metanorma 1.2.6 → 1.3.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: e4552898da027404dc0a7556a0c3b97d8c55c014c8ef397dff1d421f495a748d
-  data.tar.gz: a9a7f45f7e35f5a06bdc05c367a8ff3f25369251f5de1993fdbd166604a9349e
+  metadata.gz: 6da8527ed559d4b6833977c169022db5dfec3a9d93926257586d9e676a11e578
+  data.tar.gz: cf9cc8d31d2ae7cbd08787dcb3f4a79747e85fad5c142bc02fd377df91e467e0
 SHA512:
-  metadata.gz: 9be3cea69411bf8f1b48dde44a432353f9b93741ff13ce388312386817e6a8a90a2290dafa222013b7397838cd948b40228882e329bb2d89270924c1b0a08469
-  data.tar.gz: 1eff396a38c708948620c489664f8d9713ac0b76e7df72d1631e60e31f1bda0d2aea93ac7015a6a6f7863b9ed466eac731db6ec90fd42ca831d6ffead3f0ecfc
+  metadata.gz: 07f86288c180813daf6ceed810dec2bfecc1cdb2605bf45de5f363cf0a7187babffa37095f208679fd1d1a3cdc6aeebfc879a5293f51c4f49ecc9c473a077295
+  data.tar.gz: bc111d4ca32a5b3135cf518c748370654b9f99803b4123de42b2603965bba4a1e6164e6b3307f7f9afa8b53b7b721b1b01941eee22fd3dd5d63d95a8597cb71e

data/.github/workflows/rake.yml

@@ -16,35 +16,28 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        ruby: [ '2.6', '2.5', '2.4' ]
+        ruby: [ '2.7', '2.6', '2.5', '2.4' ]
         os: [ ubuntu-latest, windows-latest, macos-latest ]
         experimental: [ false ]
         include:
-          - ruby: '2.7'
+          - ruby: '3.0'
             os: 'ubuntu-latest'
             experimental: true
-          - ruby: '2.7'
+          - ruby: '3.0'
             os: 'windows-latest'
             experimental: true
-          - ruby: '2.7'
+          - ruby: '3.0'
             os: 'macos-latest'
             experimental: true
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v2
+        with:
+          submodules: true
 
       - uses: ruby/setup-ruby@v1
         with:
           ruby-version: ${{ matrix.ruby }}
-
-      - uses: actions/cache@v2
-        with:
-          path: vendor/bundle
-          key: bundle-${{ matrix.os }}-${{ matrix.ruby }}-${{ hashFiles('**/*.gemspec') }}
-          restore-keys: bundle-${{ matrix.os }}-${{ matrix.ruby }}
-
-      - run: bundle config set path 'vendor/bundle'
-
-      - run: bundle install --jobs 4 --retry 3
+          bundler-cache: true
 
       - run: bundle exec rake
 
@@ -54,7 +47,7 @@ jobs:
     steps:
       - uses: peter-evans/repository-dispatch@v1
         with:
-          token: ${{ secrets.GITHUB_TOKEN }}
+          token: ${{ secrets.METANORMA_CI_PAT_TOKEN || secrets.GITHUB_TOKEN }}
           repository: ${{ github.repository }}
-          event-type: notify
-          client-payload: '{"ref": "${{ github.ref }}"}'
+          event-type: tests-passed
+          client-payload: '{"ref": "${{ github.ref }}", "sha": "${{ github.sha }}"}'

data/.gitignore

@@ -20,3 +20,5 @@
 Gemfile.lock
 relaton/
 .vscode/
+
+.rubocop-https--*

data/.hound.yml

@@ -1,3 +1,5 @@
+# Auto-generated by Cimas: Do not edit it manually!
+# See https://github.com/metanorma/cimas
 ruby:
-  Enabled: true
+  enabled: true
   config_file: .rubocop.yml

data/.rubocop.yml

@@ -1,6 +1,10 @@
-# This project follows the Ribose OSS style guide.
-# https://github.com/riboseinc/oss-guides
-# All project-specific additions and overrides should be specified in this file.
-
+# Auto-generated by Cimas: Do not edit it manually!
+# See https://github.com/metanorma/cimas
 inherit_from:
   - https://raw.githubusercontent.com/riboseinc/oss-guides/master/ci/rubocop.yml
+
+# local repo-specific modifications
+# ...
+
+AllCops:
+  TargetRubyVersion: 2.4

data/Rakefile

@@ -3,4 +3,4 @@ require "rspec/core/rake_task"
 
