Almirah 0.2.8 → 0.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 04afed7a81d07d1789a115c7c31e4d09df1c638eaf2eacf390f7ec7611e522ef
-  data.tar.gz: 403f2c7cb9381b4ee12859b27f9fc584ce73274ced9254a7b08b5cda4b316849
+  metadata.gz: be9e792ca43617f09611a801b8e8c8efde741ec531a97295de8d65378232c0d2
+  data.tar.gz: 492000cb9aadaf0731e077b46ec3a32b573da9c8cd2acfaff6f282dec75c394d
 SHA512:
-  metadata.gz: 3db8f92b780657bc4109b96dc64f19c28249c509ba9a7d8c33b71c37fa6fb821a7a140d32bd955e20a7f49e5401b55d64d8732cccd2c7a5800de494dc05660db
-  data.tar.gz: eeab5aa32a82b0efbe0cc3c3f1e576cd99b9ec1eadd9e5b1e46b7e5616d8c715d8b52640a83e9e14ce47ec443239a477f3cc8488441b356dceda6a88a22e306e
+  metadata.gz: 51e65415ee9d0a8c0f77d19d21ab525a01cbc4c025bc5572f92f2df13bc56ceed8b04be5e18d3c0308c468c43986dd267046d9b1c125e281ad01476b08a93569
+  data.tar.gz: b64d9b5a0da5d254ecbc6dd861db05017b8cd81e13c0f58071413816d9b20d879187cbda5b2a703d5eae9f92ec044000010fc6b1b103fa30a9de04b265562cde

data/lib/almirah/doc_fabric.rb

@@ -1,8 +1,12 @@
 require_relative 'doc_types/base_document'
 require_relative 'doc_types/specification'
+require_relative 'doc_types/source_file'
 require_relative 'doc_types/protocol'
 require_relative 'doc_types/coverage'
+require_relative 'doc_types/implementation'
+require_relative 'doc_types/traceability'
 require_relative 'doc_parser'
+require_relative 'source_file_parser'
 require_relative 'dom/document'
 require_relative 'doc_items/heading'
 
@@ -51,8 +55,22 @@ class DocFabric
     doc
   end
 
-  def self.parse_document(doc)
+  def self.create_implementation_document(top_document)
+    doc = Implementation.new top_document
+    Heading.reset_global_section_number
+    doc.headings << Heading.new(doc, doc.title, 0)
+    # Build dom
+    doc.dom = Document.new(doc.headings)
+    doc
+  end
 
+  def self.create_source_file(repository_path, path, repository_name)
+    doc = SourceFile.new repository_path, path, repository_name
+    DocFabric.parse_source_file doc
+    doc
+  end
+
+  def self.parse_document(doc)
     file = File.open(doc.path)
     file_lines = file.readlines
     file.close
@@ -62,4 +80,12 @@ class DocFabric
     # Build dom
     doc.dom = Document.new(doc.headings) if doc.is_a?(Specification) || doc.is_a?(Protocol)
   end
+
+  def self.parse_source_file(doc)
+    file = File.open(doc.path)
+    file_lines = file.readlines
+    file.close
+
+    SourceFileParser.parse(doc, file_lines)
+  end
 end

data/lib/almirah/doc_items/controlled_paragraph.rb

@@ -1,7 +1,8 @@
 require_relative 'paragraph'
 
+# <REQ> Implementa a controlled paragraph as a subclass of the DocItem >[SRS-001] </REQ>
 class ControlledParagraph < Paragraph
-  attr_accessor :id, :up_link_ids, :down_links, :coverage_links
+  attr_accessor :id, :up_link_ids, :down_links, :coverage_links, :source_code_links
 
   def initialize(doc, text, id)
     super(doc, text)
@@ -10,6 +11,7 @@ class ControlledParagraph < Paragraph
     @up_link_ids = nil
     @down_links = nil
     @coverage_links = nil
+    @source_code_links = nil
   end
 
   def to_html
@@ -32,7 +34,7 @@ class ControlledParagraph < Paragraph
           up_link_doc_name = tmp[1].downcase
         end
         s += "\t\t<td class=\"item_id\">\
-            <a href=\"./../#{up_link_doc_name}/#{up_link_doc_name}.html##{@up_link_ids[0]}\" \
+            <a href=\"#{parent_doc.specifications_path}#{up_link_doc_name}/#{up_link_doc_name}.html##{@up_link_ids[0]}\" \
             class=\"external\" title=\"Linked to\">#{@up_link_ids[0]}</a></td>\n"
       else
         s += "\t\t<td class=\"item_id\">"
@@ -45,7 +47,7 @@ class ControlledParagraph < Paragraph
           if tmp = /^([a-zA-Z]+)-\d+/.match(lnk)
             up_link_doc_name = tmp[1].downcase
           end
-          s += "\t\t\t<a href=\"./../#{up_link_doc_name}/#{up_link_doc_name}.html##{lnk}\" \
+          s += "\t\t\t<a href=\"#{parent_doc.specifications_path}#{up_link_doc_name}/#{up_link_doc_name}.html##{lnk}\" \
             class=\"external\" title=\"Linked to\">#{lnk}</a>\n<br>"
         end
         s += '</div>'

data/lib/almirah/doc_items/paragraph.rb

@@ -1,5 +1,6 @@
 require_relative 'doc_item'
 
