{% from "variants/indicators.html" import clinical_assessments_badge, research_assessments_badge %}

{% macro matchmaker_modal(institute, case, suspects, mme_nodes ) %}
<div class="modal fade" id="matchmaker_modal" tabindex="-1" role="dialog" aria-hidden="true">
  <div class="modal-dialog modal-xl modal-dialog-centered" role="document">
    <div class="modal-content">
      <div class="modal-header">
        <h5 class="modal-title" id="exampleModalLabel">Matchmaker Exchange patient submission</h5>
        <button type="button" class="close" data-bs-dismiss="modal" aria-label="Close">
          <span aria-hidden="true">&times;</span>
        </button>
      </div> <!-- end of modal title -->
      <div class="modal-body">
        {% if case.mme_submission %} <!-- case was already submitted to Matchmaker -->
          <div class="row">
            <div class="col-6">
              <a href="{{url_for('cases.matchmaker_matches', institute_id=institute._id, case_name=case.display_name)}}" class="btn btn-secondary text-white" role="button" target="_blank">Submission details <span class="fas fa-people-arrows"></span></a>
            </div>
            <div class="col-6">
              <select class="btn btn-secondary" onchange="window.open(this.value,'_self');" style="width:auto;">
                   <option selected>Match against</option>
                   <option value="{{ url_for('cases.matchmaker_match', institute_id=institute._id, case_name=case.display_name, target='internal') }}">Scout patients in Matchmaker</option>
                   {% if mme_nodes %}
                      {% for node in mme_nodes %}
                        <option value="{{ url_for('cases.matchmaker_match', institute_id=institute._id, case_name=case.display_name, target=node.id) }}">{{node.description}}</option>
                      {% endfor %}
                  {% endif %}
              </select>
            </div>
          </div>
          <hr>
          <p><a href="#mme_form" data-bs-toggle="collapse">Modify submission</a></p>
        {% else %} <!-- display option to submit case to Matchmaker -->
          <p>This case is not yet in Matchmaker!&nbsp;<a href="#mme_form" data-bs-toggle="collapse">Submission form</a></p>
        {% endif %}
        <form id="mme_submit" method="POST" action="{{ url_for('cases.matchmaker_add', institute_id=institute._id, case_name=case.display_name )}}" >
            <div id="mme_form" class="collapse">
              <div class="d-flex justify-content-center">
                <ul class="list-group w-75">
                  <li class="list-group-item">
                    <div class="d-flex justify-content-between">
                      <div data-bs-placement="top" title="hpo">
                        Include patient gender
                      </div>
                      <div class="form-check form-switch">
                        <input type="checkbox" class="form-check-input" id="sex" name="sex" {% if not case.mme_submission or case.mme_submission.sex %}checked{% endif %}>
                        <label class="form-check-label" for="sex"></label>
                      </div>
                    </div>
                  </li>
                  <li class="list-group-item">
                    <div class="d-flex justify-content-between">
                      <div data-bs-placement="top" title="hpo">
                        Include HPO terms
                      </div>
                      <div class="form-check form-switch">
                        <input type="checkbox" class="form-check-input" id="features" name="features" {% if not case.mme_submission or case.mme_submission.features %}checked{% endif %}>
                        <label class="form-check-label" for="features"></label>
                      </div>
                    </div>
                  </li>
                  <li class="list-group-item">
                    <div class="d-flex justify-content-between">
                      <div data-bs-placement="top" title="disorders">
                        Include OMIM diagnoses
                      </div>
                      <div class="form-check form-switch">
                        <input type="checkbox" class="form-check-input" id="disorders" name="disorders" {% if not case.mme_submission or case.mme_submission.disorders %}checked{% endif %}>
                        <label class="form-check-label" for="disorders"></label>
                      </div>
                    </div>
                  </li>
                  <li class="list-group-item">
                    Select <u><b>max 3</b></u> variants/genes from the pinned variants list (only gene names can be shared for SVs)<br>
                    <div style="max-height:200px; overflow-y: scroll;"">
                      {% set count = namespace(value=0) %}
                      {% for var in suspects %}
                        {% set count.value = count.value + 1 %}
                        {% if var.category == "snv" %} <!-- Share either gene names or variant details for SNVs -->

