class Jekyll::Generators::APIGenerator

# File _plugins/api.rb, line 72
def copy(site, source, dest)
  # It isn't unusual that some of these might not exist in dev envs.
  if File.exist?(site.in_source_dir(source))
    if ! Dir.exist?(File.dirname(site.in_dest_dir(dest)))
      FileUtils.mkdir_p(File.dirname(site.in_dest_dir(dest)))
    end

    FileUtils.cp(site.in_source_dir(source), site.in_dest_dir(dest))
  end
end

# File _plugins/api.rb, line 106
def generate(site)
  Jekyll.logger.info '[GTN/API] Generating API'

  write(site, 'api/configuration.json', site.config.reject { |k, _v| k.to_s.start_with?('cached_') })
  write(site, 'api/swagger.json', site.data['swagger'])
  write(site, 'api/version.json', Gtn::Git.discover)

  # Full Bibliography
  Jekyll.logger.debug '[GTN/API] Bibliography'
  write(site, 'api/gtn.bib', site.config['cached_global_bib'].to_s, json: false)

  # Metrics endpoint, /metrics
  write(site, 'api/metrics', Gtn::Metrics.generate_metrics(site), json: false)

  # Public tool listing
  write(site, 'api/psl.json', site.data['public-server-tools'], pretty: false)

  # Tool Categories
  write(site, 'api/toolcats.json', site.data['toolcats'], pretty: false)

  # Tool Categories
  write(site, 'api/toolshed-revisions.json', site.data['toolshed-revisions'], pretty: false)

  # Feedback Data
  write(site, 'api/feedback2.json', site.data['feedback2'], pretty: false)
  copy(site, 'metadata/feedback.csv', 'api/feedback.csv')
  copy(site, 'metadata/feedback2.yaml', 'api/feedback2.yaml')

  # Contributors
  Jekyll.logger.debug '[GTN/API] Contributors, Funders, Organisations'
  %w[contributors grants organisations].each do |type|
    pfo = site.data[type].map { |c, _| mapContributor(site, c) }
    write(site, "api/#{type}.json", pfo, pretty: false)

    site.data['contributors'].each do |c, _|
      write(site, "api/#{type}/#{c}.json", mapContributor(site, c))
    end
  end

  geojson = {
    'type' => 'FeatureCollection',
    'features' => site.data['contributors']
      .select { |_k, v| v.key? 'location' }
      .map do |k, v|
        {
          'type' => 'Feature',
          'geometry' => { 'type' => 'Point', 'coordinates' => [v['location']['lon'], v['location']['lat']] },
          'properties' => {
            'name' => v.fetch('name', k),
            'url' => "https://training.galaxyproject.org/training-material/hall-of-fame/#{k}/",
            'joined' => v['joined'],
            'orcid' => v['orcid'],
            'id' => k,
            'contact_for_training' => v.fetch('contact_for_training', false),
          }
        }
      end
  }
  write(site, "api/contributors.geojson", geojson)


  # Trigger the topic cache to generate if it hasn't already
  Jekyll.logger.debug '[GTN/API] Tutorials'
  Gtn::TopicFilter.topic_filter(site, 'does-not-matter')
  Gtn::TopicFilter.list_topics(site).map do |topic|
    out = site.data[topic].dup
    out['materials'] = Gtn::TopicFilter.topic_filter(site, topic).map do |x|
      q = x.dup
      q['contributors'] = Gtn::Contributors.get_contributors(q).dup.map do |c|
        mapContributor(site, c)
      end

      q['urls'] = {}

      if !q['hands_on'].nil?
        q['urls']['hands_on'] = site.config['url'] + site.config['baseurl'] + "/api/topics/#{q['url'][8..-6]}.json"
      end

      if !q['slides'].nil?
        q['urls']['slides'] = site.config['url'] + site.config['baseurl'] + "/api/topics/#{q['url'][8..-6]}.json"
      end

      # Write out the individual page
      # Delete the ref to avoid including it by accident
      q.delete('ref')
      q.delete('ref_tutorials')
      q.delete('ref_slides')
      write(site, "api/topics/#{q['url'][7..-6]}.json", q)

      q
    end
    out['editorial_board'] = out['editorial_board'].map do |c|
      mapContributor(site, c)
    end

    write(site, "api/topics/#{topic}.json", out)
  end

  topics = {}
  Jekyll.logger.debug '[GTN/API] Topics'
  # Individual Topic Indexes
  site.data.each_pair do |k, v|
    if v.is_a?(Hash) && v.key?('type') && v.key?('editorial_board')

      topics[k] = {
        'name' => v['name'],
        'title' => v['title'],
        'summary' => v['summary'],
        'url' => site.config['url'] + site.config['baseurl'] + "/api/topics/#{k}.json",
        'editorial_board' => v['editorial_board'].map { |c| mapContributor(site, c) }
      }
    end
  end

  # Videos.json
  # {
  # "id": "transcriptomics/tutorials/mirna-target-finder/slides",
  # "topic": "Transcriptomics",
  # "title": "Whole transcriptome analysis of Arabidopsis thaliana"
  # },

  videos = Gtn::TopicFilter.list_videos(site).map do |m|
    {
      id: "#{m['topic_name']}/tutorials/#{m['tutorial_name']}/slides",
      topic: m['topic_name_human'],
      title: m['title']
    }
  end
  write(site, "api/videos.json", videos)


  # Overall topic index
  write(site, "api/topics.json", topics)

  Jekyll.logger.debug '[GTN/API] Tutorial and Slide pages'

  # Deploy the feedback file as well
  write(site, "api/feedback.json", site.data['feedback'])

  # Top Tools
  Jekyll.logger.debug '[GTN/API] Top Tools'
  write(site, "api/top-tools.json", Gtn::TopicFilter.list_materials_by_tool(site))

  # GA4GH TRS Endpoint
  # Please note that this is all a fun hack
  Gtn::TopicFilter.list_all_materials(site).select { |m| m['workflows'] }.each do |material|
    material['workflows'].each do |workflow|
      wfid = workflow['wfid']
      wfname = workflow['wfname']

      ga4gh_blob =  {
        'id' => wfname,
        'url' => site.config['url'] + site.config['baseurl'] + material['url'],
        'name' => 'v1',
        'author' => [],
        'descriptor_type' => ['GALAXY'],
      }
      write(site, "api/ga4gh/trs/v2/tools/#{wfid}/versions/#{wfname}.json", ga4gh_blob)



      descriptor = {
        'content' => File.read("#{material['dir']}/workflows/#{workflow['workflow']}"),
        'checksum' => [],
        'url' => nil,
      }
      write(site, "api/ga4gh/trs/v2/tools/#{wfid}/versions/#{wfname}/GALAXY/descriptor.json", descriptor)
    end
  end
end

# File _plugins/api.rb, line 83
def write(site, dest, data, json: true, pretty: true)
  # Since we're doing this ourselves, need to be responsible for ensuring
  # the directory exists.
  if ! Dir.exist?(File.dirname(site.in_dest_dir(dest)))
    FileUtils.mkdir_p(File.dirname(site.in_dest_dir(dest)))
  end

  if json
    if pretty
      File.write(site.in_dest_dir(dest), JSON.pretty_generate(data))
    else
      File.write(site.in_dest_dir(dest), JSON.generate(data))
    end
  else
    # Pretty isn't relevant.
    File.write(site.in_dest_dir(dest), data)
  end
end