{% extends "cases/case_tabular_view.html" %}
{% from "utils.html" import comments_panel, activity_panel %}
{% from "cases/utils.html" import individuals_table, sex_table_cell_content %}
{% from "variants/components.html" import gene_link %}
{% from "variant/gene_disease_relations.html" import incomplete_penetrance_badge, inheritance_badge %}

{% block title %}
  {{ super() }}
{% endblock %}

{% block css %}
{{ super() }}
<style>
  /* Paraphrase nested table styling for consistent alignment */
  .paraphrase-nested-table {
    width: 100%;
    margin: 0;
  }
  .paraphrase-nested-table thead tr th {
    padding: 0.25rem 0;
    font-size: 0.75rem;
    font-weight: 600;
    word-break: break-word;
    white-space: normal;
    border-bottom: 1px solid #dee2e6;
  }
  .paraphrase-nested-table tbody tr td {
    padding: 0.25rem 0;
    word-break: break-word;
    white-space: normal;
    font-size: 0.875rem;
    line-height: 1.25;
    vertical-align: top;
  }
</style>
{% endblock %}

{% block top_nav %}
  {{ super() }}
  <li class="nav-item active d-flex align-items-center">
    <span class="navbar-text">SMN - Dark regions</span>
  </li>
{% endblock %}

{% block content_main %}
<div class="container-float">
  <div class="row" id="body-row">
    {% if case.smn_tsv %}
      {{ smn_case_page() }}
    {% endif %}

    {% if case.paraphrase %}
      {{ paraphrase_case_page() }}
    {% endif %}

    <div class="container_spaced">
      <div class="row">
        <div class="col-4">
          {% if case.madeline_info and case.individuals|length > 1 %}
            {{ pedigree_panel() }}
          {% else %}
            <p>No pedigree picture available.</p>
          {% endif %}
        </div>
        <div class="col-8">
          {{ synopsis_panel() }}
          <div class="panel-default">
          {{ comments_panel(institute, case, current_user, comments) }}
          </div>
        </div>
      </div> <!-- end of div class row -->

      <div class="row">
        <div class="col-12">{{activity_panel(events)}}</div>
      </div>
    </div>
  </div> <!-- end of div id body-row -->
</div>
{% endblock %}

{% macro paraphrase_case_page() %}
<div class="container_spaced col-12">
  <div class="card">
    <div class="card-body">
      <div class="card-title"> Dark regions - <a href="https://github.com/Clinical-Genomics/paraphrase" target="_blank" rel="noopener">Paraphrase</a> annotation of <a href="https://github.com/PacificBiosciences/paraphase" target="_blank" rel="noopener">Paraphase</a> - Individuals</div>
      <div class="accordion accordion-flush" id="paraphrase">
      {% for region_name, region in paraphrase_regions.items() %}
        <div class="accordion-item">
          <div class="accordion-header" data-bs-toggle="tooltip" title="Status {{ region.status }} - {{ region.status_matches }}">
           <button class="accordion-button {% if region.get("status", "normal") == "pathological" %}
                  bg-danger
                {% elif region.get("status", "normal") == "intermediate" %}
                  bg-warning
                {% endif %}" type="button" data-bs-toggle="collapse" data-bs-target="#collapse_{{ region_name }}" aria-expanded="false" aria-controls="collapse_{{ region_name }}">
              <span class="col-1" data-bs-toggle="tooltip" title="Region name from Paraphase configuration">{{ region_name|upper }}</span>
              <span class="col-1" data-bs-toggle="tooltip" title="Region status from Paraphrase annotation">{{ region.status |capitalize }}</span>
              <span class="col-9">
                {% for gene in region.get("genes_in_region",[]) %}
                  {% if gene %}
                    {{ gene_link(gene) }}
                    {% for model in gene.inheritance_models %}
                      {{ inheritance_badge(model, inherit_palette) }}
                    {% endfor %}
                    {{ incomplete_penetrance_badge(gene, inherit_palette) }}
                  {% endif %}
                {% endfor %}
              </span>
           </button>
          </div>
        </div>
        <div id="collapse_{{ region_name }}" class="accordion-collapse collapse" data-bs-parent="#paraphrase">
          <div class="accordion-body">
            {% set ns = namespace(paraphrase_keys=[]) %}
            {% for ind in case.individuals %}
              {% for subtable_key in ind.paraphrase[region_name].keys() %}
                {% if subtable_key not in ["status", "status_matches", "genes_in_region", "phase_region"] and subtable_key not in ns.paraphrase_keys %}
                  {% set ns.paraphrase_keys = ns.paraphrase_keys + [subtable_key] %}
                {% endif %}
              {% endfor %}
            {% endfor %}