                          <!-- Share variant it is, could be a multi-gene variant, resulting into multiple gene submission-->
                          <input type="checkbox" name="selected_var" id="var_details" value="{{var._id}}"> ~ Variant {{count.value}} {% if var.genes|length > 1 %} ({{var.genes|length}} genes) {%endif%} ~ {{ pretty_variant(var) }}<span class="badge bg-success">SNV</span><br>

                          {% if var.genes|length > 1 %} <!-- Share single gene variants from a multi-gene variant -->
                            {% for gene in var.genes %}
                              <input type="checkbox" name="selected_var" id="var_details" value="{{var._id}}|{{gene.hgnc_symbol or gene.hgnc_id}}"> ~ Variant {{count.value}} (1 gene) ~
                              {{ gene.hgnc_symbol or gene.hgnc_id }}
                              <span class="badge bg-success">SNV</span><br>
                            {% endfor %}
                          {% endif %}

                        {% elif var.category == "sv" %} <!-- Share only gene names from SVs -->
                          {% for gene in var.genes %}
                            <input type="checkbox" name="selected_var" id="var_details" value="{{var._id}}|{{gene.hgnc_symbol or gene.hgnc_id}}"> ~ Variant {{count.value}} ~  {{gene.hgnc_symbol or gene.hgnc_id}} - {{ pretty_variant(var) }} <span class="badge bg-warning">SV</span><br>
                          {% endfor %}
                        {% endif %}
                      {% endfor %}
                    </div>
                  </li>
                  <li class="list-group-item">
                    <div class="row">
                      <div class="col-6">
                        <div data-bs-placement="top" id="share_variants">
                          Share variant details for SNVs and gene names for SVs
                        </div>
                        <div>
                          <input type="radio" id="genomicfeatures" name="genomicfeatures" value="variants" checked>
                          <label for="share_variants"></label>
                        </div>
                      </div>
                      <div class="col-6">
                        <div data-bs-placement="top" id="share_genes">
                          Share only gene names from all selected variants
                        </div>
                        <div>
                          <input type="radio" id="genomicfeatures" name="genomicfeatures" value="genes" {% if case.mme_submission and case.mme_submission.genes_only %}checked{% endif %}>
                          <label for="share_genes"></label>
                        </div>
                      </div>
                    </div>
                  </li>
                </ul>
              </div>
              <div>
                <br>
                <button class="btn btn-secondary mx-auto d-block" data-bs-toggle="modal" type="submit">
                  {% if case.mme_submission %}
                    Update case
                  {% else %}
                    Share to Matchmaker
                  {% endif %}</button>
              </div>
            </div>
            <br>
          </form>
          {% if case.mme_submission %}
            {{ modal_mme_delete(institute, case) }}
          {% endif %}
      </div> <!-- end of modal body -->
    </div> <!--end of modal-content -->
  </div> <!--end of modal-dialog modal-lg -->
</div> <!--end of MatchMaker modal -->
{% endmacro %}

{% macro modal_mme_delete(institute, case) %}
  <form id="mme_delete" method="POST" action="{{ url_for('cases.matchmaker_delete', institute_id=institute._id, case_name=case.display_name )}}">
    <!-- Button trigger modal -->
    <button type="submit" class="btn btn-danger form-control">
    Remove case from Matchmaker
    </button>
  </form>
{% endmacro %}

{% macro beacon_modal(institute, case) %}
<form method="POST" action="{{url_for('cases.beacon_add_variants', institute_id=institute._id, case_name=case.display_name)}}">
<div class="modal fade" id="beacon_modal" tabindex="-1" role="dialog" aria-hidden="true">
  <div class="modal-dialog modal-lg" role="document">
    <div class="modal-content">
      <div class="modal-header">
        <h5 class="modal-title" id="exampleModalLabel">Beacon submission</h5>
        <button type="button" class="close" data-bs-dismiss="modal" aria-label="Close">
          <span aria-hidden="true">&times;</span>
        </button>
      </div>
      <div class="modal-body">
          {% if not "beacon" in case %}
            <!-- form to submit variants to beacon -->
            <input type="hidden" name="case" value="{{case._id}}">

            <!--Sample selection-->
            <div class="d-flex justify-content-center">
              <div class="form-check form-check-inline">
                <input class="form-check-input" type="radio" id="sampleradio1" name="samples" value="affected" checked>
                <label class="form-check-label" for="sampleradio1">
                  Affected individuals
                </label>
              </div>
              <div class="form-check form-check-inline">
                <input class="form-check-input" type="radio" id="sampleradio2" name="samples" value="all">
                <label class="form-check-label" for="sampleradio2">
                  All individuals
                </label>
              </div>
            </div>

