metanorma 1.3.1 → 1.3.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: e823c389c083ead32851781abb9fa3e28d7744d7fcd3ebacb60b051c118157ed
-  data.tar.gz: 6a3ef75f087f322c0fcf317f72cf5d91c52576b3f322c0935c368e9c74fb7e6d
+  metadata.gz: 1858cecb1db05debaa3cb36f970a2bcb76b403508067ea2fa8569720fd294a98
+  data.tar.gz: 90f6e4bca7bd431a9d40a989c77837e6cfa47a12e436e0934624592bac0707f0
 SHA512:
-  metadata.gz: b942d2fadf478c4aa4e8f27437a29a75c37d9515541bc1c13aec1fece10c8d81b07ad8d60cdce455341fc8f65b35d1a53b3d20bf6005281753774e21e1130354
-  data.tar.gz: f744d5316edcd92e46fcfff79128a20353849b8a5d7037cc808afbc39aeb5c1feecb503d3e47fffad4f5fd175129f152be83c5208dc3f8ca771d748d4deb5736
+  metadata.gz: 8aec70e8a44751d4ab8557b793718c0bd02be3d90715a0048864257a8faf4bf23a5f4b60b780cf6d24658179eb2ecb572bf8b870ca9313b5d6f70839d2df03a5
+  data.tar.gz: 58814116504a8ec8c80961e836adf50b7e50bc049d2a259031e7dc92b9a8f8909ddd8bbc26219197057a6e4a9dfec4ee05cb16144f1b69fdfdc66d46d9408e9b

data/.github/workflows/rake.yml

@@ -16,19 +16,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        ruby: [ '2.7', '2.6', '2.5', '2.4' ]
+        ruby: [ '3.0', '2.7', '2.6', '2.5' ]
         os: [ ubuntu-latest, windows-latest, macos-latest ]
         experimental: [ false ]
-        include:
-          - ruby: '3.0'
-            os: 'ubuntu-latest'
-            experimental: true
-          - ruby: '3.0'
-            os: 'windows-latest'
-            experimental: true
-          - ruby: '3.0'
-            os: 'macos-latest'
-            experimental: true
     steps:
       - uses: actions/checkout@v2
         with:
@@ -49,5 +39,5 @@ jobs:
         with:
           token: ${{ secrets.METANORMA_CI_PAT_TOKEN || secrets.GITHUB_TOKEN }}
           repository: ${{ github.repository }}
-          event-type: notify
+          event-type: tests-passed
           client-payload: '{"ref": "${{ github.ref }}", "sha": "${{ github.sha }}"}'

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

@@ -1,14 +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:
-  DisplayCopNames: false
-  StyleGuideCopsOnly: false
-  TargetRubyVersion: 2.4
-Rails:
-  Enabled: true
+  TargetRubyVersion: 2.5

data/Gemfile

@@ -6,6 +6,6 @@ git_source(:github) { |repo| "https://github.com/#{repo}" }
 
 gemspec
 
-if File.exist? 'Gemfile.devel'
-  eval File.read('Gemfile.devel'), nil, 'Gemfile.devel' # rubocop:disable Security/Eval
+if File.exist? "Gemfile.devel"
+  eval File.read("Gemfile.devel"), nil, "Gemfile.devel" # rubocop:disable Security/Eval
 end

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

@@ -4,6 +4,7 @@ require "relaton"
 require "relaton/cli"
 require "metanorma/collection_manifest"
 require "metanorma-utils"
+require_relative "util"
 
 module Metanorma
   # Metanorma collection of documents
@@ -18,6 +19,8 @@ module Metanorma
     # @return [Hash<String, Metanorma::Document>]
     attr_accessor :documents
 
+    attr_accessor :disambig
+
     # @param file [String] path to source file
     # @param directives [Array<String>] documents-inline to inject the XML into
     #   the collection manifest; documents-external to keeps them outside
@@ -41,25 +44,32 @@ module Metanorma
       @prefatory = args[:prefatory]
       @final = args[:final]
       @log = Metanorma::Utils::Log.new
+      @disambig = Util::DisambigFiles.new
     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
-      Nokogiri::XML::Builder.new do |xml|
+      b = Nokogiri::XML::Builder.new do |xml|
         xml.send("metanorma-collection",
                  "xmlns" => "http://metanorma.org") do |mc|
-          mc << @bibdata.to_xml(bibdata: true, date_format: :full)
-          @manifest.to_xml mc
-          content_to_xml "prefatory", mc
-          doccontainer mc
-          content_to_xml "final", mc
+          collection_body(mc)
         end
-      end.to_xml
+      end
+      b.to_xml
+    end
+
+    def collection_body(coll)
+      coll << @bibdata.to_xml(bibdata: true, date_format: :full)
+      @manifest.to_xml coll
+      content_to_xml "prefatory", coll
+      doccontainer coll
+      content_to_xml "final", coll
     end
 
