metanorma 1.3.4 → 1.3.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 066d89b3df0a8865f52e3e70b257a1a4ce3c71eb9f8b6840a87b9046743536d1
+  metadata.gz: d4ccf8d6a09fd9345faa44ae7201b4f7ee8816a6f36245c26b2482abd3f7afa9
+  data.tar.gz: 7997e0bea6b752e07f7db96f19b6d136b7a9740c046a0850022b477a2223a85b
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+  data.tar.gz: a92a8a6ddd41e404cb6a1e00e0a0aaa2ecd645723486769b8656bb09e10f9e595a9df81231713224f6f9781d17c1c6943135d978b5865d0c02842b5e0ccbb84c

data/.rubocop.yml

@@ -7,4 +7,4 @@ inherit_from:
 # ...
 
 AllCops:
-  TargetRubyVersion: 2.4
+  TargetRubyVersion: 2.5

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
@@ -41,6 +44,7 @@ module Metanorma
       @prefatory = args[:prefatory]
       @final = args[:final]
       @log = Metanorma::Utils::Log.new
+      @disambig = Util::DisambigFiles.new
     end
 
     # rubocop:enable Metrics/AbcSize,Metrics/MethodLength

data/lib/metanorma/collection_fileparse.rb

@@ -11,12 +11,14 @@ module Metanorma
       xrefs = @isodoc.xref_init(@lang, @script, @isodoc, @isodoc.i18n, {})
       xrefs.parse xml
       xrefs.get.each_with_object({}) do |(k, v), ret|
+        v[:type] ||= "clause"
         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
+        ret[v[:type]][v[:value]] = k if v[:value]
       end
     end
 
@@ -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}."
@@ -41,11 +43,12 @@ 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
+      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
@@ -69,7 +72,7 @@ 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 "\
+      docxml.xpath(ns("//references[bibitem][not(./bibitem[not(@hidden) or "\
                       "@hidden = 'false'])]")).each do |f|
         f["hidden"] = "true"
       end
@@ -135,7 +138,7 @@ module Metanorma
     # 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)
@@ -161,11 +164,12 @@ module Metanorma
 
     # 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

data/lib/metanorma/collection_fileprocess.rb

@@ -15,7 +15,7 @@ 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
+        identifier = d.at(ns("./identifier")).children.to_xml
         files[identifier] = file_entry(d, identifier, path)
         if files[identifier][:attachment]
           files[identifier][:bibdata] = Metanorma::Document
@@ -34,15 +34,16 @@ module Metanorma
     # 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(docref, identifier, _path)
-      ret = if docref["fileref"]
+    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: docref["fileref"],
-                out_path: Util::source2dest_filename(docref["fileref"]) }
+                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
 
@@ -74,9 +75,9 @@ module Metanorma
     # @return [Array<String, nil>]
     def targetfile(data, options)
       options = { read: false, doc: true, relative: false }.merge(options)
-      path = options[:relative] ? data[:out_path] : data[:ref]
+      path = options[:relative] ? data[:rel_path] : data[:ref]
       if data[:type] == "fileref"
-        ref_file path, options[:read], options[:doc]
+        ref_file path, data[:out_path], options[:read], options[:doc]
       else
         xml_file data[:id], options[:read]
       end
@@ -86,9 +87,9 @@ 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$/, ".html") if doc
       [file, filename]
     end
@@ -96,6 +97,8 @@ module Metanorma
     # compile and output individual file in collection
     def file_compile(file, filename, identifier)
       # warn "metanorma compile -x html #{f.path}"
+      Array(@directives).include?("presentation-xml") and
+        @compile_options.merge!(passthrough_presentation_xml: true)
       c = Compile.new
       c.compile file.path, { format: :asciidoc,
                              extension_keys: @format }.merge(@compile_options)
@@ -103,23 +106,24 @@ module Metanorma
       @format.each do |e|
         ext = c.processor.output_formats[e]
         fn = File.basename(filename).sub(/(?<=\.)[^\.]+$/, ext.to_s)
-        FileUtils.mv file.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, read: true, doc: false)
       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, read: true)

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
@@ -43,7 +45,7 @@ module Metanorma
       # @return [Hash{String=>String}]
       def parse_docref(mnf)
         mnf.xpath("xmlns:docref").map do |dr|
-          h = { "identifier" => dr.at("identifier").text }
+          h = { "identifier" => dr.at("identifier").children.to_xml }
           dr[:fileref] and h["fileref"] = dr[:fileref]
           h["attachment"] = dr[:attachment] if dr[:attachment]
           h
@@ -100,14 +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] = Util::source2dest_filename(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
@@ -38,9 +39,12 @@ module Metanorma
       @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
@@ -103,15 +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
@@ -168,11 +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
 

data/lib/metanorma/compile.rb

@@ -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
@@ -217,6 +223,8 @@ 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) ?

data/lib/metanorma/util.rb

@@ -12,8 +12,32 @@ module Metanorma
       end
     end
 
-    def self.source2dest_filename(name)
-      name.sub(%r{^(\./)?(\.\./)+}, "")
+    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 = "1.3.4".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: 1.3.4
+  version: 1.3.5
 platform: ruby
 authors:
 - Ribose Inc.
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-06-07 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:
   - - ">="