+# <REQ> Implementa a non-controlled paragraph as a subclass of the DocItem >[SRS-004] </REQ>
 class Paragraph < DocItem
   attr_accessor :text
 

data/lib/almirah/doc_items/source_code_paragraph.rb

@@ -0,0 +1,7 @@
+class SourceCodeParagraph < ControlledParagraph
+  @@source_code_links_counter = 'AAAA'
+  def initialize(doc, text)
+    super(doc, text, "SC-#{@@source_code_links_counter}")
+    @@source_code_links_counter.next!
+  end
+end

data/lib/almirah/doc_types/base_document.rb

@@ -49,10 +49,21 @@ class BaseDocument # rubocop:disable Style/Documentation
         elsif instance_of? Coverage
           file.puts '<link rel="stylesheet" href="../../css/main.css">'
           file.puts '<script src="../../scripts/main.js"></script>'
+        elsif instance_of? Implementation
+          file.puts '<link rel="stylesheet" href="../../css/main.css">'
+          file.puts '<script src="../../scripts/main.js"></script>'
         elsif instance_of? Protocol
           file.puts '<link rel="stylesheet" href="../../../css/main.css">'
           file.puts '<script src="../../../scripts/main.js"></script>'
         end
+      elsif s.include?('{{HOME_BUTTON}}')
+        if @id == 'index'
+          file.puts '<a id="home_menu_item" href="./index.html"><span><i class="fa fa-home" aria-hidden="true"></i></span>&nbsp;Home</a>'
+        elsif instance_of? Protocol
+          file.puts '<a id="index_menu_item" href="./../../../index.html"><span><i class="fa fa-info" aria-hidden="true"></i></span>&nbsp;Index</a>'
+        else
+           file.puts '<a id="index_menu_item" href="./../../index.html"><span><i class="fa fa-info" aria-hidden="true"></i></span>&nbsp;Index</a>'
+        end
       elsif s.include?('{{GEM_VERSION}}')
         file.puts "(#{Gem.loaded_specs['Almirah'].version.version})"
       else

data/lib/almirah/doc_types/implementation.rb

@@ -0,0 +1,104 @@
+require_relative 'base_document'
+
+class Implementation < BaseDocument
+    attr_accessor :top_doc, :bottom_doc, :items, :is_agregated, :traced_items
+
+    def initialize(top_doc)
+        super()
+        @top_doc = top_doc
+
+        @is_agregated = true
+        @traced_items = {}
+
+        @id = if @is_agregated
+                top_doc.id + '-sources'
+              else
+                top_doc.id + '-' + bottom_doc.id
+              end
+
+        @title = 'Implementation Matrix: ' + @id
+    end
+
+    def to_console
+        puts "\e[35m" + 'Implementation: ' + @id + "\e[0m"
+    end
+
+    def to_html(nav_pane, output_file_path)
+        html_rows = []
+
+        html_rows.append('')
+        s = "<h1>#{@title}</h1>\n"
+        s += "<table class=\"controlled\">\n"
+        s += "\t<thead>"
+        s += "\t\t<th>#</th>"
+        s += "\t\t<th style='font-weight: bold;'>#{@top_doc.title}</th>"
+        s += "\t\t<th>#</th>"
+        s += "\t\t<th style='font-weight: bold;'>Repository</th>"
+        s += "\t\t<th style='font-weight: bold;'>File Name</th>"
+        s += "\t\t<th style='font-weight: bold;'>Comment</th>"
+        s += "\t</thead>\n"
+        html_rows.append s
+
+        sorted_items = @top_doc.controlled_items.sort_by { |w| w.id }
+
+        sorted_items.each do |top_item|
+            row = render_table_row top_item
+            html_rows.append row
+        end
+        html_rows.append "</table>\n"
+
+        save_html_to_file(html_rows, nav_pane, output_file_path)
+    end
+
+    def render_table_row(top_item)
+        s = ''
+        top_f_text = top_item.format_string(top_item.text)
+        id_color = ''
+
+        if top_item.source_code_links && top_item.source_code_links.length.positive?
+
+            top_item_rendered = false
+
+            top_item.source_code_links.each do |bottom_item|
+                id_color = "style='background-color: #cff4d2;'"
+                bottom_f_text = bottom_item.format_string(bottom_item.text)
+                file_name = bottom_item.parent_doc.id
+                repository = bottom_item.parent_doc.repository
+
+                p = bottom_item.parent_doc.html_file_path.split('/build/source_files/').last
+                html_source_file_relative_path = "./../../source_files/#{p}"
+
+                s += "\t<tr>\n"
+                s += "\t\t<td class=\"item_id\"><a href=\"./../#{top_item.parent_doc.id}/#{top_item.parent_doc.id}.html##{top_item.id}\" class=\"external\">#{top_item.id}</a></td>\n"
+                s += "\t\t<td class=\"item_text\" style='width: 28%;'>#{top_f_text}</td>\n"
+                s += "\t\t<td class=\"item_id\"><a href=\"#{html_source_file_relative_path}##{bottom_item.id}\" class=\"external\">#{bottom_item.id}</a></td>\n"
+                s += "\t\t<td class=\"item_text\" style='width: 16%;'>#{repository}</td>\n"
+                s += "\t\t<td class=\"item_text\" style='width: 16%;'>#{file_name}</td>\n"
+                s += "\t\t<td class=\"item_text\" style='width: 28%;'>#{bottom_f_text}</td>\n"
+                s += "\t</tr>\n"
+                top_item_rendered = true
+                @traced_items[top_item.id.to_s.downcase] = top_item
+            end
+            unless top_item_rendered
+                s += "\t<tr>\n"
+                s += "\t\t<td class=\"item_id\"><a href=\"./../#{top_item.parent_doc.id}/#{top_item.parent_doc.id}.html##{top_item.id}\" class=\"external\">#{top_item.id}</a></td>\n"
+                s += "\t\t<td class=\"item_text\" style='width: 28%;'>#{top_f_text}</td>\n"
+                s += "\t\t<td class=\"item_id\"></td>\n"
+                s += "\t\t<td class=\"item_text\" style='width: 16%;'></td>\n"
+                s += "\t\t<td class=\"item_text\" style='width: 16%;'></td>\n"
+                s += "\t\t<td class=\"item_text\" style='width: 28%;'></td>\n"
+                s += "\t</tr>\n"
+            end
+        else
+            s += "\t<tr>\n"
+            s += "\t\t<td class=\"item_id\"><a href=\"./../#{top_item.parent_doc.id}/#{top_item.parent_doc.id}.html##{top_item.id}\" class=\"external\">#{top_item.id}</a></td>\n"
+            s += "\t\t<td class=\"item_text\" style='width: 28%;'>#{top_f_text}</td>\n"
+            s += "\t\t<td class=\"item_id\"></td>\n"
+            s += "\t\t<td class=\"item_text\" style='width: 16%;'></td>\n"
+            s += "\t\t<td class=\"item_text\" style='width: 16%;'></td>\n"
+            s += "\t\t<td class=\"item_text\" style='width: 28%;'></td>\n"
+            s += "\t</tr>\n"
+        end
+        s
+    end
+end

