module GTNNotebooks

# File _plugins/notebook.rb, line 193
def self.add_metadata_cell(site, notebook, metadata)
  by_line = construct_byline(site, metadata)

  meta_header = [
    "<div style=\"border: 2px solid #8A9AD0; margin: 1em 0.2em; padding: 0.5em;\">\n\n",
    "# #{metadata['title']}\n",
    "\n",
    "by #{by_line}\n",
    "\n",
    "#{metadata.fetch('license', 'CC-BY')} licensed content from the [Galaxy Training Network]" \
    "(https://training.galaxyproject.org/)\n",
    "\n",
    "**Objectives**\n",
    "\n"
  ] + metadata.fetch2('questions', []).map { |q| "- #{q}\n" } + [
    "\n",
    "**Objectives**\n",
    "\n"
  ] + metadata.fetch2('objectives', []).map { |q| "- #{q}\n" } + [
    "\n",
    "**Time Estimation: #{metadata['time_estimation']}**\n",
    "\n",
    "</div>\n"
  ]
  metadata_cell = {
    'id' => 'metadata',
    'cell_type' => 'markdown',
    'source' => meta_header
  }
  notebook['cells'].unshift(metadata_cell)
  notebook
end

# File _plugins/notebook.rb, line 185
def self.construct_byline(site, metadata)
  folks = Gtn::Contributors.get_authors(metadata)
  folks.map do |c|
    name = Gtn::Contributors.fetch_name(site, c)
    "[#{name}](https://training.galaxyproject.org/hall-of-fame/#{c}/)"
  end.join(', ')
end

# File _plugins/notebook.rb, line 67
def self.convert_notebook_markdown(content, accepted_languages)
  out = []
  inside_block = false
  cur_lang = nil
  val = []
  data = content.split("\n")
  data.each.with_index do |line, i|
    m = line.match(/^```(#{accepted_languages.join('|')})\s*$/)
    if m
      if inside_block
        puts data[i - 2..i + 2]
        raise "[GTN/Notebook] L#{i} Error! we're already in a block:"
      end
      # End the previous block
      out.push([val, inside_block, cur_lang])
      val = []

      inside_block = true
      cur_lang = m[1]
    elsif inside_block && line == '```'
      # End of code block
      out.push([val, inside_block, cur_lang])
      val = []
      inside_block = false
    else
      val.push(line)
    end
  end
  # final flush
  out.push([val, inside_block, cur_lang]) if !val.nil?

  notebook = {
    'metadata' => {},
    'nbformat' => 4,
    'nbformat_minor' => 5,
  }

  notebook['cells'] = out.map.with_index do |data2, index|
    res = {
      'id' => "cell-#{index}",
      'source' => data2[0].map { |x| "#{x.rstrip}\n" }
    }
    # Strip the trailing newline in the last cell.
    res['source'][-1] = res['source'][-1].rstrip if res['source'].length.positive?

    # Remove any remaining language tagged code blocks, e.g. in
    # tip/solution/etc boxes. These do not render well.
    res['source'] = res['source'].map { |x| x.gsub(/```(#{accepted_languages.join('|')})/, '```') }

    if data2[1]
      res.update({
                   'cell_type' => 'code',
                   'execution_count' => nil,
                   'outputs' => [],
                   'metadata' => {
                     'attributes' => {
                       'classes' => [
                         data[2]
                       ],
                       'id' => '',
                     }
                   }
                 })
    else
      res['cell_type'] = 'markdown'
    end
    res
  end
  notebook
end

# File _plugins/notebook.rb, line 253
def self.fixBashNotebook(notebook)
  # Set the bash kernel
  notebook['metadata'] = {
    'kernelspec' => {
      'display_name' => 'Bash',
      'language' => 'bash',
      'name' => 'bash'
    },
    'language_info' => {
      'codemirror_mode' => 'shell',
      'file_extension' => '.sh',
      'mimetype' => 'text/x-sh',
      'name' => 'bash'
    }
  }
  # Strip out %%bash since we'll use the bash kernel
  notebook['cells'].map do |cell|
    if cell.fetch('cell_type') == 'code' && (cell['source'][0] == "%%bash\n")
      cell['source'] = cell['source'].slice(1..-1)
    end
    cell
  end
  notebook
end