 RSpec::Core::RakeTask.new(:spec)
 
-task :default => :spec
+task default: :spec

data/lib/metanorma/asciidoctor_extensions/glob_include_processor.rb

@@ -1,20 +1,18 @@
 module Metanorma::AsciidoctorExtensions
-
   class GlobIncludeProcessor < ::Asciidoctor::Extensions::IncludeProcessor
-    def process doc, reader, target_glob, attributes
+    def process(_doc, reader, target_glob, attributes)
       Dir[File.join reader.dir, target_glob].sort.reverse_each do |target|
         content = IO.readlines target
-        content.unshift '' unless attributes['adjoin-option']
+        content.unshift "" unless attributes["adjoin-option"]
         reader.push_include content, target, target, 1, attributes
       end
       reader
     end
 
-    def handles? target
-      target.include? '*'
+    def handles?(target)
+      target.include? "*"
     end
   end
-
 end
 
 Asciidoctor::Extensions.register do

data/lib/metanorma/collection.rb

@@ -44,9 +44,10 @@ module Metanorma
     end
 
     # rubocop:enable Metrics/AbcSize,Metrics/MethodLength
-     def clean_exit
-       @log.write(File.join(File.dirname(@file), File.basename(@file, ".*") + ".err"))
-     end
+    def clean_exit
+      @log.write(File.join(File.dirname(@file),
+                           "#{File.basename(@file, '.*')}.err"))
+    end
 
     # @return [String] XML
     def to_xml
@@ -110,7 +111,7 @@ module Metanorma
       # @parma mnf [Metanorma::CollectionManifest]
       # @return [Hash{String=>Metanorma::Document}]
       def docs_from_xml(xml, mnf)
-        xml.xpath("//xmlns:doc-container/*/xmlns:bibdata")
+        xml.xpath("//xmlns:doc-container//xmlns:bibdata")
           .each_with_object({}) do |b, m|
           bd = Relaton::Cli.parse_xml b
           docref = mnf.docref_by_id bd.docidentifier.first.id
@@ -153,7 +154,7 @@ module Metanorma
 
       require "metanorma-#{doctype}"
       out = sections(dummy_header + cnt)
-      builder.send(elm + "-content") { |b| b << out }
+      builder.send("#{elm}-content") { |b| b << out }
     end
 
     # @param cnt [String] prefatory/final content
@@ -169,7 +170,13 @@ module Metanorma
 
       documents.each_with_index do |(_, d), i|
         id = format("doc%<index>09d", index: i)
-        builder.send("doc-container", id: id) { |b| d.to_xml b }
+        builder.send("doc-container", id: id) do |b|
+          if d.attachment
+            d.bibitem and b << d.bibitem.root.to_xml
+            b.attachment Metanorma::Utils::datauri(d.file)
+          else d.to_xml b
+          end
+        end
       end
     end
 