data/lib/almirah/doc_types/index.rb

@@ -36,9 +36,10 @@ class Index < BaseDocument # rubocop:disable Metrics/ClassLength,Style/Documenta
     s += "\t\t<th title=\"Number of 'TODO:' blocks in document\">TODOs</th>\n"
     s += "\t\t<th title=\"The last Controlled Paragraph sequence number (ID) used in the document\">Last Used<br>ID</th>\n"
     s += "</thead>\n"
+
     html_rows.append s
 
-    sorted_items = @project.specifications.sort_by(&:id)
+    sorted_items = @project.project_data.specifications.sort_by(&:id)
 
     sorted_items.each do |doc| # rubocop:disable Metrics/BlockLength
       s = "\t<tr>\n"
@@ -101,7 +102,7 @@ class Index < BaseDocument # rubocop:disable Metrics/ClassLength,Style/Documenta
     s += "</thead>\n"
     html_rows.append s
 
-    sorted_items = @project.traceability_matrices.sort_by(&:id)
+    sorted_items = @project.project_data.traceability_matrices.sort_by(&:id)
     # buble-up design inputs
     design_inputs = []
     others = []
@@ -131,7 +132,7 @@ class Index < BaseDocument # rubocop:disable Metrics/ClassLength,Style/Documenta
     html_rows.append "</table>\n"
 
     # Coverage Matrices
-    unless @project.coverage_matrices.empty?
+    unless @project.project_data.coverage_matrices.empty?
       s = "<h2>Coverage Matrices</h2>\n"
       s += "<table class=\"controlled\">\n"
       s += "\t<thead>\n"
@@ -142,7 +143,7 @@ class Index < BaseDocument # rubocop:disable Metrics/ClassLength,Style/Documenta
       s += "</thead>\n"
       html_rows.append s
 
-      sorted_items = @project.coverage_matrices.sort_by(&:id)
+      sorted_items = @project.project_data.coverage_matrices.sort_by(&:id)
 
       sorted_items.each do |doc|
         s = "\t<tr>\n"
@@ -168,6 +169,40 @@ class Index < BaseDocument # rubocop:disable Metrics/ClassLength,Style/Documenta
       html_rows.append "</table>\n"
     end
 
+    # Implementation Matrices
+    unless @project.project_data.implementation_matrices.empty?
+      s = "<h2>Implementation Matrices</h2>\n"
+      s += "<table class=\"controlled\">\n"
+      s += "\t<thead>\n"
+      s += "\t\t<th>Title</th>\n"
+      s += "\t\t<th title=\"The ratio of Controlled Paragraphs mentioned in source code files and total number of Controlled Paragraphs\">Status</th>\n"
+      s += "\t\t<th>Specification Implemented</th>\n"
+      s += "</thead>\n"
+      html_rows.append s
+
+      sorted_items = @project.project_data.implementation_matrices.sort_by(&:id)
+
+      sorted_items.each do |doc|
+        s = "\t<tr>\n"
+
+        implemented_items = 0
+        doc.top_doc.controlled_items.each do |i|
+          implemented_items += 1 if i.source_code_links && i.source_code_links.length.positive? # rubocop:disable Style/SafeNavigation
+        end
+
+        coverage = implemented_items.to_f / doc.top_doc.controlled_items.length * 100.0
+
+        s += "\t\t<td class=\"item_text\" style='padding: 5px;'><a href=\"./specifications/#{doc.id}/#{doc.id}.html\" class=\"external\">#{doc.title}</a></td>\n"
+        s += "\t\t<td class=\"item_id\" style='width: 7%;'>#{'%.2f' % coverage}%</td>\n" # rubocop:disable Style/FormatString
+        s += "\t\t<td class=\"item_text\" style='width: 25%; padding: 5px;'>\
+                    <i class=\"fa fa-file-text-o\" style='background-color: ##{doc.top_doc.color};'> </i>\
+                    #{doc.top_doc.title}</td>\n"
+        s += "</tr>\n"
+        html_rows.append s
+      end
+      html_rows.append "</table>\n"
+    end
+
     save_html_to_file(html_rows, nil, output_file_path)
   end
 end