# File _plugins/notebook.rb, line 278
def self.fixPythonNotebook(notebook)
  # TODO
  # prefix bash cells with `!`
  notebook['cells'].map do |cell|
    if cell.fetch('metadata', {}).fetch('attributes', {}).fetch('classes', [])[0] == 'bash'
      cell['source'] = cell['source'].map { |line| "!#{line}" }
    end
    cell
  end
  notebook
end

# File _plugins/notebook.rb, line 226
def self.fixRNotebook(notebook)
  # Set the bash kernel
  notebook['metadata'] = {
    'kernelspec' => {
      'display_name' => 'R',
      'language' => 'R',
      'name' => 'r'
    },
    'language_info' => {
      'codemirror_mode' => 'r',
      'file_extension' => '.r',
      'mimetype' => 'text/x-r-source',
      'name' => 'R',
      'pygments_lexer' => 'r',
      'version' => '4.1.0'
    }
  }
  # Strip out %%R since we'll use the bash kernel
  notebook['cells'].map do |cell|
    if cell.fetch('cell_type') == 'code' && (cell['source'][0] == "%%R\n")
      cell['source'] = cell['source'].slice(1..-1)
    end
    cell
  end
  notebook
end

# File _plugins/notebook.rb, line 290
def self.fixSqlNotebook(notebook)
  # Add in a %%sql at the top of each cell
  notebook['cells'].map do |cell|
    if cell.fetch('cell_type') == 'code' && cell['source'].join.index('load_ext').nil?
      cell['source'] = ["%%sql\n"] + cell['source']
    end
    cell
  end
  notebook
end

# File _plugins/notebook.rb, line 61
def self.generate_css
  COLORS.map do |key, val|
    ".#{key} { padding: 0 1em; margin: 1em 0.2em; border: 2px solid #{val} }"
  end.join("\n")
end

# File _plugins/notebook.rb, line 138
def self.group_doc_by_first_char(data)
  out = []
  first_char = nil
  val = []
  data = data.split("\n")

  # Here we collapse running groups of `>` into single blocks.
  data.each do |line|
    if first_char.nil?
      first_char = line[0]
      val = [line]
    elsif line[0] == first_char
      val.push(line)
    elsif line[0..1] == '{:' && first_char == '>'
      val.push(line)
    else
      # flush
      out.push(val)
      first_char = if line.size.positive?
                     line[0]
                   else
                     ''
                   end
      val = [line]
    end
  end
  # final flush
  out.push(val)

  out.reject! do |v|
    (v[0][0] == '>' && v[-1][0..1] == '{:' && v[-1].match(/.agenda/))
  end
  out.map! do |v|
    if v[0][0] == '>' && v[-1][0..1] == '{:'
      cls = v[-1][2..-2].strip
      res = [":::{#{cls}}"]
      res += v[0..-2].map { |c| c.sub(/^>\s*/, '') }
      res += [':::']
      res
    else
      v
    end
  end

  out.flatten(1).join("\n")
end

# File _plugins/notebook.rb, line 301
def self.markdownify(site, text)
  site.find_converter_instance(
    Jekyll::Converters::Markdown
  ).convert(text.to_s)
rescue StandardError
  require 'kramdown'
  Kramdown::Document.new(text).to_html
end

# File _plugins/notebook.rb, line 310
def self.notebook_filter(data, language = nil)
  data['layout'] == 'tutorial_hands_on' \
    and data.key?('notebook') \
    and (language.nil? or data['notebook']['language'].downcase == language)
end

# File _plugins/notebook.rb, line 442
def self.renderMarkdownCells(site, notebook, metadata, _page_url, dir)
  seen_abbreviations = {}
  notebook['cells'].map do |cell|
    if cell.fetch('cell_type') == 'markdown'

      # The source is initially a list of strings, we'll merge it together
      # to make it easier to work with.
      source = cell['source'].join.strip

      # Here we replace individual `s with codeblocks, they screw up
      # rendering otherwise by going through rouge
      source = source.gsub(/ `([^`]*)`([^`])/, ' <code>\1</code>\2')
                     .gsub(/([^`])`([^`]*)` /, '\1<code>\2</code> ')

      # Strip out includes, snippets
      source.gsub!(/{% include .* %}/, '')
      source.gsub!(/{% snippet .* %}/, '')

      # Replace all the broken icons that can't render, because we don't
      # have access to the full render pipeline.
      cell['source'] = markdownify(site, source)

      ICONS.each do |key, val|
        # Replace the new box titles with h3s.
        cell['source'].gsub!(%r{<div class="box-title #{key}-title".*?</span>(.*?)</div>},
                             "<div style=\"font-weight:900;font-size: 125%\">#{val} \\1</div>")