     def render(opts)
@@ -81,7 +91,9 @@ module Metanorma
       private
 
       def parse_xml(file)
-        xml = Nokogiri::XML File.read(file, encoding: "UTF-8")
+        xml = Nokogiri::XML File.read(file, encoding: "UTF-8") do |config|
+          config.huge
+        end
         if (b = xml.at("/xmlns:metanorma-collection/xmlns:bibdata"))
           bd = Relaton::Cli.parse_xml b
         end
@@ -110,7 +122,7 @@ 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
@@ -127,7 +139,7 @@ module Metanorma
         <<~CONT
 
           == #{xml.at('title')&.text}
-          #{xml.at('p')&.text}
+        #{xml.at('p')&.text}
         CONT
       end
     end
@@ -152,8 +164,8 @@ module Metanorma
       return unless (cnt = send(elm))
 
       require "metanorma-#{doctype}"
-      out = sections(dummy_header + cnt)
-      builder.send(elm + "-content") { |b| b << out }
+      out = sections(dummy_header + cnt.strip)
+      builder.send("#{elm}-content") { |b| b << out }
     end
 
     # @param cnt [String] prefatory/final content
@@ -168,9 +180,18 @@ module Metanorma
       return unless Array(@directives).include? "documents-inline"
 
       documents.each_with_index do |(_, d), i|
-        next if d.attachment
-        id = format("doc%<index>09d", index: i)
-        builder.send("doc-container", id: id) { |b| d.to_xml b }
+        doccontainer1(builder, d, i)
+      end
+    end
+
+    def doccontainer1(builder, doc, idx)
+      id = format("doc%<index>09d", index: idx)
+      builder.send("doc-container", id: id) do |b|
+        if doc.attachment
+          doc.bibitem and b << doc.bibitem.root.to_xml
+          b.attachment Metanorma::Utils::datauri(doc.file)
+        else doc.to_xml b
+        end
       end
     end
 

data/lib/metanorma/collection_fileparse.rb

@@ -8,16 +8,22 @@ module Metanorma
     # 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 = v[:container] || v[:label].nil? || v[:label].empty? ?
-          UUIDTools::UUID.random_create.to_s : v[:label]
-        ret[v[:type]][index] = k
+      xrefs.get.each_with_object({}) do |(k, v), ret|
+        read_anchors1(k, v, ret)
       end
-      ret
+    end
+
+    def read_anchors1(key, val, ret)
+      val[:type] ||= "clause"
+      ret[val[:type]] ||= {}
+      index = if val[:container] || val[:label].nil? || val[:label].empty?
+                UUIDTools::UUID.random_create.to_s
+              else val[:label]
+              end
+      ret[val[:type]][index] = key
+      ret[val[:type]][val[:value]] = key if val[:value]
     end
 
     # @param id [String]
@@ -31,28 +37,36 @@ module Metanorma
 
     # @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, !@files[docid][:attachment])
+    def update_bibitem(bib, identifier) # rubocop:disable Metrics/AbcSize
+      docid = bib&.at(ns("./docidentifier"))&.children&.to_xml
+      return fail_update_bibitem(docid, identifier) unless @files[docid]
+
+      newbib = dup_bibitem(docid, bib)
+      bib.replace(newbib)
+      _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
 
+    def fail_update_bibitem(docid, identifier)
+      error = "[metanorma] Cannot find crossreference to document #{docid} "\
+        "in document #{identifier}."
+      @log.add("Cross-References", nil, error)
+      Util.log(error, :warning)
+    end
+
+    def dup_bibitem(docid, bib)
+      newbib = @files[docid][:bibdata].dup
+      newbib.name = "bibitem"
+      newbib["hidden"] = "true"
+      newbib&.at("./*[local-name() = 'ext']")&.remove
+      newbib["id"] = bib["id"]
+      newbib
+    end
+
     # Resolves direct links to other files in collection
     # (repo(current-metanorma-collection/x),
     # and indirect links to other files in collection
@@ -63,12 +77,13 @@ module Metanorma
     # @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)
+      docxml = Nokogiri::XML(file) { |config| config.huge }
       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|
+      docxml.xpath(ns("//references[bibitem][not(./bibitem[not(@hidden) or "\
+                      "@hidden = 'false'])]")).each do |f|
         f["hidden"] = "true"
       end
       docxml.to_xml
@@ -85,11 +100,9 @@ module Metanorma
       isodoc = IsoDoc::Convert.new({})
       docxml.xpath(ns("//svgmap//eref")).each do |e|
         href = isodoc.eref_target(e)
-        next if href == "##{e['bibitemid']}"
+        next if href == "##{e['bibitemid']}" ||
+          href =~ /^#/ && !docxml.at("//*[@id = '#{href.sub(/^#/, '')}']")
 