data/lib/almirah/doc_types/source_file.rb

@@ -0,0 +1,112 @@
+# frozen_string_literal: true
+
+require_relative 'persistent_document'
+require 'fileutils'
+require 'rouge'
+
+class SourceFile < PersistentDocument
+  attr_accessor :root_path, :repository, :dictionary, :wrong_links_hash,
+                :items_with_uplinks_number, :html_file_path, :specifications_path
+
+  def initialize(repository_path, fele_path, repository_name)
+    super fele_path
+    @root_path = repository_path
+    @id = File.basename(fele_path).downcase
+    @repository = repository_name
+    @html_file_path = '' # available only afer rendering
+
+    @dictionary = {}
+    @wrong_links_hash = {}
+
+    @items_with_uplinks_number = 0
+
+    # Calculate the relative path depth to determine correct number of parent directory symbols
+    relative_path = @path.sub("#{@root_path}/", '')
+    depth = relative_path.count('/') + 1 # +1 for the repository folder
+    depth += 1 # for the source_files folder
+    @specifications_path = "./#{'../' * depth}specifications/"
+    puts @specifications_path
+  end
+
+  def to_console
+    puts "\e[32mSource File: [#{@repository}] #{@id}\e[0m"
+  end
+
+  def to_html(output_file_path)
+    html_rows = []
+
+    html_rows.append('')
+
+    @items.each do |item|
+      a = item.to_html
+      html_rows.append a
+    end
+
+    # make some nice lexed html
+    source = File.read(@path.to_s)
+    # Detect lexer from file extension
+    # lexer = Rouge::Lexer.find_fancy(@path.to_s, source) || Rouge::Lexers::PlainText.new
+    lexer = Rouge::Lexer.guess_by_filename(@path.to_s) || Rouge::Lexers::PlainText.new
+    formatter = Rouge::Formatters::HTML.new
+
+    # Add Base16 theme CSS
+    theme_css = Rouge::Themes::Pastie.render(scope: '.highlight')
+    html_rows.append "<style>\n#{theme_css}\n</style>"
+
+    # Format the source code with syntax highlighting
+    formatted_html = formatter.format(lexer.lex(source))
+
+    # Add formatted code with highlighting styles
+    html_rows.append '<div class="highlight" style="background-color:#f6f7f8;"><pre>'
+    html_rows.append formatted_html
+    html_rows.append '</pre></div>'
+
+    save_to_file(html_rows, nil, output_file_path)
+  end
+
+  def save_to_file(html_rows, nav_pane, output_file_path) # rubocop:disable Metrics/AbcSize,Metrics/CyclomaticComplexity,Metrics/MethodLength,Metrics/PerceivedComplexity
+    gem_root = File.expand_path './../../..', File.dirname(__FILE__)
+    template_file = "#{gem_root}/lib/almirah/templates/page.html"
+
+    file = File.open(template_file)
+    file_data = file.readlines
+    file.close
+
+    output_file_path += "#{@repository}/"
+    output_file_path += @path.sub("#{@root_path}/", '')
+    output_file_path += '.html'
+    @html_file_path = output_file_path
+    FileUtils.mkdir_p(File.dirname(output_file_path))
+
+    # Calculate the relative path depth to determine correct number of parent directory symbols
+    relative_path = @path.sub("#{@root_path}/", '')
+    depth = relative_path.count('/') + 1 # +1 for the repository folder
+    depth += 1 # for the source_files folder
+    css_path = "#{'../' * depth}css/main.css"
+    js_path = "#{'../' * depth}scripts/main.js"
+    index_path = "#{'../' * depth}index.html"
+
+    file = File.open(output_file_path, 'w')
+    file_data.each do |s|
+      if s.include?('{{CONTENT}}')
+        html_rows.each do |r|
+          file.puts r
+        end
+      elsif s.include?('{{NAV_PANE}}')
+        file.puts nav_pane.to_html if nav_pane
+      elsif s.include?('{{DOCUMENT_TITLE}}')
+        file.puts s.gsub! '{{DOCUMENT_TITLE}}', @title
+      elsif s.include?('{{STYLES_AND_SCRIPTS}}')
+        file.puts "<link rel=\"stylesheet\" href=\"#{css_path}\">"
+        file.puts "<script src=\"#{js_path}\"></script>"
+      elsif s.include?('{{HOME_BUTTON}}')
+        file.puts "<a id=\"index_menu_item\" href=\"#{index_path}\"><span><i class=\"fa fa-info\" aria-hidden=\"true\"></i></span>&nbsp;Index</a>"
+      elsif s.include?('{{GEM_VERSION}}')
+        file.puts "(#{Gem.loaded_specs['Almirah'].version.version})"
+      else
+        file.puts s
+      end
+    end
+    file.close
+  end
+end

data/lib/almirah/doc_types/specification.rb

@@ -5,7 +5,7 @@ require_relative 'persistent_document'
 class Specification < PersistentDocument
   attr_accessor :dictionary, :todo_blocks, :wrong_links_hash, :items_with_uplinks_number, :items_with_downlinks_number,
                 :items_with_coverage_number, :duplicated_ids_number, :duplicates_list, :last_used_id,
-                :last_used_id_number, :color
+                :last_used_id_number, :color, :source_code_links, :specifications_path
 
   def initialize(fele_path)
     super
@@ -13,6 +13,7 @@ class Specification < PersistentDocument
     @duplicates_list = []
     @todo_blocks = []
     @wrong_links_hash = {}
+    @source_code_links = []
 
     @items_with_uplinks_number = 0
     @items_with_downlinks_number = 0
@@ -24,6 +25,7 @@ class Specification < PersistentDocument
     @color = 'bbb'
 
     @id = File.basename(fele_path, File.extname(fele_path)).downcase
+    @specifications_path = './../'
   end
 
