bio-miga/miga-web

require 'miga/tax_dist'

module QueryDatasetsHelper
  def aai_intax(aai, project, ds_miga)
    opts = {}
    if project.miga && project.miga.metadata[:aai_p]
      opts[:engine] = project.miga.metadata[:aai_p]
    end
    res = MiGA::TaxDist.aai_taxtest(aai, :intax, opts)
    tax = ds_miga.metadata[:tax]
    tax = {} if tax.nil?
    phrases = []
    res.each do |k,v|
      o = k.to_s.unmiga_name + ' belongs to the '
      if tax == {} || tax[v.first].nil?
        o += "same <b>#{MiGA::Taxonomy.LONG_RANKS[v.first]}</b> of " +
          link_to(ds_miga.name.unmiga_name,
            reference_dataset_path(project.id, ds_miga.name))
      else
        tag = %i[root ns p ssp str ds].include?(v.first) ? :span : :i
        o += content_tag(:b, MiGA::Taxonomy.LONG_RANKS[v.first]) + ' '
        o += content_tag(tag, tax[v.first].unmiga_name, class: 'tax-name')
      end
      o += ' (p-value: %.2g)' % v.second
      phrases << o
    end
    all = '<div class="small comment">'
    all_c = ''
    MiGA::TaxDist.aai_pvalues(aai, :intax, opts).each do |k,v|
      sig = ''
      [0.5,0.1,0.05,0.01].each{ |i| sig << '*' if v<i }
      all << '<div class="taxonomy-tree">' +
              "<b" + (v>0.5 ? ' class="text-muted"' : '') +
              "><span class=badge>#{MiGA::Taxonomy.LONG_RANKS[k]}</span> "
      if tax[k]
        tag = %i[root ns p ssp str ds].include?(k) ? :span : :i
        all << content_tag(tag, class: 'tax-name') do
          link_to(tax[k],
            project_search_path(project.id, q: "tax:\"#{tax[k]}\""))
        end
      end
      all << " (p-value #{"%.3g" % v}#{sig})</b>"
      all_c << '</div>'
    end
    all << "#{all_c}<br/><span class=text-muted>Significance at p-value " +
            "below: *0.5, **0.1, ***0.05, ****0.01</span></div>"
    return (phrases.empty? ?
            "The dataset doesn't have any close relative in the database " +
              "that can be used to determine its taxonomy. #{all}" :
            "The dataset #{phrases.to_sentence}. #{all}"
      ).html_safe
  end

  def aai_novel(aai, project)
    opts = {}
    if project.miga && project.miga.metadata[:aai_p]
      opts[:engine] = project.miga.metadata[:aai_p]
    end
    res = MiGA::TaxDist.aai_taxtest(aai, :novel, opts)
    thr = {most_likely:0.01, probably:0.1, possibly_even:0.5}
    phrases = []
    res.each do |k,v|
      next if [:d, :root].include? v.first
      rank = MiGA::Taxonomy.LONG_RANKS[v.first]
      phrases << '' + k.to_s.unmiga_name +
        " belongs to #{rank[0] == 'o' ? 'an' : 'a'} <b>#{rank}</b> not " +
        "represented in the database (p-value: #{"%.2g" % v.second}), " +
        "highest taxonomic rank with p-value &le; #{thr[k]}"
    end
    all = '<div class="text-muted small comment"><b>P-values:</b> ' +
            MiGA::TaxDist.aai_pvalues(aai, :novel, opts).map do |k,v|
              "<b>#{MiGA::Taxonomy.LONG_RANKS[k]}</b> #{"%.3g" % v}"
            end.join(", ") + '.</div>'
    conn = ". It "
    return (phrases.empty? ?
          "The dataset doesn't have any determinable degree of novelty with " +
            "respect to the database. #{all}" :
          "The dataset #{phrases.to_sentence(words_connector: conn,
            two_words_connector: conn, last_word_connector: conn)}. #{all}"
      ).html_safe
  end
end