        # Remove the fa-icon spans
        cell['source'].gsub!(%r{<span role="button" class="fold-unfold fa fa-minus-square"></span>}, '')

        # just removing the buttons from solutions since they'll be changed
        # into summary/details in the parent notebook-jupyter.
        cell['source'].gsub!(%r{<button class="gtn-boxify-button solution".*?</button>}, '')
      end

      if metadata.key?('abbreviations')
        metadata['abbreviations'].each do |abbr, defn|
          cell['source'].gsub(/\{#{abbr}\}/) do
            if seen_abbreviations.key?(abbr)
              firstdef = false
            else
              firstdef = true
              seen_abbreviations[abbr] = true
            end

            if firstdef
              "#{defn} (#{abbr})"
            else
              "<abbr title=\"#{defn}\">#{abbr}</abbr>"
            end
          end
        end
      end

      # Here we give a GTN-ish styling that doesn't try to be too faithful,
      # so we aren't spending time keeping up with changes to GTN css,
      # we're making it 'our own' a bit.

      COLORS.each do |key, val|
        val = "#{val};#{COLORS_EXTRA[key]}" if COLORS_EXTRA.key? key

        cell['source'].gsub!(/<blockquote class="#{key}">/,
                             "<blockquote class=\"#{key}\" style=\"border: 2px solid #{val}; margin: 1em 0.2em\">")
      end

      # Images are referenced in the through relative URLs which is
      # fab, but in a notebook this doesn't make sense as it will live
      # outside of the GTN. We need real URLs.
      #
      # So either we'll embed the images directly via base64 encoding (cool,
      # love it) or we'll link to the production images and folks can live
      # without their images for a bit until it's merged.

      if cell['source'].match(/<img src="\.\./)
        cell['source'].gsub!(/<img src="(\.\.[^"]*)/) do |img|
          path = img[10..]
          image_path = File.join(dir, path)

          if img[-3..].downcase == 'png'
            data = Base64.encode64(File.binread(image_path))
            %(<img src="data:image/png;base64,#{data}")
          elsif (img[-3..].downcase == 'jpg') || (img[-4..].downcase == 'jpeg')
            data = Base64.encode64(File.binread(image_path))
            %(<img src="data:image/jpeg;base64,#{data}")
          elsif img[-3..].downcase == 'svg'
            data = Base64.encode64(File.binread(image_path))
            %(<img src="data:image/svg+xml;base64,#{data}")
          else
            # Falling back to non-embedded images
            "<img src=\"https://training.galaxyproject.org/training-material/#{page_url.split('/')[0..-2].join('/')}/.."
          end
        end
      end

      # Strip out the highlighting as it is bad on some platforms.
      cell['source'].gsub!(/<pre class="highlight">/, '<pre style="color: inherit; background: transparent">')
      cell['source'].gsub!(/<div class="highlight">/, '<div>')
      cell['source'].gsub!(/<code>/, '<code style="color: inherit">')

      # There is some weirdness in the processing of $s in Jupyter. After a
      # certain number of them, it will give up, and just render everything
      # like with a '<pre>'. We remove this to prevent that result.
      cell['source'].gsub!(/^\s*</, '<')
      # Additionally leading spaces are sometimes interpreted as <pre>s and
      # end up causing paragraphs to be rendered as code. So we wipe out
      # all leading space.
      # 'editable' is actually CoCalc specific but oh well.
      cell['metadata'] = { 'editable' => false, 'collapsed' => false }
      cell['source'].gsub!(/\$/, '&#36;')
    end
    cell
  end
  notebook
end

# File _plugins/notebook.rb, line 391
def self.render_jupyter_notebook(data, content, url, _last_modified, notebook_language, site, dir)
  # Here we read use internal methods to convert the tutorial to a Hash
  # representing the notebook
  accepted_languages = [notebook_language]
  accepted_languages << 'bash' if notebook_language == 'python'

  if !data['zenodo_link'].nil?
    Jekyll.logger.debug "Replacing zenodo links in #{url}, #{data['zenodo_link']}"
    content.gsub!(/{{\s*page.zenodo_link\s*}}/, data['zenodo_link'])
  end
  notebook = convert_notebook_markdown(content, accepted_languages)
  # This extracts the metadata yaml header and does manual formatting of
  # the header data to make for a nicer notebook.
  notebook = add_metadata_cell(site, notebook, data)