-        if href.match(/^#/)
-          next unless docxml.at("//*[@id = '#{href.sub(/^#/, '')}']")
-        end
         e["target"] = href.strip
         e.name = "link"
         e&.elements&.remove
@@ -103,11 +116,18 @@ module Metanorma
     # Preferably with anchor, and is a job to realise dynamic lookup
     # of localities.
     def update_direct_refs_to_docs(docxml, identifier)
+      erefs = docxml.xpath(ns("//eref"))
+        .each_with_object({ citeas: {}, bibitemid: {} }) do |i, m|
+        m[:citeas][i["citeas"]] = true
+        m[:bibitemid][i["bibitemid"]] = true
+      end
       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)
+        docid = b&.at(ns("./docidentifier"))&.children&.to_xml or next
+        erefs[:citeas][docid] and update_anchors(b, docxml, docid)
       end
     end
 
@@ -124,6 +144,9 @@ module Metanorma
     def update_indirect_refs_to_docs1(docxml, schema, id, file)
       docxml.xpath(ns("//eref[@bibitemid = '#{schema}_#{id}']")).each do |e|
         e["citeas"] = file
+        if a = e.at(ns(".//locality[@type = 'anchor']/referenceFrom"))
+          a.children = "#{a.text}_#{Metanorma::Utils::to_ncname(file)}"
+        end
       end
       docid = docxml.at(ns("//bibitem[@id = '#{schema}_#{id}']/"\
                            "docidentifier[@type = 'repository']")) or return
@@ -131,53 +154,52 @@ module Metanorma
       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
+    # update crossrefences to other documents, to include
+    # disambiguating document suffix on id
+    def update_anchors(bib, docxml, docid) # rubocop:disable Metrics/AbcSize
       docxml.xpath("//xmlns:eref[@citeas = '#{docid}']").each do |e|
-        if @files[docid]
-          update_anchor_loc(bib, e, docid)
+        if @files[docid] then update_anchor_loc(bib, e, docid)
         else
-          e << "<strong>** Unresolved reference to document #{docid}, id #{e['bibitemid']}</strong>"
+          e << "<strong>** Unresolved reference to document #{docid} "\
+            "from eref</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)
+    def update_anchor_loc(bib, eref, docid)
+      loc = eref.at(ns(".//locality[@type = 'anchor']")) or
+        return update_anchor_create_loc(bib, eref, 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
+        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
+    def update_anchor_create_loc(_bib, eref, docid)
+      ins = eref.at(ns("./localityStack")) or return
       type = ins&.at(ns("./locality/@type"))&.text
+      type = "clause" if type == "annex"
       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
+      anchor = @files[docid][:anchors].dig(type, ref) or return
+      ins << "<locality type='anchor'><referenceFrom>#{anchor.sub(/^_/, '')}"\
+        "</referenceFrom></locality>"
     end
 
     # gather internal bibitem references
     def gather_internal_refs
       @files.each_with_object({}) do |(_, x), refs|
         next if x[:attachment]
-        file, _ = targetfile(x, true)
+
+        file, = targetfile(x, read: true)
         Nokogiri::XML(file)
           .xpath(ns("//bibitem[@type = 'internal']/"\
-        "docidentifier[@type = 'repository']")).each do |d|
+                    "docidentifier[@type = 'repository']")).each do |d|
           a = d.text.split(%r{/}, 2)
           a.size > 1 or next
           refs[a[0]] ||= {}
@@ -189,18 +211,8 @@ module Metanorma
     # 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, 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
+      @files.keys.reject { |k| @files[k][:attachment] }.each do |identifier|
+        locate_internal_refs1(refs, identifier, @files[identifier])
       end
       refs.each do |schema, ids|
         ids.each do |id, key|
@@ -209,5 +221,18 @@ module Metanorma
       end
       refs
     end
+
+    def locate_internal_refs1(refs, identifier, filedesc)
+      file, _filename = targetfile(filedesc, read: true)
+      xml = Nokogiri::XML(file) { |config| config.huge }
+      t = xml.xpath("//*/@id").each_with_object({}) { |i, x| x[i.text] = true }
+      refs.each do |schema, ids|
+        ids.keys.select { |id| t[id] }.each do |id|
+          n = xml.at("//*[@id = '#{id}']") and
+            n.at("./ancestor-or-self::*[@type = '#{schema}']") and
+            refs[schema][id] = identifier
+        end
+      end
+    end
   end
 end