data/lib/metanorma/collection_fileparse.rb

@@ -0,0 +1,243 @@
+module Metanorma
+  # XML collection renderer
+  class CollectionRenderer
+    # map locality type and label (e.g. "clause" "1") to id = anchor for
+    # a document
+    # Note: will only key clauses, which have unambiguous reference label in
+    # locality. Notes, examples etc with containers are just plunked against
+    # UUIDs, so that their IDs can at least be registered to be tracked
+    # as existing.
+    def read_anchors(xml)
+      ret = {}
+      xrefs = @isodoc.xref_init(@lang, @script, @isodoc, @isodoc.i18n, {})
+      xrefs.parse xml
+      xrefs.get.each do |k, v|
+        ret[v[:type]] ||= {}
+        index = if v[:container] || v[:label].nil? || v[:label].empty?
+                  UUIDTools::UUID.random_create.to_s
+                else
+                  v[:label]
+                end
+        ret[v[:type]][index] = k
+      end
+      ret
+    end
+
+    # @param id [String]
+    # @param read [Boolean]
+    # @return [Array<String, nil>]
+    def xml_file(id, read)
+      file = @xml.at(ns("//doc-container[@id = '#{id}']")).to_xml if read
+      filename = "#{id}.html"
+      [file, filename]
+    end
+
+    # @param bib [Nokogiri::XML::Element]
+    # @param identifier [String]
+    def update_bibitem(bib, identifier) # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
+      docid = bib&.at(ns("./docidentifier"))&.text
+      unless @files[docid]
+        error = "[metanorma] Cannot find crossreference to document #{docid} "\
+          "in document #{identifier}."
+        @log.add("Cross-References", nil, error)
+        Util.log(error, :warning)
+        return
+      end
+      id = bib["id"]
+      newbib = bib.replace(@files[docid][:bibdata])
+      newbib.name = "bibitem"
+      newbib["id"] = id
+      newbib["hidden"] = "true"
+      newbib&.at(ns("./ext"))&.remove
+      _file, url = targetfile(@files[docid], relative: true, read: false,
+                                             doc: !@files[docid][:attachment])
+      uri_node = Nokogiri::XML::Node.new "uri", newbib
+      uri_node[:type] = "citation"
+      uri_node.content = url
+      newbib.at(ns("./docidentifier")).previous = uri_node
+    end
+
+    # Resolves direct links to other files in collection
+    # (repo(current-metanorma-collection/x),
+    # and indirect links to other files in collection
+    # (bibitem[@type = 'internal'] pointing to a file anchor
+    # in another file in the collection)
+    # @param file [String] XML content
+    # @param identifier [String] docid
+    # @param internal_refs [Hash{String=>Hash{String=>String}] schema name to anchor to filename
+    # @return [String] XML content
+    def update_xrefs(file, identifier, internal_refs)
+      docxml = Nokogiri::XML(file)
+      update_indirect_refs_to_docs(docxml, internal_refs)
+      add_document_suffix(identifier, docxml)
+      update_direct_refs_to_docs(docxml, identifier)
+      svgmap_resolve(datauri_encode(docxml))
+      docxml.xpath(ns("//references[not(./bibitem[not(@hidden) or @hidden = 'false'])]")).each do |f|
+        f["hidden"] = "true"
+      end
+      docxml.to_xml
+    end
+
+    def datauri_encode(docxml)
+      docxml.xpath(ns("//image")).each do |i|
+        i["src"] = Metanorma::Utils::datauri(i["src"])
+      end
+      docxml
+    end
+
+    def svgmap_resolve(docxml)
+      isodoc = IsoDoc::Convert.new({})
+      docxml.xpath(ns("//svgmap//eref")).each do |e|
+        href = isodoc.eref_target(e)
+        next if href == "##{e['bibitemid']}"
+
+        # XML collection renderer
+        # map locality type and label (e.g. "clause" "1") to id = anchor for
+        # a document
+        # Note: will only key clauses, which have unambiguous reference label in
+        # locality. Notes, examples etc with containers are just plunked against
+        # UUIDs, so that their IDs can at least be registered to be tracked
+        # as existing.
+        # @param id [String]
+        # @param read [Boolean]
+        # @return [Array<String, nil>]
+        # @param bib [Nokogiri::XML::Element]
+        # @param identifier [String]
+        # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
+        # Resolves direct links to other files in collection
+        # (repo(current-metanorma-collection/x),
+        # and indirect links to other files in collection
+        # (bibitem[@type = 'internal'] pointing to a file anchor
+        # in another file in the collection)
+        # @param file [String] XML content
+        # @param identifier [String] docid
+        # @param internal_refs [Hash{String=>Hash{String=>String}] schema name to anchor to filename
+        # @return [String] XML content