   def to_console

data/lib/almirah/project/doc_linker.rb

@@ -0,0 +1,105 @@
+# frozen_string_literal: true
+
+require_relative 'project_data'
+
+class DocLinker
+  def self.link_all_source_files(project_data)
+    result = false
+    project_data.source_files.each do |f|
+      project_data.specifications.each do |s|
+        next unless f.up_link_docs.key?(s.id.to_s)
+
+        link_source_file_to_spec(f, s)
+        project_data.implemented_specifications_dictionary[s.id.to_s] = s
+        result = true
+      end
+    end
+    result
+  end
+
+  def self.link_protocol_to_spec(protocol, specification) # rubocop:disable Metrics/AbcSize,Metrics/CyclomaticComplexity,Metrics/MethodLength,Metrics/PerceivedComplexity
+    top_document = specification
+    bottom_document = protocol
+
+    bottom_document.controlled_items.each do |item|
+      next unless item.up_link_ids
+
+      item.up_link_ids.each do |up_lnk|
+        if top_document.dictionary.key?(up_lnk.to_s)
+
+          top_item = top_document.dictionary[up_lnk.to_s]
+
+          unless top_item.coverage_links
+            top_item.coverage_links = []
+            top_document.items_with_coverage_number += 1 # for statistics
+          end
+          top_item.coverage_links.append(item)
+        elsif tmp = /^([a-zA-Z]+)-\d+/.match(up_lnk)
+          # check if there is a non existing link with the right doc_id
+          if tmp[1].downcase == top_document.id.downcase
+            bottom_document.wrong_links_hash[up_lnk] = item
+          end # SRS
+        end
+      end
+    end
+  end
+
+  def self.link_source_file_to_spec(source_file, specification) # rubocop:disable Metrics/AbcSize,Metrics/CyclomaticComplexity,Metrics/MethodLength,Metrics/PerceivedComplexity
+    top_document = specification
+    bottom_document = source_file
+
+    bottom_document.controlled_items.each do |item|
+      next unless item.up_link_ids
+
+      item.up_link_ids.each do |up_lnk|
+        if top_document.dictionary.key?(up_lnk.to_s)
+
+          top_item = top_document.dictionary[up_lnk.to_s]
+
+          top_item.source_code_links = [] unless top_item.source_code_links
+          top_item.source_code_links.append(item)
+        elsif tmp = /^([a-zA-Z]+)-\d+/.match(up_lnk)
+          # check if there is a non existing link with the right doc_id
+          if tmp[1].downcase == top_document.id.downcase
+            bottom_document.wrong_links_hash[up_lnk] = item
+          end # SRS
+        end
+      end
+    end
+  end
+
+  def self.link_two_specifications(doc_a, doc_b) # rubocop:disable Metrics/AbcSize,Metrics/CyclomaticComplexity,Metrics/MethodLength,Metrics/PerceivedComplexity
+    if doc_b.up_link_docs.key?(doc_a.id.to_s)
+      top_document = doc_a
+      bottom_document = doc_b
+    elsif doc_a.up_link_docs.key?(doc_b.id.to_s)
+      top_document = doc_b
+      bottom_document = doc_a
+    else
+      return false # no links
+    end
+    # puts "Link: #{doc_a.id} - #{doc_b.id}"
+    bottom_document.controlled_items.each do |item|
+      next unless item.up_link_ids
+
+      item.up_link_ids.each do |up_lnk|
+        if top_document.dictionary.key?(up_lnk.to_s)
+
+          top_item = top_document.dictionary[up_lnk.to_s]
+
+          unless top_item.down_links
+            top_item.down_links = []
+            top_document.items_with_downlinks_number += 1 # for statistics
+          end
+          top_item.down_links.append(item)
+        elsif tmp = /^([a-zA-Z]+)-\d+/.match(up_lnk)
+          # check if there is a non existing link with the right doc_id
+          if tmp[1].downcase == top_document.id.downcase
+            bottom_document.wrong_links_hash[up_lnk] = item
+          end # SRS
+        end
+      end
+    end
+    true
+  end
+end

data/lib/almirah/project/project_data.rb

@@ -0,0 +1,18 @@
+class ProjectData
+  attr_reader :specifications, :protocols, :traceability_matrices, :coverage_matrices, :source_files,
+              :specifications_dictionary, :covered_specifications_dictionary, :implemented_specifications_dictionary,
+              :implementation_matrices
+
+  def initialize
+    @specifications = []
+    @protocols = []
+    @traceability_matrices = []
+    @coverage_matrices = []
+    @source_files = []
+    @implementation_matrices = []
+
+    @specifications_dictionary = {}
+    @covered_specifications_dictionary = {}
+    @implemented_specifications_dictionary = {}
+  end
+end

data/lib/almirah/project.rb

@@ -6,19 +6,17 @@ require_relative 'navigation_pane'
 require_relative 'doc_types/traceability'
 require_relative 'doc_types/index'
 require_relative 'search/specifications_db'
+require_relative 'project/doc_linker'
+require_relative 'project_configuration'
+require_relative 'project/project_data'
 
 class Project # rubocop:disable Metrics/ClassLength,Style/Documentation
-  attr_accessor :specifications, :protocols, :traceability_matrices, :coverage_matrices, :specifications_dictionary,
-                :index, :project, :configuration
+  attr_accessor :index, :project, :configuration, :project_data
 
   def initialize(configuration)
     @configuration = configuration
-    @specifications = []
-    @protocols = []
-    @traceability_matrices = []
-    @coverage_matrices = []
-    @specifications_dictionary = {}
-    @covered_specifications_dictionary = {}
+    @project_data = ProjectData.new
+
     @index = nil
     @project = self
     FileUtils.remove_dir("#{@configuration.project_root_directory}/build", true)
@@ -42,14 +40,18 @@ class Project # rubocop:disable Metrics/ClassLength,Style/Documentation
   def specifications_and_protocols # rubocop:disable Metrics/MethodLength
     parse_all_specifications
     parse_all_protocols
+    parse_all_source_files
     link_all_specifications
     link_all_protocols
+    link_all_source_files
     check_wrong_specification_referenced
     create_index
-    render_all_specifications(@specifications)
-    render_all_specifications(@traceability_matrices)
-    render_all_specifications(@coverage_matrices)
+    render_all_specifications(@project_data.specifications)
+    render_all_specifications(@project_data.traceability_matrices)
+    render_all_specifications(@project_data.coverage_matrices)
     render_all_protocols
+    render_all_source_files
+    render_all_specifications(@project_data.implementation_matrices) # intentionally after source file rendering
     render_index
     create_search_data
   end
@@ -57,14 +59,18 @@ class Project # rubocop:disable Metrics/ClassLength,Style/Documentation
   def specifications_and_results(test_run) # rubocop:disable Metrics/MethodLength
     parse_all_specifications
     parse_test_run test_run
+    parse_all_source_files
     link_all_specifications
     link_all_protocols
+    link_all_source_files
     check_wrong_specification_referenced
     create_index
-    render_all_specifications(@specifications)
-    render_all_specifications(@traceability_matrices)
-    render_all_specifications(@coverage_matrices)
+    render_all_specifications(@project_data.specifications)
+    render_all_specifications(@project_data.traceability_matrices)
+    render_all_specifications(@project_data.coverage_matrices)
     render_all_protocols
+    render_all_source_files
+    render_all_specifications(@project_data.implementation_matrices) # intentionally after source file rendering
     render_index
     create_search_data
   end
@@ -78,8 +84,8 @@ class Project # rubocop:disable Metrics/ClassLength,Style/Documentation
     # parse documents in the second pass
     Dir.glob("#{path}/specifications/**/*.md").each do |f| # rubocop:disable Style/CombinableLoops
       doc = DocFabric.create_specification(f)
-      @specifications.append(doc)
-      @specifications_dictionary[doc.id.to_s.downcase] = doc
+      @project_data.specifications.append(doc)
+      @project_data.specifications_dictionary[doc.id.to_s.downcase] = doc
     end
   end
 
