metanorma 1.3.0 → 1.3.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: c6503cb40980d520fe14a15845b75b748a6cdd40c9206e2218676ac9f2500ff5
-  data.tar.gz: cb169e73038bae1a2c8d70170af1eb4956342056bd4d2c88341f0f08d86462ee
+  metadata.gz: d4ccf8d6a09fd9345faa44ae7201b4f7ee8816a6f36245c26b2482abd3f7afa9
+  data.tar.gz: 7997e0bea6b752e07f7db96f19b6d136b7a9740c046a0850022b477a2223a85b
 SHA512:
-  metadata.gz: 66fb9df1d800763aafccdbb696d755627dfda9d29530200d048f91b59f46e081ff3ffe5f5504579d54ef2667ae33d821d1642329bf21eec6b04e1503e992454c
-  data.tar.gz: d46d5ba951e50d47e75cd86c627c65958a490a4cb6e74ba4f61523b301caa53ae6eddc57a72dd58653b0b5a2894110ff5e0d55d795ac764ef303d0f607424667
+  metadata.gz: 162c6e5e79ff9f7f4f41b17444c68ec23168ee593173b72c251c8623f9a16916f6ae557bc581f39d220c2c6d68d6350c2e4f4de7c000a87e90f39bed7e825609
+  data.tar.gz: a92a8a6ddd41e404cb6a1e00e0a0aaa2ecd645723486769b8656bb09e10f9e595a9df81231713224f6f9781d17c1c6943135d978b5865d0c02842b5e0ccbb84c

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', '2.4' ]
         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/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)
@@ -110,7 +120,7 @@ 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 +137,7 @@ module Metanorma
         <<~CONT
 
           == #{xml.at('title')&.text}
-          #{xml.at('p')&.text}
+        #{xml.at('p')&.text}
         CONT
       end
     end
@@ -152,8 +162,8 @@ 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 +178,18 @@ 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 +8,18 @@ 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|
+      xrefs.get.each_with_object({}) do |(k, v), ret|
+        v[:type] ||= "clause"
         ret[v[:type]] ||= {}
-        index = v[:container] || v[:label].nil? || v[:label].empty? ?
-          UUIDTools::UUID.random_create.to_s : v[:label]
+        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
+        ret[v[:type]][v[:value]] = k if v[:value]
       end
-      ret
     end
 
     # @param id [String]
@@ -32,7 +34,7 @@ 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
+      docid = bib&.at(ns("./docidentifier"))&.children&.to_xml
       unless @files[docid]
         error = "[metanorma] Cannot find crossreference to document #{docid} "\
           "in document #{identifier}."
@@ -41,12 +43,14 @@ module Metanorma
         return
       end
       id = bib["id"]
-      newbib = bib.replace(@files[docid][:bibdata])
+      newbib = @files[docid][:bibdata].dup
       newbib.name = "bibitem"
       newbib["id"] = id
       newbib["hidden"] = "true"
-      newbib&.at(ns("./ext"))&.remove
-      _file, url = targetfile(@files[docid], false, !@files[docid][:attachment])
+      newbib&.at("./*[local-name() = 'ext']")&.remove
+      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
@@ -68,7 +72,8 @@ module Metanorma
       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 +90,9 @@ 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
@@ -106,6 +109,7 @@ module Metanorma
       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
@@ -131,14 +135,16 @@ module Metanorma
       docid.previous = "<docidentifier type='X'>#{file}</docidentifier>"
     end
 
-    # update crossrefences to other documents, to include disambiguating document suffix on id
+    # 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
+      docid = bib&.at(ns("./docidentifier"))&.children.to_xml
       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>"
+          e << "<strong>** Unresolved reference to document #{docid}, "\
+            "id #{e['bibitemid']}</strong>"
         end
       end
     end
@@ -150,18 +156,20 @@ module Metanorma
       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
+      anchor = @files[docid][:anchors].dig(type, ref) or return
       ref_from = Nokogiri::XML::Node.new "referenceFrom", bib
       ref_from.content = anchor.sub(/^_/, "")
       locality = Nokogiri::XML::Node.new "locality", bib
@@ -174,7 +182,8 @@ module Metanorma
     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|
@@ -189,18 +198,8 @@ 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 +208,17 @@ module Metanorma
       end
       refs
     end
+
+    def locate_internal_refs1(refs, identifier, filedesc)
+      file, _filename = targetfile(filedesc, 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
   end
 end