+        if href =~ /^#/ && !docxml.at("//*[@id = '#{href.sub(/^#/, '')}']")
+          next
+        end
+
+        e["target"] = href.strip
+        e.name = "link"
+        e&.elements&.remove
+      end
+      Metanorma::Utils::svgmap_rewrite(docxml, "")
+    end
+
+    # repo(current-metanorma-collection/ISO 17301-1:2016)
+    # replaced by bibdata of "ISO 17301-1:2016" in situ as bibitem.
+    # Any erefs to that bibitem id are replaced with relative URL
+    # Preferably with anchor, and is a job to realise dynamic lookup
+    # of localities.
+    def update_direct_refs_to_docs(docxml, identifier)
+      docxml.xpath(ns("//bibitem[not(ancestor::bibitem)]")).each do |b|
+        docid = b&.at(ns("./docidentifier[@type = 'repository']"))&.text
+        next unless docid && %r{^current-metanorma-collection/}.match(docid)
+
+        update_bibitem(b, identifier)
+        update_anchors(b, docxml, docid)
+      end
+    end
+
+    # Resolve erefs to a container of ids in another doc,
+    # to an anchor eref (direct link)
+    def update_indirect_refs_to_docs(docxml, internal_refs)
+      internal_refs.each do |schema, ids|
+        ids.each do |id, file|
+          update_indirect_refs_to_docs1(docxml, schema, id, file)
+        end
+      end
+    end
+
+    def update_indirect_refs_to_docs1(docxml, schema, id, file)
+      docxml.xpath(ns("//eref[@bibitemid = '#{schema}_#{id}']")).each do |e|
+        e["citeas"] = file
+      end
+      docid = docxml.at(ns("//bibitem[@id = '#{schema}_#{id}']/"\
+                           "docidentifier[@type = 'repository']")) or return
+      docid.children = "current-metanorma-collection/#{file}"
+      docid.previous = "<docidentifier type='X'>#{file}</docidentifier>"
+    end
+
+    # update crossrefences to other documents, to include disambiguating document suffix on id
+    def update_anchors(bib, docxml, _id) # rubocop:disable Metrics/MethodLength, Metrics/AbcSize
+      docid = bib&.at(ns("./docidentifier"))&.text
+      docxml.xpath("//xmlns:eref[@citeas = '#{docid}']").each do |e|
+        if @files[docid]
+          update_anchor_loc(bib, e, docid)
+        else
+          e << "<strong>** Unresolved reference to document #{docid}, id #{e['bibitemid']}</strong>"
+        end
+      end
+    end
+
+    def update_anchor_loc(bib, e, docid)
+      loc = e.at(ns(".//locality[@type = 'anchor']")) or
+        return update_anchor_create_loc(bib, e, docid)
+      document_suffix = Metanorma::Utils::to_ncname(docid)
+      ref = loc.at(ns("./referenceFrom")) || return
+      anchor = "#{ref.text}_#{document_suffix}"
+      return unless @files[docid][:anchors].inject([]) do |m, (_, x)|
+        m += x.values
+      end.include?(anchor)
+
+      ref.content = anchor
+    end
+
+    # if there is a crossref to another document, with no anchor, retrieve the
+    # anchor given the locality, and insert it into the crossref
+    def update_anchor_create_loc(bib, e, docid)
+      ins = e.at(ns("./localityStack")) || return
+      type = ins&.at(ns("./locality/@type"))&.text
+      ref = ins&.at(ns("./locality/referenceFrom"))&.text
+      (anchor = @files[docid][:anchors][type][ref]) || return
+      ref_from = Nokogiri::XML::Node.new "referenceFrom", bib
+      ref_from.content = anchor.sub(/^_/, "")
+      locality = Nokogiri::XML::Node.new "locality", bib
+      locality[:type] = "anchor"
+      locality.add_child ref_from
+      ins << locality
+    end
+
+    # gather internal bibitem references
+    def gather_internal_refs
+      @files.each_with_object({}) do |(_, x), refs|
+        next if x[:attachment]
+
+        file, = targetfile(x, read: true)
+        Nokogiri::XML(file)
+          .xpath(ns("//bibitem[@type = 'internal']/"\
+        "docidentifier[@type = 'repository']")).each do |d|
+          a = d.text.split(%r{/}, 2)
+          a.size > 1 or next
+          refs[a[0]] ||= {}
+          refs[a[0]][a[1]] = true
+        end
+      end
+    end
+
+    # resolve file location for the target of each internal reference
+    def locate_internal_refs
+      refs = gather_internal_refs
+      @files.each do |identifier, x|
+        next if x[:attachment]
+
+        file, _filename = targetfile(x, read: true)
+        docxml = Nokogiri::XML(file)
+        refs.each do |schema, ids|
+          ids.each_key do |id|
+            n = docxml.at("//*[@id = '#{id}']") and
+              n.at("./ancestor-or-self::*[@type = '#{schema}']") and
+              refs[schema][id] = identifier
+          end
+        end
+      end
+      refs.each do |schema, ids|
+        ids.each do |id, key|
+          key == true and refs[schema][id] = "Missing:#{schema}:#{id}"
+        end
+      end
+      refs
+    end
+  end
+end