@@ -87,7 +93,24 @@ class Project # rubocop:disable Metrics/ClassLength,Style/Documentation
     path = @configuration.project_root_directory
     Dir.glob("#{path}/tests/protocols/**/*.md").each do |f|
       doc = DocFabric.create_protocol(f)
-      @protocols.append(doc)
+      @project_data.protocols.append(doc)
+    end
+  end
+
+  def parse_all_source_files
+    @configuration.get_repositories.each do |repos|
+      # puts "Processing repository: #{repos['name']}, #{repos['path']}"
+      next unless repos['path'] && Dir.exist?(repos['path'])
+
+      file_path = repos['path']
+      Dir.glob("#{repos['path']}/**/*.*").each do |f|
+        next unless File.file?(f) && f.end_with?('.c', '.cpp', '.h', '.hpp', '.py', '.java', '.rb', '.js', '.ts', '.go',
+                                                 '.rs')
+
+        doc = DocFabric.create_source_file(file_path, f, repos['name'])
+        # puts "Source file: #{doc.id}"
+        @project_data.source_files.append(doc)
+      end
     end
   end
 
@@ -95,52 +118,62 @@ class Project # rubocop:disable Metrics/ClassLength,Style/Documentation
     path = @configuration.project_root_directory
     Dir.glob("#{path}/tests/runs/#{test_run}/**/*.md").each do |f|
       doc = DocFabric.create_protocol(f)
-      @protocols.append(doc)
+      @project_data.protocols.append(doc)
     end
   end
 
-  def link_all_specifications # rubocop:disable Metrics/MethodLength
-    comb_list = @specifications.combination(2)
+  def link_all_specifications # rubocop:disable Metrics/MethodLength,Metrics/AbcSize
+    comb_list = @project_data.specifications.combination(2)
     comb_list.each do |c|
       link_two_specifications(c[0], c[1])
       # puts "Link: #{c[0].id} - #{c[1].id}"
     end
     # separatelly create design inputs treceability
     @configuration.get_design_inputs.each do |i|
-      next unless @specifications_dictionary.key? i.to_s.downcase
+      next unless @project_data.specifications_dictionary.key? i.to_s.downcase
 
-      document = @specifications_dictionary[i.to_s.downcase]
+      document = @project_data.specifications_dictionary[i.to_s.downcase]
       if document
         doc = DocFabric.create_traceability_document(document, nil)
-        @traceability_matrices.append doc
+        @project_data.traceability_matrices.append doc
       end
     end
   end
 
   def link_all_protocols # rubocop:disable Metrics/MethodLength
-    @protocols.each do |p|
-      @specifications.each do |s|
+    @project_data.protocols.each do |p|
+      @project_data.specifications.each do |s|
         if p.up_link_docs.key?(s.id.to_s)
-          link_protocol_to_spec(p, s)
-          @covered_specifications_dictionary[s.id.to_s] = s
+          DocLinker.link_protocol_to_spec(p, s)
+          @project_data.covered_specifications_dictionary[s.id.to_s] = s
         end
       end
     end
     # create coverage documents
-    @covered_specifications_dictionary.each do |_key, value|
+    @project_data.covered_specifications_dictionary.each do |_key, value|
       doc = DocFabric.create_coverage_matrix(value)
-      @coverage_matrices.append doc
+      @project_data.coverage_matrices.append doc
+    end
+  end
+
+  def link_all_source_files
+    return unless DocLinker.link_all_source_files(@project_data)
+
+    # create implementation documents
+    @project_data.implemented_specifications_dictionary.each do |_key, value|
+      doc = DocFabric.create_implementation_document(value)
+      @project_data.implementation_matrices.append doc
     end
   end
 
   def check_wrong_specification_referenced # rubocop:disable Metrics/AbcSize,Metrics/CyclomaticComplexity,Metrics/MethodLength,Metrics/PerceivedComplexity
     available_specification_ids = {}
 
-    @specifications.each do |s|
+    @project_data.specifications.each do |s|
       available_specification_ids[s.id.to_s.downcase] = s
     end
 
-    @specifications.each do |s| # rubocop:disable Style/CombinableLoops
+    @project_data.specifications.each do |s| # rubocop:disable Style/CombinableLoops
       s.up_link_docs.each do |key, _value|
         next if available_specification_ids.key?(key)
 