data/lib/metanorma/collection_fileprocess.rb

@@ -15,27 +15,35 @@ module Metanorma
     def read_files(path) # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
       files = {}
       @xml.xpath(ns("//docref")).each do |d|
-        identifier = d.at(ns("./identifier")).text
-        files[identifier] = file_entry(d, path)
-        next if files[identifier][:attachment]
-
-        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"))
+        identifier = d.at(ns("./identifier")).children.to_xml
+        files[identifier] = file_entry(d, identifier, 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"] }
+    # rel_path is the source file address, determined relative to the YAML.
+    # out_path is the destination file address, with any references outside
+    # the working directory (../../...) truncated
+    def file_entry(ref, identifier, _path)
+      out = ref["attachment"] ? ref["fileref"] : File.basename(ref["fileref"])
+      ret = if ref["fileref"]
+              { type: "fileref", ref: @documents[identifier].file,
+                rel_path: ref["fileref"],
+                out_path: out }
             else
-              { type: "id", ref: docref["id"] }
+              { type: "id", ref: ref["id"] }
             end
-      ret[:attachment] = docref["attachment"] if docref["attachment"]
+      ret[:attachment] = ref["attachment"] if ref["attachment"]
       ret
     end
 
@@ -58,12 +66,20 @@ module Metanorma
 
     # 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 output path,
+    # formed relative to YAML file, not input path, relative to calling function
     # @return [Array<String, nil>]
-    def targetfile(data, read = false, doc = true)
-      if data[:type] == "fileref" then ref_file data[:ref], read, doc
-      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, data[:out_path], options[:read], options[:doc]
+      else
+        xml_file data[:id], options[:read]
       end
     end
 
@@ -71,43 +87,46 @@ module Metanorma
     # @param read [Boolean]
     # @param doc [Boolean]
     # @return [Array<String, nil>]
-    def ref_file(ref, read, doc)
+    def ref_file(ref, out, read, doc)
       file = File.read(ref, encoding: "utf-8") if read
-      filename = ref.dup
+      filename = out.dup
       filename.sub!(/\.xml$/, ".html") if doc
       [file, filename]
     end
 
     # compile and output individual file in collection
-    def file_compile(f, filename, identifier)
+    def file_compile(file, filename, identifier)
       # warn "metanorma compile -x html #{f.path}"
+      Array(@directives).include?("presentation-xml") and
+        @compile_options.merge!(passthrough_presentation_xml: true)
       c = Compile.new
-      c.compile f.path, { format: :asciidoc,
-                          extension_keys: @format }.merge(@compile_options)
+      c.compile file.path, { format: :asciidoc,
+                             extension_keys: @format }.merge(@compile_options)
       @files[identifier][:outputs] = {}
       @format.each do |e|
         ext = c.processor.output_formats[e]
         fn = File.basename(filename).sub(/(?<=\.)[^\.]+$/, ext.to_s)
-        FileUtils.mv f.path.sub(/\.xml$/, ".#{ext}"), File.join(@outdir, fn)
+        FileUtils.cp file.path.sub(/\.xml$/, ".#{ext}"), File.join(@outdir, fn)
         @files[identifier][:outputs][e] = File.join(@outdir, fn)
       end
     end
 
     def copy_file_to_dest(fileref)
-      _file, filename = targetfile(fileref, true, false)
-      dest = File.join(@outdir, fileref[:rel_path])
+      dest = File.join(@outdir, fileref[:out_path])
       FileUtils.mkdir_p(File.dirname(dest))
-      FileUtils.cp filename, dest
+      FileUtils.cp fileref[:ref], dest
     end
 
