{% extends "base.html" %}
{% block content %}
  <div class="section">
    <div class="toc card">
      <h3>Table of contents</h3>
      <ol>
        <li><a href="#summary">Report Summary</a></li>
        <li><a href="#inputs">Input files</a></li>
        <li><a href="#lengths">Sequence length distribution</a></li>
        <li><a href="#dataset">Metadata description</a></li>
        <li><a href="#filtered-sequences">Filtered sequences</a></li>
        <li><a href="#final">Final IDs</a></li>
        <li><a href="#report-metadata">Report metadata</a></li>
      </ol>
    </div>

    <div id="summary" class="card">
      <h3>1. Report Summary</h3>
      <p>FASTA files: {{ summary.fasta_file_count }}<br>
        Metadata files: {{ summary.metadata_file_count }}</p>
      <p>Total sequences: {{ summary.total_sequences }}</p>
      <p>Filters: {{ summary.filters }}<br>
        Filtered: {{ summary.filtered_count }}</p>
      <p>Unique locations: {{ summary.locations }}</p>
      <p>Date range: {{ summary.date_range }}</p>
    </div>

    <div id="inputs" class="card">
      <h3>2. Input files</h3>
      <p>{{ fasta_summary }}</p>
      {% for row in records_summary %}
        {% set file_block = (seq_details_by_file | selectattr('file', 'equalto', row.file) | list | first) %}
        <details class="file-details">
          <summary>
            <button type="button" class="expand-button">Expand</button>
            <div class="table-wrap">
              <table>
                <thead>
                  <tr>
                    <th>File</th><th>Seqs</th><th>Length (min)</th><th>Length (max)</th><th>Length (mean)</th><th>N (min)</th><th>N (max)</th><th>N (mean)</th>
                  </tr>
                </thead>
                <tbody>
                  <tr>
                    <td>{{ row.file }}</td>
                    <td>{{ row.sequences }}</td>
                    <td>{{ row.len_min }}</td>
                    <td>{{ row.len_max }}</td>
                    <td>{{ row.len_mean }}</td>
                    <td>{{ row.n_min }}</td>
                    <td>{{ row.n_max }}</td>
                    <td>{{ row.n_mean }}</td>
                  </tr>
                </tbody>
              </table>
            </div>
          </summary>
          {% if file_block %}
            <div class="table-wrap table-scroll">
              <table class="datatable">
                <thead>
                  <tr><th>ID</th><th>Length</th><th>N content</th><th>Status</th></tr>
                </thead>
                <tbody>
                  {% for detail in file_block.details %}
                    {% set key = file_block.file ~ '::' ~ detail.id %}
                    {% set is_filtered = key in filtered_keys %}
                    <tr class="{% if is_filtered %}filtered{% endif %}">
                      <td>{{ detail.id }}</td>
                      <td>{{ detail.length }}</td>
                      <td>{{ detail.n_content | round(4) }}</td>
                      <td>{{ 'filtered' if is_filtered else 'kept' }}</td>
                    </tr>
                  {% endfor %}
                </tbody>
              </table>
            </div>
          {% endif %}
        </details>
      {% endfor %}
      <p>{{ metadata_summary }}</p>
      {% if metadata_tables %}
        {% for table in metadata_tables %}
          <details class="metadata-block">
            <summary>
              <button type="button" class="expand-button">Expand</button>
              <div class="table-wrap">
                <table>
                  <thead>
                    <tr>
                      <th>Metadata file</th><th>Rows</th>
                      {% for header in table.headers %}
                        <th>{{ header }}</th>
                      {% endfor %}
                    </tr>
                  </thead>
                  <tbody>
                    <tr>
                      <td>{{ table.title }}</td>
                      <td>{{ table.row_count }}</td>
                      {% for _ in table.headers %}
                        <td></td>
                      {% endfor %}
                    </tr>
                  </tbody>
                </table>
              </div>
            </summary>
            <div class="table-wrap table-scroll">
              <table class="datatable">
                <thead>
                  <tr>
                    {% for header in table.headers %}
                      <th>{{ header }}</th>
                    {% endfor %}
                  </tr>
                </thead>
                <tbody>
                  {% for row in table.rows %}
                    <tr>
                      {% for cell in row %}
                        <td>{{ cell }}</td>
                      {% endfor %}
                    </tr>
                  {% endfor %}
                </tbody>
              </table>
            </div>
          </details>
        {% endfor %}
      {% else %}
        <p>No metadata tables available.</p>
      {% endif %}
    </div>

    <div id="lengths" class="card">
      <h3>3. Sequence length distribution</h3>
      {% if length_plot_html %}
        <p class="caption">Distribution of sequence lengths across all input FASTA files. If a minimum length threshold is specified, it will be shown in the plot.</p>
        {{ length_plot_html | safe }}
      {% else %}
        <p>No length data available for plotting.</p>
      {% endif %}
    </div>


    <div id="dataset" class="card">
      <h3>4. Metadata description</h3>
      <p>Unique locations: {{ summary.locations }}</p>
      <p>Date range: {{ summary.date_range }}</p>
      {% if dataset_plot_html %}
          <p class="caption">Date distribution by location.</p>
        {{ dataset_plot_html | safe }}
      {% else %}
        <p>No date/location data available for plotting. To include this information, ensure your metadata files contain valid date and location fields and specify the date and location columns when running raccoon.</p>
      {% endif %}
    </div>

    <div id="filtered-sequences" class="card">
      <h3>5. Filtered sequences</h3>
      {% if filter_failures_table %}
      <p>The following sequences failed the length or N-content filters and will not be present in the output FASTA file:</p>
        <div class="table-wrap table-scroll">
          <table class="datatable">
            <thead>
              <tr>
                {% for header in filter_failures_table.headers %}
                  <th>{{ header }}</th>
                {% endfor %}
              </tr>
            </thead>
            <tbody>
              {% for row in filter_failures_table.rows %}
                <tr>
                  {% for cell in row %}
                    <td>{{ cell }}</td>
                  {% endfor %}
                </tr>
              {% endfor %}
            </tbody>
          </table>
        </div>
      {% else %}
        <p>No sequences failed length or N-content filters.</p>
      {% endif %}
    </div>

    <div id="final" class="card">
      <h3>6. Final dataset</h3>
      <div class="table-wrap table-scroll">
        <table class="datatable">
          <thead>
            <tr><th>ID</th><th>Length</th><th>N content</th></tr>
          </thead>
          <tbody>
            {% for row in final_rows %}
              <tr>
                <td>{{ row.id }}</td>
                <td>{{ row.length }}</td>
                <td>{{ row.n_content }}</td>
              </tr>
            {% endfor %}
          </tbody>
        </table>
      </div>
    </div>

    <div id="metadata-issues" class="card">
      <h3>7. Metadata issues</h3>
      {% if metadata_issues_table %}
        <div class="table-wrap table-scroll">
          <table class="datatable">
            <thead>
              <tr>
                {% for header in metadata_issues_table.headers %}
                  <th>{{ header }}</th>
                {% endfor %}
              </tr>
            </thead>
            <tbody>
              {% for row in metadata_issues_table.rows %}
                <tr>
                  {% for cell in row %}
                    <td>{{ cell }}</td>
                  {% endfor %}
                </tr>
              {% endfor %}
            </tbody>
          </table>
        </div>
      {% else %}
        <p>No metadata issues detected.</p>
      {% endif %}
    </div>
  </div>
{% endblock %}