@@ -197,34 +230,7 @@ class Project # rubocop:disable Metrics/ClassLength,Style/Documentation
     end
     # create treceability document
     doc = DocFabric.create_traceability_document(top_document, bottom_document)
-    @traceability_matrices.append doc
-  end
-
-  def link_protocol_to_spec(protocol, specification) # rubocop:disable Metrics/AbcSize,Metrics/CyclomaticComplexity,Metrics/MethodLength,Metrics/PerceivedComplexity
-    top_document = specification
-    bottom_document = protocol
-
-    bottom_document.controlled_items.each do |item|
-      next unless item.up_link_ids
-
-      item.up_link_ids.each do |up_lnk|
-        if top_document.dictionary.key?(up_lnk.to_s)
-
-          top_item = top_document.dictionary[up_lnk.to_s]
-
-          unless top_item.coverage_links
-            top_item.coverage_links = []
-            top_document.items_with_coverage_number += 1 # for statistics
-          end
-          top_item.coverage_links.append(item)
-        elsif tmp = /^([a-zA-Z]+)-\d+/.match(up_lnk)
-          # check if there is a non existing link with the right doc_id
-          if tmp[1].downcase == top_document.id.downcase
-            bottom_document.wrong_links_hash[up_lnk] = item
-          end # SRS
-        end
-      end
-    end
+    @project_data.traceability_matrices.append doc
   end
 
   def create_index
@@ -256,7 +262,7 @@ class Project # rubocop:disable Metrics/ClassLength,Style/Documentation
 
     FileUtils.mkdir_p("#{path}/build/tests/protocols")
 
-    @protocols.each do |doc|
+    @project_data.protocols.each do |doc|
       img_src_dir = "#{path}/tests/protocols/#{doc.id}/img"
       img_dst_dir = "#{path}/build/tests/protocols/#{doc.id}/img"
 
@@ -269,6 +275,17 @@ class Project # rubocop:disable Metrics/ClassLength,Style/Documentation
     end
   end
 
+  def render_all_source_files
+    path = @configuration.project_root_directory
+    FileUtils.mkdir_p("#{path}/build/source_files")
+
+    @project_data.source_files.each do |doc|
+      doc.to_console
+
+      doc.to_html("#{path}/build/source_files/")
+    end
+  end
+
   def render_index
     path = @configuration.project_root_directory
 
@@ -279,7 +296,7 @@ class Project # rubocop:disable Metrics/ClassLength,Style/Documentation
   end
 
   def create_search_data
-    db = SpecificationsDb.new @specifications
+    db = SpecificationsDb.new @project_data.specifications
     data_path = "#{@configuration.project_root_directory}/build/data"
     FileUtils.mkdir_p(data_path)
     db.save(data_path)

data/lib/almirah/project_configuration.rb

@@ -1,42 +1,42 @@
 require 'yaml'
 
 class ProjectConfiguration
-
-    attr_accessor :project_root_directory
-    attr_accessor :parameters
+    attr_accessor :project_root_directory, :parameters
 
     def initialize(path)
         @project_root_directory = path
         @parameters = {}
-        load_project_file()
+        load_project_file
     end
 
     def load_project_file
-        begin
-            @parameters = YAML.load_file(@project_root_directory + '/project.yml') 
-        rescue Psych::SyntaxError => e
+            @parameters = YAML.load_file(@project_root_directory + '/project.yml')
+    rescue Psych::SyntaxError => e
             puts "YAML syntax error: #{e.message}"
-          rescue Errno::ENOENT
-            puts "Project file not found: project.yml"
-        end
+    rescue Errno::ENOENT
+            puts 'Project file not found: project.yml'
     end
 
     def get_design_inputs
         if (@parameters.key? 'specifications') and (@parameters['specifications'].key? 'input')
             return @parameters['specifications']['input']
         end
-        return []
+
+        []
+    end
+
+    def get_repositories
+        return @parameters['repositories'] if @parameters.key? 'repositories'
+
+        []
     end
 
     def is_spec_db_shall_be_created
-        if (@parameters.key? 'output')
+        if @parameters.key? 'output'
             @parameters['output'].each do |p|
-               if p == 'specifications_db'
-                return true
-               end
+               return true if p == 'specifications_db'
             end
         end
-        return false
+        false
     end
-
-end
+end

data/lib/almirah/source_file_parser.rb

@@ -0,0 +1,91 @@
+require_relative 'doc_items/doc_item'
+require_relative 'doc_items/heading'
+require_relative 'doc_items/source_code_paragraph'
+
+class SourceFileParser # rubocop:disable Style/Documentation
+  def self.parse(doc, file_lines)
+    # restart section numbering for each new document
+    Heading.reset_global_section_number
+
+    # There is no document without heading
+    title = "[#{doc.repository}] : #{doc.id}"
+    item = Heading.new(doc, title, 0)
+    doc.items.append(item)
+    doc.headings.append(item)
+    doc.title = title
+
+    item = Heading.new(doc, 'References', 2)
+    doc.items.append(item)
+    doc.headings.append(item)
+
+    # main loop
+    file_lines.each do |s| # rubocop:disable Metrics/BlockLength
+      res = %r{<REQ>(.*)</REQ>}.match(s) # Document Referece Item
+      next unless res
+
+      # extract text between <REQ> and </REQ>
+      # id will be generated automatically
+      text = res[1].strip
+      up_links = nil
+
+      # check if it contains the uplink (one or many)
+      # TODO: check this regular expression
+      first_pos = text.length # for trailing commas
+      tmp = text.scan(/(>\[(?>[^\[\]]|\g<0>)*\])/) # >[SRS-001], >[SYS-002]
+      if tmp.length.positive?
+        up_links = []
+        tmp.each do |ul|
+          lnk = ul[0]
+          #
+          doc_id = /([a-zA-Z]+)-\d+/.match(lnk) # SRS
+          up_links << lnk.upcase if doc_id
+          # try to find the real end of text
+          pos = text.index(lnk)
+          first_pos = pos if pos < first_pos
+          # remove uplink from text
+          text = text.split(lnk, 1).join('')
+        end
+        # remove trailing commas and spaces
+        if text.length > first_pos
+          first_pos -= 1
+          text = text[0..first_pos].strip
+        end
+      end
+
+      # since we already know id and text
+      item = SourceCodeParagraph.new(doc, text)
+
+      if up_links
+        up_links.uniq! # remove duplicates
+        doc.items_with_uplinks_number += 1 # for statistics
+        up_links.each do |ul|
+          next unless tmp = />\[(\S*)\]$/.match(ul) # >[(SRS-001)]
+
+          up_link_id = tmp[1]
+
+          item.up_link_ids = [] unless item.up_link_ids
+
+          item.up_link_ids.append(up_link_id)
+
+          if tmp = /^([a-zA-Z]+)-\d+/.match(up_link_id) # SRS
+            doc.up_link_docs[tmp[1].downcase.to_s] = tmp[1].downcase # multiple documents could be up-linked
+          end
+        end
+      end
+
+      doc.items.append(item)
+      # for statistics
+      if doc.dictionary.has_key?(item.id.to_s)
+        doc.duplicated_ids_number += 1
+        doc.duplicates_list.append(item)
+      else
+        doc.dictionary[item.id.to_s] = item # for fast search
+      end
+      doc.controlled_items.append(item) # for fast search
+    end
+
+    item = Heading.new(doc, 'Source Code', 2)
+    doc.items.append(item)
+    doc.headings.append(item)
+  end
+end