     # process each file in the collection
     # files are held in memory, and altered as postprocessing
     def files # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
       internal_refs = locate_internal_refs
-      @files.each do |identifier, x|
+      @files.each_with_index do |(identifier, x), i|
+        i.positive? && Array(@directives).include?("bare-after-first") and
+          @compile_options.merge!(bare: true)
         if x[:attachment] then copy_file_to_dest(x)
         else
-          file, filename = targetfile(x, true)
+          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)

data/lib/metanorma/collection_manifest.rb

@@ -1,4 +1,5 @@
 # frozen_string_literal: true
+require_relative "util"
 
 module Metanorma
   # Metanorma collection's manifest
@@ -15,6 +16,7 @@ module Metanorma
       @title = title
       @docref = docref
       @manifest = manifest
+      @disambig = Util::DisambigFiles.new
     end
 
     class << self
@@ -43,8 +45,8 @@ module Metanorma
       # @return [Hash{String=>String}]
       def parse_docref(mnf)
         mnf.xpath("xmlns:docref").map do |dr|
-          h = { "identifier" => dr.at("identifier").text }
-          h["fileref"] = dr[:fileref] if dr[:fileref]
+          h = { "identifier" => dr.at("identifier").children.to_xml }
+          dr[:fileref] and h["fileref"] = dr[:fileref]
           h["attachment"] = dr[:attachment] if dr[:attachment]
           h
         end
@@ -63,12 +65,13 @@ module Metanorma
       docs = @docref.each_with_object({}) do |dr, m|
         next m unless dr["fileref"]
 
-        m[dr["identifier"]] = Document.parse_file(File.join(dir, dr["fileref"]), dr["attachment"])
+        m[dr["identifier"]] = Document.parse_file(
+          File.join(dir, dr["fileref"]),
+          dr["attachment"], dr["identifier"]
+        )
         m
       end
-      @manifest.reduce(docs) do |mem, mnf|
-        mem.merge mnf.documents(dir)
-      end
+      @manifest.reduce(docs) { |mem, mnf| mem.merge mnf.documents(dir) }
     end
 
     # @param builder [Nokogiri::XML::Builder]
@@ -99,14 +102,25 @@ module Metanorma
 
     # @param builder [Nokogiri::XML::Builder]
     def docref_to_xml(builder)
+      @disambig = Util::DisambigFiles.new
       @docref.each do |dr|
-        drf = builder.docref { |b| b.identifier dr["identifier"] }
-        drf[:fileref] = dr["fileref"]
-        drf[:attachment] = dr["attachment"] if dr["attachment"]
-        if collection.directives.include?("documents-inline")
-          id = collection.documents.find_index { |k, _| k == dr["identifier"] }
-          drf[:id] = format("doc%<index>09d", index: id)
+        drf = builder.docref do |b|
+          b.identifier do |i|
+            i << dr["identifier"]
+          end
+        end
+        docref_to_xml_attrs(drf, dr)
+      end
+    end
+
+    def docref_to_xml_attrs(elem, docref)
+      elem[:fileref] = @disambig.source2dest_filename(docref["fileref"])
+      elem[:attachment] = docref["attachment"] if docref["attachment"]
+      if collection.directives.include?("documents-inline")
+        id = collection.documents.find_index do |k, _|
+          k == docref["identifier"]
         end
+        elem[:id] = format("doc%<index>09d", index: id)
       end
     end
   end

data/lib/metanorma/collection_renderer.rb

@@ -3,6 +3,7 @@
 require "isodoc"
 require_relative "collection_fileprocess"
 require_relative "fontist_utils"
+require_relative "util"
 
 module Metanorma
   # XML collection renderer
@@ -21,9 +22,9 @@ module Metanorma
     # the collection, and that the flavour gem can sensibly process it. We may
     # need to enhance metadata in the flavour gems isodoc/metadata.rb with
     # collection metadata
-    def initialize(xml, folder, options = {}) # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
+    def initialize(collection, folder, options = {}) # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
       check_options options
-      @xml = Nokogiri::XML xml # @xml is the collection manifest
+      @xml = Nokogiri::XML collection.to_xml # @xml is the collection manifest
       @lang = @xml&.at(ns("//bibdata/language"))&.text || "en"
       @script = @xml&.at(ns("//bibdata/script"))&.text || "Latn"
       @doctype = doctype
@@ -37,9 +38,13 @@ module Metanorma
       @format = options[:format]
       @compile_options = options[:compile] || {}
       @log = options[:log]
+      @documents = collection.documents
+      @directives = collection.directives
+      @disambig = Util::DisambigFiles.new
 