  # Apply language specific conventions
  case notebook_language
  when 'bash'
    notebook = fixBashNotebook(notebook)
  when 'sql'
    notebook = fixSqlNotebook(notebook)
  when 'r'
    notebook = fixRNotebook(notebook)
  when 'python'
    notebook = fixPythonNotebook(notebook)
  end

  # Here we loop over the markdown cells and render them to HTML. This
  # allows us to get rid of classes like {: .tip} that would be left in
  # the output by Jupyter's markdown renderer, and additionally do any
  # custom CSS which only seems to work when inline on a cell, i.e. we
  # can't setup a style block, so we really need to render the markdown
  # to html.
  notebook = renderMarkdownCells(site, notebook, data, url, dir)

  # Here we add a close to the notebook
  notebook['cells'] = notebook['cells'] + [{
    'cell_type' => 'markdown',
    'id' => 'final-ending-cell',
    'metadata' => { 'editable' => false, 'collapsed' => false },
    'source' => [
      "# Key Points\n\n"
    ] + data.fetch2('key_points', []).map { |k| "- #{k}\n" } + [
      "\n# Congratulations on successfully completing this tutorial!\n\n",
      'Please [fill out the feedback on the GTN website](https://training.galaxyproject.org/training-material' \
      "#{url}#feedback) and check there for further resources!\n"
    ]
  }]
  notebook
end

# File _plugins/notebook.rb, line 316
def self.render_rmarkdown(site, page_data, page_content, page_url, page_last_modified, fn)
  by_line = construct_byline(site, page_data)

  # Replace top level `>` blocks with fenced `:::`
  content = group_doc_by_first_char(page_content)

  # Re-run a second time to catch singly-nested Q&A?
  content = group_doc_by_first_char(content)

  # Replace zenodo links, the only replacement we do
  if !page_data['zenodo_link'].nil?
    Jekyll.logger.debug "Replacing zenodo links in #{page_url}, #{page_data['zenodo_link']}"
    content.gsub!(/{{\s*page.zenodo_link\s*}}/, page_data['zenodo_link'])
  end

  ICONS.each do |key, val|
    content.gsub!(/{% icon #{key} %}/, val)
  end
  ICONS_FA.each do |key, val|
    content.gsub!(%r{<i class="#{key}" aria-hidden="true"></i>}, ICONS[val])
  end

  content += %(\n\n# References\n\n<div id="refs"></div>\n)

  # https://raw.githubusercontent.com/rstudio/cheatsheets/master/rmarkdown-2.0.pdf
  # https://bookdown.org/yihui/rmarkdown/

  fnparts = fn.split('/')
  rmddata = {
    'title' => page_data['title'],
    'author' => "#{by_line}, #{page_data.fetch('license',
                                               'CC-BY')} licensed content from the [Galaxy Training Network](https://training.galaxyproject.org/)",
    'bibliography' => "#{fnparts[2]}-#{fnparts[4]}.bib",
    'output' => {
      'html_notebook' => {
        'toc' => true,
        'toc_depth' => 2,
        'css' => 'gtn.css',
        'toc_float' => {
          'collapsed' => false,
          'smooth_scroll' => false,
        },
        # 'theme' => {'bootswatch' => 'journal'}
      },
      'word_document' => {
        'toc' => true,
        'toc_depth' => 2,
        'latex_engine' => 'xelatex',
      },
      'pdf_document' => {
        'toc' => true,
        'toc_depth' => 2,
        'latex_engine' => 'xelatex',
      },
    },
    'date' => page_last_modified.to_s,
    'link-citations' => true,
    'anchor_sections' => true,
    'code_download' => true,
  }
  rmddata['output']['html_document'] = JSON.parse(JSON.generate(rmddata['output']['html_notebook']))

  final_content = [
    "# Introduction\n",
    content.gsub(/```[Rr]/, '```{r}'),
    "# Key Points\n"
  ] + page_data.fetch2('key_points', []).map { |k| "- #{k}" } + [
    "\n# Congratulations on successfully completing this tutorial!\n",
    'Please [fill out the feedback on the GTN website](https://training.galaxyproject.org/' \
    "training-material#{page_url}#feedback) and check there for further resources!\n"
  ]

  "#{rmddata.to_yaml(line_width: rmddata['author'].size + 10)}---\n#{final_content.join("\n")}"
end