data/lib/almirah/templates/page.html

@@ -9,8 +9,7 @@
 </head>
 <body>
     <div id="top_nav">
-        <a id="home_menu_item" href="javascript:void(0)" onclick="navigate_to_home()"><span><i class="fa fa-home" aria-hidden="true"></i></span>&nbsp;Home</a>
-        <a id="index_menu_item" href="javascript:void(0)" onclick="navigate_to_home()" style="display: none;"><span><i class="fa fa-info" aria-hidden="true"></i></span>&nbsp;Index</a>
+        {{HOME_BUTTON}}
         <a id="document_tree_menu_item" href="javascript:void(0)" onclick="openNav()" style="display: none;" title="Navigation Pane"><span><i class="fa fa-folder-open-o" aria-hidden="true"></i></span></a>
         <input type="text" id="searchInput" placeholder="Search.." style="display: none;">
         <a class="split">{{DOCUMENT_TITLE}}</a>

data/lib/almirah/templates/scripts/main.js

@@ -21,14 +21,10 @@ function openNav() {
     }
     if (document.title == "Document Index"){
       document.getElementById('document_tree_menu_item').style.display = "none";
-      document.getElementById('home_menu_item').style.display = "block";
-      document.getElementById('index_menu_item').style.display = "none";
       if (document.URL.includes('http')){
         document.getElementById("searchInput").style.display = "block";
       }
     }else{
-      document.getElementById('home_menu_item').style.display = "none";
-      document.getElementById('index_menu_item').style.display = "block";
       if (document.title.includes("Traceability Matrix:")){
         document.getElementById('document_tree_menu_item').style.display = "none";
       } else {
@@ -63,19 +59,6 @@ function openNav() {
     document.getElementById(required_id).style.display = 'block';  
   }
   
-  function navigate_to_home(){
-      if (document.title != "Document Index")
-      {
-        if (document.URL.includes('protocols')){
-          window.location.href = "./../../../index.html";
-        }else{
-          window.location.href = "./../../index.html";
-        }
-      }else{
-          window.location.href = "./index.html";
-      }
-  }
-  
   // Modal window for image zoom
   function image_OnClick(clicked){
   

metadata

@@ -1,15 +1,34 @@
 --- !ruby/object:Gem::Specification
 name: Almirah
 version: !ruby/object:Gem::Version
-  version: 0.2.8
+  version: 0.3.1
 platform: ruby
 authors:
 - Oleksandr Ivanov
-autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-10-28 00:00:00.000000000 Z
+date: 1980-01-02 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: rouge
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.6'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 4.6.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.6'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 4.6.1
 - !ruby/object:Gem::Dependency
   name: thor
   requirement: !ruby/object:Gem::Requirement
@@ -53,24 +72,30 @@ files:
 - lib/almirah/doc_items/markdown_list.rb
 - lib/almirah/doc_items/markdown_table.rb
 - lib/almirah/doc_items/paragraph.rb
+- lib/almirah/doc_items/source_code_paragraph.rb
 - lib/almirah/doc_items/text_line.rb
 - lib/almirah/doc_items/todo_block.rb
 - lib/almirah/doc_parser.rb
 - lib/almirah/doc_types/base_document.rb
 - lib/almirah/doc_types/coverage.rb
+- lib/almirah/doc_types/implementation.rb
 - lib/almirah/doc_types/index.rb
 - lib/almirah/doc_types/persistent_document.rb
 - lib/almirah/doc_types/protocol.rb
+- lib/almirah/doc_types/source_file.rb
 - lib/almirah/doc_types/specification.rb
 - lib/almirah/doc_types/traceability.rb
 - lib/almirah/dom/doc_section.rb
 - lib/almirah/dom/document.rb
 - lib/almirah/navigation_pane.rb
 - lib/almirah/project.rb
+- lib/almirah/project/doc_linker.rb
+- lib/almirah/project/project_data.rb
 - lib/almirah/project_configuration.rb
 - lib/almirah/project_template.rb
 - lib/almirah/project_utility.rb
 - lib/almirah/search/specifications_db.rb
+- lib/almirah/source_file_parser.rb
 - lib/almirah/templates/css/main.css
 - lib/almirah/templates/css/search.css
 - lib/almirah/templates/page.html
@@ -80,7 +105,6 @@ homepage: http://almirah.site
 licenses:
 - MIT
 metadata: {}
-post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -95,8 +119,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.17
-signing_key:
+rubygems_version: 4.0.1
 specification_version: 4
 summary: Almirah
 test_files: []