       # list of files in the collection
       @files = read_files folder
+      isodoc_populate(@isodoc)
       FileUtils.rm_rf @outdir
       FileUtils.mkdir_p @outdir
     end
@@ -51,7 +56,7 @@ module Metanorma
     # @option options [Strong] :ourput_folder output directory
     def self.render(col, options = {})
       folder = File.dirname col.file
-      cr = new(col.to_xml, folder, options)
+      cr = new(col, folder, options)
       cr.files
       cr.concatenate(col, options)
       cr.coverpage if options[:format]&.include?(:html)
@@ -61,11 +66,13 @@ module Metanorma
       options[:format] << :presentation if options[:format].include?(:pdf)
       options[:format].uniq.each do |e|
         next unless %i(presentation xml).include?(e)
+
         ext = e == :presentation ? "presentation.xml" : e.to_s
         out = col.clone
         out.directives << "documents-inline"
         out.documents.keys.each do |id|
           next if @files[id][:attachment]
+
           filename = @files[id][:outputs][e]
           out.documents[id] = Metanorma::Document.raw_file(filename)
         end
@@ -100,15 +107,21 @@ module Metanorma
     end
 
     # The isodoc class for the metanorma flavour we are using
-    def isodoc # rubocop:disable Metrics/MethodLength
+    def isodoc
       x = Asciidoctor.load nil, backend: @doctype.to_sym
       isodoc = x.converter.html_converter(Dummy.new)
       isodoc.i18n_init(@lang, @script) # read in internationalisation
+      isodoc.metadata_init(@lang, @script, isodoc.i18n)
+      isodoc.info(@xml, nil)
+      isodoc
+    end
+
+    def isodoc_populate(isodoc)
       # create the @meta class of isodoc, with "navigation" set to the index bar
       # extracted from the manifest
       nav = indexfile(@xml.at(ns("//manifest")))
       i18n = isodoc.i18n
-      i18n.set(:navigation, nav)
+      i18n.set("navigation", nav)
       isodoc.metadata_init(@lang, @script, i18n)
       # populate the @meta class of isodoc with the various metadata fields
       # native to the flavour; used to populate Liquid
@@ -135,6 +148,8 @@ module Metanorma
     # populate liquid template of ARGV[1] with metadata extracted from
     # collection manifest
     def coverpage
+      return unless @coverpage
+
       File.open(File.join(@outdir, "index.html"), "w:UTF-8") do |f|
         f.write @isodoc.populate_template(File.read(@coverpage))
       end
@@ -163,11 +178,19 @@ module Metanorma
     # @param builder [Nokogiri::XML::Builder]
     def docrefs(elm, builder)
       elm.xpath(ns("./docref")).each do |d|
-        identifier = d.at(ns("./identifier")).text
-        link = if d["fileref"] then d["fileref"].sub(/\.xml$/, ".html")
-               else d["id"] + ".html"
-               end
-        builder.li { builder.a identifier, href: link }
+        ident = d.at(ns("./identifier")).children.to_xml
+        builder.li do |li|
+          li.a **{ href: index_link(d, ident) } do |a|
+            a << ident
+          end
+        end
+      end
+    end
+
+    def index_link(docref, ident)
+      if docref["fileref"]
+        @files[ident][:out_path].sub(/\.xml$/, ".html")
+      else "#{docref['id']}.html"
       end
     end
 
@@ -199,8 +222,6 @@ module Metanorma
       unless options[:format].is_a?(Array) && (FORMATS & options[:format]).any?
         raise ArgumentError, "Need to specify formats (xml,html,pdf,doc)"
       end
-      return if !options[:format].include?(:html) || options[:coverpage]
-      raise ArgumentError, "Need to specify a coverpage to render HTML"
     end
   end
 end

data/lib/metanorma/compile.rb

@@ -20,7 +20,7 @@ module Metanorma
     def compile(filename, options = {})
       require_libraries(options)
       options = options_extract(filename, options)
-      validate_type(options) && validate_format(options) || (return nil)
+      validate_options(options)
       @processor = @registry.find_processor(options[:type].to_sym)
       extensions = get_extensions(options) or return nil
       (file, isodoc = process_input(filename, options)) or return nil
@@ -74,7 +74,9 @@ module Metanorma
           memo
         end
       end
-      if !extensions.include?(:presentation) and extensions.any? { |e| @processor.use_presentation_xml(e) }
+      if !extensions.include?(:presentation) && extensions.any? do |e|
+        @processor.use_presentation_xml(e)
+      end
         extensions << :presentation
       end
       extensions
@@ -88,7 +90,7 @@ module Metanorma
         options[:asciimath] and
           file.sub!(/^(=[^\n]+\n)/, "\\1:mn-keep-asciimath:\n")
         dir = File.dirname(filename)
-        dir != '.' and
+        dir != "." and
           file.gsub!(/^include::/, "include::#{dir}/")
         [file, @processor.input_to_isodoc(file, filename, options)]
       when ".xml"
@@ -108,15 +110,17 @@ module Metanorma
 