data/lib/metanorma/collection_fileprocess.rb

@@ -2,6 +2,7 @@
 
 require "isodoc"
 require "metanorma-utils"
+require_relative "collection_fileparse"
 
 module Metanorma
   # XML collection renderer
@@ -15,20 +16,32 @@ module Metanorma
       files = {}
       @xml.xpath(ns("//docref")).each do |d|
         identifier = d.at(ns("./identifier")).text
-        files[identifier] = if d["fileref"]
-                              { type: "fileref",
-                                ref: File.join(path, d["fileref"]) }
-                            else { type: "id", ref: d["id"] }
-                            end
-        file, _filename = targetfile(files[identifier], true)
-        xml = Nokogiri::XML(file)
-        add_document_suffix(identifier, xml)
-        files[identifier][:anchors] = read_anchors(xml)
-        files[identifier][:bibdata] = xml.at(ns("//bibdata"))
+        files[identifier] = file_entry(d, path)
+        if files[identifier][:attachment]
+          files[identifier][:bibdata] = Metanorma::Document
+            .attachment_bibitem(identifier).root
+        else
+          file, _filename = targetfile(files[identifier], read: true)
+          xml = Nokogiri::XML(file)
+          add_document_suffix(identifier, xml)
+          files[identifier][:anchors] = read_anchors(xml)
+          files[identifier][:bibdata] = xml.at(ns("//bibdata"))
+        end
       end
       files
     end
 
+    def file_entry(docref, path)
+      ret = if docref["fileref"]
+              { type: "fileref", ref: File.join(path, docref["fileref"]),
+                rel_path: docref["fileref"] }
+            else
+              { type: "id", ref: docref["id"] }
+            end
+      ret[:attachment] = docref["attachment"] if docref["attachment"]
+      ret
+    end
+
     def add_suffix_to_attributes(doc, suffix, tag_name, attribute_name)
       doc.xpath(ns("//#{tag_name}[@#{attribute_name}]")).each do |elem|
         elem.attributes[attribute_name].value =
@@ -38,199 +51,50 @@ module Metanorma
 
     def add_document_suffix(identifier, doc)
       document_suffix = Metanorma::Utils::to_ncname(identifier)
-      [%w[* id],
-      %w[* bibitemid],
-      %w[review from],
-      %w[review to],
-      %w[index to],
-      %w[xref target],
-      %w[callout target]]
-      .each do |(tag_name, attribute_name)|
+      [%w[* id], %w[* bibitemid], %w[review from],
+       %w[review to], %w[index to], %w[xref target],
+       %w[callout target]]
+        .each do |(tag_name, attribute_name)|
         add_suffix_to_attributes(doc, document_suffix, tag_name, attribute_name)
       end
     end
 