            <table class="table paraphrase-nested-table">
              <thead>
                <tr class="bg-secondary">
                  <th>Sample</th>
                  <th>Sex</th>
                  <th>Phenotype</th>
                  <th>Paraphrase {{ region_name }}</th>
                </tr>
              </thead>
              <tbody>
                {% for ind in case.individuals %}
                  <tr>
                    <td>{{ ind.display_name }}</td>
                    <td style="font-weight: bold; white-space: nowrap;">{{ sex_table_cell_content(ind) }}</td>
                    <td>{{ ind.phenotype_human }}</td>
                    <td>{{ show_paraphrase_value(ind.paraphrase[region_name], ns.paraphrase_keys) }}</td>
                  </tr>
                {% endfor %}
              </tbody>
            </table>

            <span class="d-flex mt-2">
              {% if case.vcf_files.vcf_snv %}
                <span class="me-3">
                  <form target="_blank" rel="noopener" action="{{url_for('variants.variants', institute_id=institute._id, case_name=case.display_name, variant_type='clinical') }}">
                    <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="{{ case.individuals[0].paraphrase[region_name].genes_in_region }}"></input>
                    <input type="hidden" id="gene_panels" name="gene_panels" value=""></input>
                    <button type="submit" class="btn btn-secondary btn-sm"  data-bs-toggle="tooltip" title="SNV and INDEL variants view filtered for the genes {{ case.individuals[0].paraphrase[region_name].genes_in_region }}">SNVs</button>
                  </form>
                </span>
              {% endif %}
              {% if case.vcf_files.vcf_sv %}
                <span class="me-3">
                  <form target="_blank" rel="noopener" action="{{url_for('variants.sv_variants', institute_id=institute._id, case_name=case.display_name, variant_type='clinical') }}">
                    <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="{{ case.individuals[0].paraphrase[region_name].genes_in_region }}"></input>
                    <input type="hidden" id="gene_panels" name="gene_panels" value=""></input>
                    <button type="submit" class="btn btn-secondary btn-sm"  data-bs-toggle="tooltip" title="Structural variants view filtered for the genes {{ case.individuals[0].paraphrase[region_name].genes_in_region }}">SVs</button>
                  </form>
                </span>
              {% endif %}
              {% if "phase_region" in region %}
                <span class="me-3" {% if not case.bam_files %}title="Alignment file(s) missing" data-bs-toggle="tooltip"{% endif %}>
                  <a href="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name'],chrom=region['phase_region']['chrom'], start=region['phase_region']['start'], stop=region['phase_region']['end'] )}}" target="_blank"
                    class="btn btn-secondary btn-sm text-white{% if not case.bam_files %} disabled{% endif %}">
                    IGV DNA
                  </a>
                </span>
              {% endif %}
            </span>
          </div>
        </div>
      {% endfor %}
      </div>
    </div>
  </div>
</div>
{% endmacro %}

{% macro show_paraphrase_value(paraphrase_value, paraphrase_keys=None) %}

  {% if paraphrase_value is mapping %}
    {% if paraphrase_keys %}
      {% set subtable_keys = paraphrase_keys %}
    {% else %}
      {% set ns = namespace(subtable_keys=[]) %}
      {% for subtable_key in paraphrase_value.keys() %}
        {% if subtable_key not in ["status", "status_matches", "genes_in_region", "phase_region"] %}
          {% set ns.subtable_keys = ns.subtable_keys + [subtable_key] %}
        {% endif %}
      {% endfor %}
      {% set subtable_keys = ns.subtable_keys %}
    {% endif %}

    <table class="table table-sm table-borderless paraphrase-nested-table">
      <thead>
        <tr>
        {% for subtable_key in subtable_keys %}
          <th>{{ subtable_key }}</th>
        {% endfor %}
        </tr>
      </thead>
      <tbody>
        <tr>
          {% for subtable_key in subtable_keys %}
            <td>{% if subtable_key in paraphrase_value %}{{ show_paraphrase_value(paraphrase_value[subtable_key]) }}{% else %}-{% endif %}</td>
          {% endfor %}
        </tr>
      </tbody>
    </table>
  {% elif paraphrase_value is string or paraphrase_value is integer or paraphrase_value is float %}
    {{ paraphrase_value }}
  {% elif paraphrase_value is sequence %}
    {{ paraphrase_value | join(', ') }}
  {% endif %}
{% endmacro %}


{% macro smn_case_page() %}
<div class="container_spaced col-12">
  <div class="card">
    <div class="card-body">
      <div class="card-title"><a href="https://github.com/Illumina/SMNCopyNumberCaller" target="_blank" rel="noopener">SMN Copy Number</a> status - Individuals</div>
      <div class="row">
        <div class="col-xs-12 col-md-12">{{ smn_individuals_table(case, institute, tissue_types) }}</div>
      </div> <!-- end of div class row -->