     def relaton_export(isodoc, options)
       return unless options[:relaton]
+
       xml = Nokogiri::XML(isodoc)
       bibdata = xml.at("//bibdata") || xml.at("//xmlns:bibdata")
-      #docid = bibdata&.at("./xmlns:docidentifier")&.text || options[:filename]
-      #outname = docid.sub(/^\s+/, "").sub(/\s+$/, "").gsub(/\s+/, "-") + ".xml"
+      # docid = bibdata&.at("./xmlns:docidentifier")&.text || options[:filename]
+      # outname = docid.sub(/^\s+/, "").sub(/\s+$/, "").gsub(/\s+/, "-") + ".xml"
       File.open(options[:relaton], "w:UTF-8") { |f| f.write bibdata.to_xml }
     end
 
     def clean_sourcecode(xml)
-      xml.xpath(".//callout | .//annotation | .//xmlns:callout | .//xmlns:annotation").each do |x|
+      xml.xpath(".//callout | .//annotation | .//xmlns:callout | "\
+                ".//xmlns:annotation").each do |x|
         x.remove
       end
       xml.xpath(".//br | .//xmlns:br").each { |x| x.replace("\n") }
@@ -125,6 +129,7 @@ module Metanorma
 
     def extract(isodoc, dirname, extract_types)
       return unless dirname
+
       if extract_types.nil? || extract_types.empty?
         extract_types = [:sourcecode, :image, :requirement]
       end
@@ -207,6 +212,7 @@ module Metanorma
         isodoc_options = @processor.extract_options(file)
         isodoc_options[:datauriimage] = true if options[:datauriimage]
         isodoc_options[:sourcefilename] = options[:filename]
+        isodoc_options[:bare] = options[:bare]
         file_extension = @processor.output_formats[ext]
         outfilename = f.sub(/\.[^.]+$/, ".#{file_extension}")
         if ext == :pdf
@@ -217,19 +223,22 @@ module Metanorma
         if ext == :rxl
           options[:relaton] = outfilename
           relaton_export(isodoc, options)
+        elsif options[:passthrough_presentation_xml] && ext == :presentation
+          FileUtils.cp f, presentationxml_name
         else
           begin
             @processor.use_presentation_xml(ext) ?
               @processor.output(nil, presentationxml_name, outfilename, ext, isodoc_options) :
               @processor.output(isodoc, xml_name, outfilename, ext, isodoc_options)
           rescue StandardError => e
-            puts e.message
-            puts e.backtrace.join("\n")
+            if e.message.include? "Fatal:"
+              @errors << e.message
+            else
+              puts e.message
+              puts e.backtrace.join("\n")
+            end
           end
         end
-        if ext == :pdf
-          # font_locations.unlink
-        end
         wrap_html(options, file_extension, outfilename)
       end
     end