-    # map locality type and label (e.g. "clause" "1") to id = anchor for
-    # a document
-    def read_anchors(xml)
-      ret = {}
-      xrefs = @isodoc.xref_init(@lang, @script, @isodoc, @isodoc.i18n, {})
-      xrefs.parse xml
-      xrefs.get.each do |k, v|
-        ret[v[:type]] ||= {}
-        index = v[:container] || v[:label].nil? || v[:label].empty? ? 
-          UUIDTools::UUID.random_create.to_s : v[:label]
-        # Note: will only key clauses, which have unambiguous reference label in locality.
-        # Notes, examples etc with containers are just plunked agaisnt UUIDs, so that their
-        # IDs can at least be registered to be tracked as existing.
-        ret[v[:type]][index] = k
-      end
-      ret
-    end
-
     # return file contents + output filename for each file in the collection,
     # given a docref entry
-    # @param data [Hash]
-    # @param read [Boolean]
+    # @param data [Hash] docref entry
+    # @param read [Boolean] read the file in and return it
+    # @param doc [Boolean] I am a Metanorma document,
+    # so my URL should end with html or pdf or whatever
+    # @param relative [Boolean] Return path relative to YAML file,
+    # not relative to calling function
     # @return [Array<String, nil>]
-    def targetfile(data, read = false)
-      if data[:type] == "fileref" then ref_file data[:ref], read
-      else xml_file data[:id], read
+    def targetfile(data, options)
+      options = { read: false, doc: true, relative: false }.merge(options)
+      path = options[:relative] ? data[:rel_path] : data[:ref]
+      if data[:type] == "fileref"
+        ref_file path, options[:read], options[:doc]
+      else
+        xml_file data[:id], options[:read]
       end
     end
 
     # @param ref [String]
     # @param read [Boolean]
+    # @param doc [Boolean]
     # @return [Array<String, nil>]
-    def ref_file(ref, read)
+    def ref_file(ref, read, doc)
       file = File.read(ref, encoding: "utf-8") if read
-      filename = ref.sub(/\.xml$/, ".html")
-      [file, filename]
-    end
-
-    # @param id [String]
-    # @param read [Boolean]
-    # @return [Array<String, nil>]
-    def xml_file(id, read)
-      file = @xml.at(ns("//doc-container[@id = '#{id}']")).to_xml if read
-      filename = id + ".html"
+      filename = ref.dup
+      filename.sub!(/\.xml$/, ".html") if doc
       [file, filename]
     end
 