      <span class="d-flex mt-2">
        {% if case.vcf_files.vcf_snv %}
        <span class="me-3">
          <form target="_blank" rel="noopener" action="{{url_for('variants.variants', institute_id=institute._id, case_name=case.display_name, variant_type='clinical') }}">
            <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="SMN1, SMN2"></input>
            <input type="hidden" id="gene_panels" name="gene_panels" value=""></input>
            <span><button type="submit" class="btn btn-secondary btn-sm"  data-bs-toggle="tooltip" title="SNV and INDEL variants view filtered for the genes SMN1 and SMN2">SNVs</button></span>
          </form>
        </span>
        {% endif %}
        {% if case.vcf_files.vcf_sv %}
          <span class="me-3">
            <form target="_blank" rel="noopener" action="{{url_for('variants.sv_variants', institute_id=institute._id, case_name=case.display_name, variant_type='clinical') }}">
              <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="SMN1, SMN2"></input>
              <input type="hidden" id="gene_panels" name="gene_panels" value=""></input>
              <button type="submit" class="btn btn-secondary btn-sm"  data-bs-toggle="tooltip" title="Structural variants view filtered for the genes SMN1 and SMN2">SVs</button>
            </form>
          </span>
        {% endif %}

        <span class="me-3"
          {% if not case.bam_files %}title="Alignment file(s) missing" data-bs-toggle="tooltip"{% endif %}>
          <a href="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name'], chrom=region['smn1']['chrom'], start=region['smn1']['start'], stop=region['smn1']['end'] )}}" target="_blank"
            class="btn btn-secondary btn-sm text-white{% if not case.bam_files %} disabled{% endif %}">
            IGV DNA SMN1
          </a>
        </span>
        <span class="me-3"
          {% if not case.bam_files %}title="Alignment file(s) missing" data-bs-toggle="tooltip"{% endif %}>
          <a href="{{url_for('alignviewers.igv', institute_id=case['owner'], case_name=case['display_name'], chrom=region['smn2']['chrom'], start=region['smn2']['start'], stop=region['smn2']['end'] )}}" target="_blank"
            class="btn btn-secondary btn-sm text-white{% if not case.bam_files %} disabled{% endif %}">
            IGV DNA SMN2
          </a>
        </span>
      </span>

      {{ modal_synopsis() }}
    </div> <!-- end of card body -->
  </div> <!-- end of card div-->
</div> <!-- end of div class col -->
{% endmacro %}

{% macro smn_individuals_table(case, institute, tissues) %}
<form method="POST" action="{{ url_for('cases.update_individual', institute_id=institute._id, case_name=case.display_name) }}">
  <div class="card panel-default">
    <div class="table-responsive">
      <table class="table table-sm">
        <thead>
          <tr>
            <th data-bs-toggle='tooltip' data-bs-container='body' style="width: 20%"
             title="Display name of sample">Sample</th>
            <th data-bs-toggle='tooltip' style="width: 5%" title="Sample sex">Sex</th>
            <th data-bs-toggle='tooltip' style="width: 5%" title="Phenotype of sample">Phenotype</th>
            <th data-bs-toggle='tooltip' data-bs-container='body'
              style="width: 5%" title="SMA affected status prediction">SMA</th>
              <th data-bs-toggle='tooltip' data-bs-container='body'
                style="width: 5%" title="SMA carrier status prediction">Carrier</th>
            <th data-bs-toggle='tooltip' data-bs-container='body'
             title="SMN1 Estimated Copy Number (None means no-call)" style="width: 5%">SMN1 CN</th>
             <th data-bs-toggle='tooltip' data-bs-container='body'
              title="SMN2 Estimated Copy Number" style="width: 5%">SMN2 CN</th>
              <th data-bs-toggle='tooltip' data-bs-container='body'
               title="SMN2Δ7–8 (SMN2 with deletion of Exon 7-8) Estimated Copy Number" style="width: 10%">SMN2Δ7–8_CN</th>
               <th data-bs-toggle='tooltip' data-bs-container='body'
                title="g.27134T>G_CN Estimated Copy Number - an SNP associated with 2+0 silent carrier" style="width: 10%">g.27134T>G CN</th>
            <th data-bs-toggle='tooltip' data-bs-container='body'
             title="Ancestry prediction from peddy" style="width: 10%">Ancestry (pred.)</th>
             <th data-bs-toggle='tooltip' data-bs-container='body'
              title="Tissue origin for the sample" style="width: 15%">Tissue</th>
          </tr>
        </thead>
        <tbody>
          {% for ind in case.individuals %}
            <tr {% if ind.is_sma  %}
                  class="bg-danger"
                {% elif ind.is_sma_carrier %}
                  class="bg-warning"
                {% endif %}>
              <td>{{ ind.display_name }}</td>
              <td style="font-weight: bold;">
                {{ sex_table_cell_content(ind) }}
              </td>
              <td>{{ ind.phenotype_human }}</td>
              <td>{{ ind.is_sma }}</td>
              <td>{{ ind.is_sma_carrier }}</td>
              <td>{{ ind.smn1_cn }}</td>
              <td>{{ ind.smn2_cn }}</td>
              <td>{{ ind.smn2delta78_cn }}</td>
              <td>{{ ind.smn_27134_cn }}</td>
              <td>{{ ind.predicted_ancestry or 'N/A' }}</td>
              <td>
                {{ ind.tissue_type }}
              </td>
            </tr>
          {% endfor %}
        </tbody>
      </table>
    </div>
  </div>
</form>
{% endmacro %}

{% block scripts %}
{{ super() }}
{% endblock %}