data/lib/metanorma/compile_validate.rb

@@ -1,45 +1,51 @@
 module Metanorma
   class Compile
+    def validate_options(options)
+      validate_type(options)
+      validate_format(options)
+    end
+
     def validate_type(options)
       unless options[:type]
         Util.log("[metanorma] Error: Please specify a standard type: "\
-                 "#{@registry.supported_backends}.", :error)
-        return nil
+                 "#{@registry.supported_backends}.", :fatal)
       end
       stdtype = options[:type].to_sym
-      metanorma_flavor = "metanorma-#{stdtype}"
+      load_flavor(stdtype)
+    end
+
+    def validate_format(options)
+      unless options[:format] == :asciidoc
+        Util.log("[metanorma] Error: Only source file format currently "\
+                 "supported is 'asciidoc'.", :fatal)
+      end
+    end
+
+    private
+
+    def load_flavor(stdtype)
+      flavor = "metanorma-#{stdtype}"
       unless @registry.supported_backends.include? stdtype
-        Util.log("[metanorma] Info: Loading `#{metanorma_flavor}` gem "\
+        Util.log("[metanorma] Info: Loading `#{flavor}` gem "\
                  "for standard type `#{stdtype}`.", :info)
       end
-      begin
-        require "metanorma-#{stdtype}"
-        Util.log("[metanorma] Info: gem `#{metanorma_flavor}` loaded.", :info)
-      rescue Gem::ConflictError
-        Util.log("[metanorma] Error: Couldn't resolve dependencies for "\
-                 "`metanorma-#{stdtype}`, Please add it to your Gemfile "\
-                 "and run bundle install first", :error)
-        return false
-      rescue LoadError
-        Util.log("[metanorma] Error: loading gem `#{metanorma_flavor}` "\
-                 "failed. Exiting.", :error)
-        return false
-      end
+      require_flavor(flavor, stdtype)
       unless @registry.supported_backends.include? stdtype
-        Util.log("[metanorma] Error: The `#{metanorma_flavor}` gem "\
-                 "still doesn't support `#{stdtype}`. Exiting.", :error)
-        return false
+        Util.log("[metanorma] Error: The `#{flavor}` gem "\
+                 "still doesn't support `#{stdtype}`. Exiting.", :fatal)
       end
-      true
     end
 
-    def validate_format(options)
-      unless options[:format] == :asciidoc
-        Util.log("[metanorma] Error: Only source file format currently "\
-                 "supported is 'asciidoc'.", :error)
-        return false
-      end
-      true
+    def require_flavor(flavor, stdtype)
+      require flavor
+      Util.log("[metanorma] Info: gem `#{flavor}` loaded.", :info)
+    rescue Gem::ConflictError
+      Util.log("[metanorma] Error: Couldn't resolve dependencies for "\
+               "`metanorma-#{stdtype}`, Please add it to your Gemfile "\
+               "and run bundle install first", :fatal)
+    rescue LoadError
+      Util.log("[metanorma] Error: loading gem `#{flavor}` "\
+               "failed. Exiting.", :fatal)
     end
   end
 end

data/lib/metanorma/config.rb

@@ -15,7 +15,7 @@ module Metanorma
     attr_accessor :logs
 
     def initialize
-      @logs ||= [:warning, :error, :fatal]
+      @logs ||= %i[warning error fatal]
     end
   end
 

data/lib/metanorma/document.rb

@@ -1,7 +1,7 @@
 module Metanorma
   class Document
     # @return [Strin]
-    attr_reader :file, :attachment
+    attr_reader :file, :attachment, :bibitem
 
     # @param bibitem [RelatonBib::BibliographicItem]
     def initialize(bibitem, file, options = {})
@@ -14,9 +14,12 @@ module Metanorma
     class << self
       # @param file [String] file path
       # @param attachment [Bool] is an attachment
+      # @param identifier [String] is the identifier assigned the file
+      # in the collection file
       # @return [Metanorma::Document]
-      def parse_file(file, attachment)
-        new bibitem(file), file, { attachment: attachment }
+      def parse_file(file, attachment, identifier = nil)
+        new(bibitem(file, attachment, identifier), file,
+            { attachment: attachment })
       end
 
       # #param xml [Nokogiri::XML::Document, Nokogiri::XML::Element]
@@ -31,6 +34,12 @@ module Metanorma
         new(doc, filename, raw: true)
       end
 
+      def attachment_bibitem(identifier)
+        Nokogiri::XML(
+          "<bibdata><docidentifier>#{identifier}</docidentifier></bibdata>",
+        )
+      end
+
       private
 
       # #param xml [Nokogiri::XML::Document, Nokogiri::XML::Element]
@@ -51,13 +60,16 @@ module Metanorma
       # @param file [String]
       # @return [RelatonBib::BibliographicItem,
       #   RelatonIso::IsoBibliographicItem]
-      def bibitem(file)
-        case format(file)
-        when :xml
-          from_xml Nokogiri::XML(File.read(file, encoding: "UTF-8"))
-        when :yaml
-          yaml = File.read(file, encoding: "UTF-8")
-          Relaton::Cli::YAMLConvertor.convert_single_file(yaml)
+      def bibitem(file, attachment, identifier)
+        if attachment then attachment_bibitem(identifier)
+        else
+          case format(file)
+          when :xml
+            from_xml Nokogiri::XML(File.read(file, encoding: "UTF-8"))
+          when :yaml
+            yaml = File.read(file, encoding: "UTF-8")
+            Relaton::Cli::YAMLConvertor.convert_single_file(yaml)
+          end
         end
       end
     end