-    # @param bib [Nokogiri::XML::Element]
-    # @param identifier [String]
-    def update_bibitem(bib, identifier) # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
-      docid = bib&.at(ns("./docidentifier"))&.text
-      unless @files[docid]
-        error = "[metanorma] Cannot find crossreference to document #{docid} in document #{identifier}."
-        @log.add("Cross-References", nil, error)
-        Util.log(error, :warning)
-        return
-      end
-      id = bib["id"]
-      newbib = bib.replace(@files[docid][:bibdata])
-      newbib.name = "bibitem"
-      newbib["id"] = id
-      newbib["hidden"] = "true"
-      newbib&.at(ns("./ext"))&.remove
-      _file, url = targetfile(@files[docid], false)
-      uri_node = Nokogiri::XML::Node.new "uri", newbib
-      uri_node[:type] = "citation"
-      uri_node.content = url
-      newbib.at(ns("./docidentifier")).previous = uri_node
-    end
-
-    # Resolves direct links to other files in collection (repo(current-metanorma-collection/x),
-    # and indirect links to other files in collection (bibitem[@type = 'internal'] pointing to a file anchor
-    # in another file in the collection)
-    # @param file [String] XML content
-    # @param identifier [String] docid
-    # @param internal_refs [Hash{String=>Hash{String=>String}] schema name to anchor to filename
-    # @return [String] XML content
-    def update_xrefs(file, identifier, internal_refs)
-      docxml = Nokogiri::XML(file)
-      update_indirect_refs_to_docs(docxml, internal_refs)
-      add_document_suffix(identifier, docxml)
-      update_direct_refs_to_docs(docxml, identifier)
-      svgmap_resolve(datauri_encode(docxml))
-      docxml.xpath(ns("//references[not(./bibitem[not(@hidden) or @hidden = 'false'])]")).each do |f|
-        f["hidden"] = "true"
-      end
-      docxml.to_xml
-    end
-
-    def datauri_encode(docxml)
-      docxml.xpath(ns("//image")).each { |i| i["src"] = Metanorma::Utils::datauri(i["src"]) }
-      docxml
-    end
-
-    def svgmap_resolve(docxml)
-      isodoc = IsoDoc::Convert.new({})
-      docxml.xpath(ns("//svgmap//eref")).each do |e|
-        href = isodoc.eref_target(e)
-        next if href == "#" + e["bibitemid"]
-        if href.match(/^#/)
-          next unless docxml.at("//*[@id = '#{href.sub(/^#/, '')}']")
-        end
-        e["target"] = href.strip
-        e.name = "link"
-        e&.elements&.remove
-      end
-      Metanorma::Utils::svgmap_rewrite(docxml, "")
-    end
-
-    # repo(current-metanorma-collection/ISO 17301-1:2016)
-    # replaced by bibdata of "ISO 17301-1:2016" in situ as bibitem.
-    # Any erefs to that bibitem id are replaced with relative URL
-    # Preferably with anchor, and is a job to realise dynamic lookup of localities.
-    def update_direct_refs_to_docs(docxml, identifier)
-      docxml.xpath(ns("//bibitem[not(ancestor::bibitem)]")).each do |b|
-        docid = b&.at(ns("./docidentifier[@type = 'repository']"))&.text
-        next unless docid && %r{^current-metanorma-collection/}.match(docid)
-        update_bibitem(b, identifier)
-        update_anchors(b, docxml, docid)
-      end
-    end
-
-    # Resolve erefs to a container of ids in another doc, to an anchor eref (direct link)
-    def update_indirect_refs_to_docs(docxml, internal_refs)
-      internal_refs.each do |schema, ids|
-        ids.each do |id, file|
-          update_indirect_refs_to_docs1(docxml, schema, id, file)
-        end
-      end
-    end
-
-    def update_indirect_refs_to_docs1(docxml, schema, id, file)
-      docxml.xpath(ns("//eref[@bibitemid = '#{schema}_#{id}']")).each do |e|
-        e["citeas"] = file
-      end
-      docid = docxml.at(ns("//bibitem[@id = '#{schema}_#{id}']/docidentifier[@type = 'repository']")) or return
-      docid.children = "current-metanorma-collection/#{file}"
-      docid.previous = "<docidentifier type='X'>#{file}</docidentifier>"
-    end
-
-    # update crossrefences to other documents, to include disambiguating document suffix on id
-    def update_anchors(bib, docxml, _id) # rubocop:disable Metrics/MethodLength, Metrics/AbcSize
-      docid = bib&.at(ns("./docidentifier"))&.text
-      docxml.xpath("//xmlns:eref[@citeas = '#{docid}']").each do |e|
-        if @files[docid]
-          update_anchor_loc(bib, e, docid)
-        else
-          e << "<strong>** Unresolved reference to document #{docid}, id #{e['bibitemid']}</strong>"
-        end
-      end
-    end
-
-    def update_anchor_loc(bib, e, docid)
-      loc = e.at(ns(".//locality[@type = 'anchor']")) or return update_anchor_create_loc(bib, e, docid)
-      document_suffix = Metanorma::Utils::to_ncname(docid)
-      ref = loc.at(ns("./referenceFrom")) || return
-      anchor = "#{ref.text}_#{document_suffix}"
-      return unless @files[docid][:anchors].inject([]) { |m, (_, x)| m+= x.values }.include?(anchor)
-      ref.content = anchor
-    end
-
-    # if there is a crossref to another document, with no anchor, retrieve the
-    # anchor given the locality, and insert it into the crossref
-    def update_anchor_create_loc(bib, e, docid)
-      ins = e.at(ns("./localityStack")) || return
-      type = ins&.at(ns("./locality/@type"))&.text
-      ref = ins&.at(ns("./locality/referenceFrom"))&.text
-      (anchor = @files[docid][:anchors][type][ref]) || return
-      ref_from = Nokogiri::XML::Node.new "referenceFrom", bib
-      ref_from.content = anchor.sub(/^_/, "")
-      locality = Nokogiri::XML::Node.new "locality", bib
-      locality[:type] = "anchor"
-      locality.add_child ref_from
-      ins << locality
-    end
-
     # compile and output individual file in collection
     def file_compile(f, filename, identifier)
       # warn "metanorma compile -x html #{f.path}"
       c = Compile.new
-      c.compile f.path, { format: :asciidoc, extension_keys: @format }.merge(@compile_options)
+      c.compile f.path, { format: :asciidoc,
+                          extension_keys: @format }.merge(@compile_options)
       @files[identifier][:outputs] = {}
       @format.each do |e|
         ext = c.processor.output_formats[e]
@@ -240,38 +104,11 @@ module Metanorma
       end
     end
 
