.read(cdx_content, false)

    @molecules.concat(cdx.molecules)
    @reactions.concat(cdx.reactions)

    base_name = File.basename(ole_path, ".bin")
    @cdx_map[base_name] = {
      cdx: cdx,
      img_ext: cdx_info[:img_ext],
      img_b64: cdx_info[:img_b64],
    }
  end

  FileUtils.remove_entry_secure dir
  true
end

#retrieve_cdx_info(dir) ⇒ Object 



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# File 'lib/chem_scanner/docx.rb', line 54

def retrieve_cdx_info(dir)
  rels = Nokogiri::XML(File.open("#{dir}/word/_rels/document.xml.rels"))
  rels.remove_namespaces!

  doc = Nokogiri::XML(File.open("#{dir}/word/document.xml"))
  ole_list = doc.xpath('//o:OLEObject[contains(@ProgID, "ChemDraw")]')

  cdx_infos = []
  ole_list.each do |ole_el|
    images = ole_el.parent.xpath(".//v:imagedata")
    next if images.empty?

    imagedata = images.first
    rid = ole_el.attr("r:id")
    img_id = imagedata.attr("r:id")

    ole_rel = rels.at("//Relationship[@Id=\"#{rid}\"]")
    img_rel = rels.at("//Relationship[@Id=\"#{img_id}\"]")
    ole_target = ole_rel.attr("Target")
    img_target = img_rel.attr("Target")

    b64_png = Base64.strict_encode64(IO.binread("#{dir}/word/#{img_target}"))
    cdx_infos.push(
      ole_path: "#{dir}/word/#{ole_target}",
      img_ext: File.extname(img_target),
      img_b64: b64_png,
    )
  end

  cdx_infos
end

#unzip_docx(file, dir) ⇒ Object 



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# File 'lib/chem_scanner/docx.rb', line 49

def unzip_docx(file, dir)
  cmd = "unzip #{file} -d #{dir}"
  Open3.popen3(cmd) { |_, _, _, wait| wait.value }
end