data/lib/metanorma/input.rb

@@ -3,6 +3,5 @@ require_relative "./input/asciidoc"
 
 module Metanorma
   module Input
-
   end
 end

data/lib/metanorma/input/asciidoc.rb

@@ -2,20 +2,14 @@ require "nokogiri"
 
 module Metanorma
   module Input
-
     class Asciidoc < Base
-
       def process(file, filename, type, options = {})
         require "asciidoctor"
         out_opts = {
-          to_file: false,
-          safe: :safe,
-          backend: type,
-          header_footer: true,
-          attributes: [
-            "nodoc", "stem", "xrefstyle=short", "docfile=#{filename}",
-            "output_dir=#{options[:output_dir]}"
-          ]
+          to_file: false, safe: :safe, backend: type, header_footer: true,
+          attributes: ["nodoc", "stem", "xrefstyle=short",
+                       "docfile=#{filename}",
+                       "output_dir=#{options[:output_dir]}"]
         }
         unless asciidoctor_validate(file, filename, out_opts)
           warn "Cannot continue compiling Asciidoctor document"
@@ -27,11 +21,12 @@ module Metanorma
       def asciidoctor_validate(file, filename, options)
         err = nil
         begin
-          previous_stderr, $stderr = $stderr, StringIO.new
+          previous_stderr = $stderr
+          $stderr = StringIO.new
           ::Asciidoctor.load(file, options)
-          %r{(\n|^)asciidoctor: ERROR: ['"]?#{Regexp.escape(filename || 
-            "<empty>")}['"]?: line \d+: include file not found: }.match($stderr.string) and
-              err = $stderr.string
+          %r{(\n|^)asciidoctor: ERROR: ['"]?#{Regexp.escape(filename ||
+            "<empty>")}['"]?: line \d+: include file not found: }
+            .match($stderr.string) and err = $stderr.string
         ensure
           $stderr = previous_stderr
         end
@@ -45,8 +40,9 @@ module Metanorma
         /\n:mn-output-extensions: (?<extensions>[^\n]+)\n/ =~ headerextract
         /\n:mn-relaton-output-file: (?<relaton>[^\n]+)\n/ =~ headerextract
         /\n(?<asciimath>:mn-keep-asciimath:[^\n]*)\n/ =~ headerextract
-        asciimath = defined?(asciimath) ?
-          (!asciimath.nil? && asciimath != ":mn-keep-asciimath: false") : nil
+        asciimath = if defined?(asciimath)
+                      (!asciimath.nil? && asciimath != ":mn-keep-asciimath: false")
+                    end
         asciimath = nil if asciimath == false
         {
           type: defined?(type) ? type : nil,
@@ -60,38 +56,39 @@ module Metanorma
         attr&.sub(/^#{name}:\s*$/, "#{name}: true")&.sub(/^#{name}:\s+/, "")
       end
 
+      ADOC_OPTIONS = %w(htmlstylesheet htmlcoverpage htmlintropage scripts
+                        scripts-override scripts-pdf wordstylesheet bare i18nyaml
+                        standardstylesheet header wordcoverpage wordintropage
+                        ulstyle olstyle htmlstylesheet-override
+                        htmltoclevels doctoclevels sectionsplit
+                        body-font header-font monospace-font title-font
+                        wordstylesheet-override).freeze
+
       def extract_options(file)
         header = file.sub(/\n\n.*$/m, "\n")
-        ret = %w(htmlstylesheet htmlcoverpage htmlintropage scripts
-                 scripts-pdf wordstylesheet
-                 standardstylesheet header wordcoverpage wordintropage i18nyaml
-                 ulstyle olstyle htmlstylesheet-override
-                 htmltoclevels doctoclevels sectionsplit
-                 body-font header-font monospace-font title-font
-                 wordstylesheet-override).each_with_object({}) do |w, acc|
+        ret = ADOC_OPTIONS.each_with_object({}) do |w, acc|
           m = /\n:#{w}: ([^\n]+)\n/.match(header) or next
           acc[w.gsub(/-/, "").sub(/override$/, "_override")
             .sub(/pdf$/, "_pdf").to_sym] = m[1]
         end
         /\n:data-uri-image: (?<datauriimage>[^\n]+)\n/ =~ header
-        /\n:(?<hierarchical_assets>hierarchical-assets:[^\n]*)\n/ =~ header
+        /\n:(?<hier_assets>hierarchical-assets:[^\n]*)\n/ =~ header
         /\n:(?<use_xinclude>use-xinclude:[^\n]*)\n/ =~ header
         /\n:(?<break_up>break-up-urls-in-tables:[^\n]*)\n/ =~ header
 