-    # gather internal bibitem references
-    def gather_internal_refs
-      @files.each_with_object({}) do |(identifier, x), refs|
-        file, _ = targetfile(x, true)
-        Nokogiri::XML(file).xpath(ns("//bibitem[@type = 'internal']/docidentifier[@type = 'repository']")).each do |d|
-          a = d.text.split(%r{/}, 2)
-          a.size > 1 or next
-          refs[a[0]] ||= {}
-          refs[a[0]][a[1]] = true
-        end
-      end
-    end
-
-    # resolve file location for the target of each internal reference
-    def locate_internal_refs
-      refs = gather_internal_refs
-      @files.each do |identifier, x|
-        file, filename = targetfile(x, true)
-        docxml = Nokogiri::XML(file)
-        refs.each do |schema, ids|
-          ids.keys.each do |id|
-            docxml.at(ns("//*[@id = '#{id}'][@type = '#{schema}']")) and
-              refs[schema][id] = identifier
-          end
-        end
-      end
-      refs.each do |schema, ids|
-        ids.each do |id, key|
-          key == true and refs[schema][id] = "Missing:#{schema}:#{id}"
-        end
-      end
-      refs
+    def copy_file_to_dest(fileref)
+      _file, filename = targetfile(fileref, read: true, doc: false)
+      dest = File.join(@outdir, fileref[:rel_path])
+      FileUtils.mkdir_p(File.dirname(dest))
+      FileUtils.cp filename, dest
     end
 
     # process each file in the collection
@@ -279,12 +116,15 @@ module Metanorma
     def files # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
       internal_refs = locate_internal_refs
       @files.each do |identifier, x|
-        file, filename = targetfile(x, true)
-        file = update_xrefs(file, identifier, internal_refs)
-        Tempfile.open(["collection", ".xml"], encoding: "utf-8") do |f|
-          f.write(file)
-          f.close
-          file_compile(f, filename, identifier)
+        if x[:attachment] then copy_file_to_dest(x)
+        else
+          file, filename = targetfile(x, read: true)
+          file = update_xrefs(file, identifier, internal_refs)
+          Tempfile.open(["collection", ".xml"], encoding: "utf-8") do |f|
+            f.write(file)
+            f.close
+            file_compile(f, filename, identifier)
+          end
         end
       end
     end