-        defined?(hierarchical_assets) and
-          hierarchical_assets = empty_attr(hierarchical_assets, "hierarchical-assets")
+        defined?(hier_assets) and
+          hier_assets = empty_attr(hier_assets, "hierarchical-assets")
         defined?(use_xinclude) and
           use_xinclude = empty_attr(use_xinclude, "use-xinclude")
         defined?(break_up) and
           break_up = empty_attr(break_up, "break-up-urls-in-tables")
-        ret.merge({
+        ret.merge(
           datauriimage: defined?(datauriimage) ? datauriimage != "false" : nil,
-          hierarchical_assets: defined?(hierarchical_assets) ? hierarchical_assets : nil,
+          hierarchical_assets: defined?(hier_assets) ? hier_assets : nil,
           use_xinclude: defined?(use_xinclude) ? use_xinclude : nil,
           break_up_urls_in_tables: defined?(break_up) ? break_up : nil,
-        }).reject { |_, val| val.nil? }
+        ).reject { |_, val| val.nil? }
       end
-
     end
   end
 end

data/lib/metanorma/output.rb

@@ -4,7 +4,5 @@ require_relative "./output/xslfo"
 
 module Metanorma
   module Output
-
   end
 end
-

data/lib/metanorma/output/utils.rb

@@ -7,7 +7,8 @@ module Metanorma
         def file_path(url_path)
           file_url = url_path
           file_url = "file://#{url_path}" if Pathname.new(file_url).absolute?
-          file_url = "file://#{Dir.pwd}/#{url_path}" unless %r{^file://} =~ file_url
+          %r{^file://}.match?(file_url) or
+            file_url = "file://#{Dir.pwd}/#{url_path}"
           file_url
         end
       end

data/lib/metanorma/util.rb

@@ -11,5 +11,33 @@ module Metanorma
         exit(1)
       end
     end
+
+    class DisambigFiles
+      def initialize
+        @seen_filenames = []
+      end
+
+      def source2dest_filename(name, disambig = true)
+        n = name.sub(%r{^(\./)?(\.\./)+}, "")
+        dir = File.dirname(n)
+        base = File.basename(n)
+        if disambig && @seen_filenames.include?(base)
+          base = disambiguate_filename(base)
+        end
+        @seen_filenames << base
+        dir == "." ? base : File.join(dir, base)
+      end
+
+      def disambiguate_filename(base)
+        m = /^(?<start>.+\.)(?!0)(?<num>\d+)\.(?<suff>[^.]*)$/.match(base) ||
+          /^(?<start>.+\.)(?<suff>[^.]*)/.match(base) ||
+          /^(?<start>.+)$/.match(base)
+        i = m.names.include?("num") ? m["num"].to_i + 1 : 1
+        while @seen_filenames.include? base = "#{m['start']}#{i}.#{m['suff']}"
+          i += 1
+        end
+        base
+      end
+    end
   end
 end

data/lib/metanorma/version.rb

@@ -1,3 +1,3 @@
 module Metanorma
-  VERSION = "1.3.0".freeze
+  VERSION = "1.3.5".freeze
 end

data/metanorma.gemspec

@@ -20,7 +20,7 @@ Gem::Specification.new do |spec|
   spec.bindir        = "bin"
   # spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
   spec.require_paths = ["lib"]
-  spec.required_ruby_version = ">= 2.4.0"
+  spec.required_ruby_version = ">= 2.5.0"
 
   spec.add_runtime_dependency "asciidoctor"
   spec.add_runtime_dependency "fontist", "~> 1.8"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: metanorma
 version: !ruby/object:Gem::Version
-  version: 1.3.0
+  version: 1.3.5
 platform: ruby
 authors:
 - Ribose Inc.
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-04-12 00:00:00.000000000 Z
+date: 2021-06-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: asciidoctor
@@ -286,7 +286,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 2.4.0
+      version: 2.5.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="