            <!--VCF files (variant type) selection-->
            <div class="row d-flex justify-content-around align-items-center mt-3">
              <label class="form-check-label" for="vcfselect">
                Variants type:
              </label>
              <select multiple name="vcf_files" id="vcfselect" class="selectpicker w-auto" data-style="btn-secondary">
                {% for file, path in case.vcf_files.items() %}
                  {% if path and file in ["vcf_snv", "vcf_cancer", "vcf_snv_research", "vcf_cancer_research"] %} <!-- support for sharing SNVs for now -->
                    <option value="{{file}}" {{ "selected" if "research" not in file }}>{{file|replace("vcf_", "")|replace("_", " ")|upper}}</option>
                  {% endif %}
                {% endfor %}
              </select>
            </div>

            <!--Gene panel selection-->
            <div class="row d-flex justify-content-around align-items-center mt-3">
              <label class="form-check-label" for="vcfselect">
                Filter by panel:
              </label>
              <select multiple name="panels" id="panelselect" class="selectpicker w-auto" data-style="btn-secondary">
                {% for panel in case.panels %}
                  <option value="{{panel.panel_id}}" {{ "selected" if panel.is_default }}>{{ panel.display_name|truncate(30, True) }} {{ panel.version }} ({{ panel.nr_genes }} genes)</option>
                {% endfor %}
              </select>
            </div>
          <!-- end of form to submit variants to beacon -->
          <!-- case variants are already in beacon, display info -->
          {% else %}
            <div class="d-flex justify-content-center">
              <table class="table table-sm">
                <tbody>
                  <tr>
                    <td><strong>Created date</strong></td>
                    <td>{{case.beacon.created_at.strftime('%Y-%m-%d %H:%M:%S')}}</td>
                  </tr>
                  <tr>
                    <td><strong>Created by</strong></td>
                    <td>{{case.beacon.user}}</td>
                  </tr>
                  <tr>
                    <td><strong>VCF samples</strong></td>
                    <td>{{ case.beacon.samples|join(", ") }}</td>
                  </tr>
                  <tr>
                    <td><strong>VCF filter</strong></td>
                    <td>{{ "gene panels" if case.beacon.panels|length > 0 else "entire VCF" }}</td>
                  </tr>
                  <tr>
                    <td><strong>VCF types</strong></td>
                    <td>{{ case.beacon.vcf_files|join(", ") }}</td>
                  </tr>
                </tbody>
              </table>
            </div>
          {% endif %}
      </div>
      <div class="modal-footer d-flex justify-content-around">
        <div>
          {% if case.beacon %}
            <a href="{{url_for('cases.beacon_remove_variants', institute_id=institute._id, case_name=case.display_name )}}" class="btn btn-danger text-white">Remove all case variants from Beacon</a>
          {% else %}
            <button type="submit" class="btn btn-primary">Add variants to beacon</button>
          {% endif %}
          <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Cancel</button>
        </div>
      </div>
    </div>
  </div>
</div>
</form>
{% endmacro %}

{% macro pretty_variant(variant) %}

  {% if variant.category %}
    {% if variant.category in "str" %}
      {% if variant.str_repid %}
        {{ variant.str_repid }}
      {% elif variant.str_trid %}
        {{ variant.str_trid  }}
      {% else %}
        {% for gene in variant.genes %} {{ gene.symbol }} {% endfor %}
      {% endif %}
      {% if variant.str_mc %}
        STR{{ variant.str_mc }}
      {% else %}
        {{ variant.alternative|truncate(20,True) }}
      {% endif %}
    {% elif variant.category in ("snv", "cancer") %}
      {% set display_genes = [] %}
      {% for gene in variant.genes %}
        {% if gene.hgvs_identifier and gene.hgnc_symbol  %}
          {{ "" if display_genes.append(gene.hgnc_symbol + ' ' + gene.hgvs_identifier|truncate(20,True)) }}
        {% elif gene.hgnc_symbol %}
          {{ "" if display_genes.append(gene.hgnc_symbol) }}
        {% elif gene.hgvs_identifier and gene.hgnc_id %}
          {{ "" if display_genes.append( gene.hgnc_id|string + ' ' + gene.hgvs_identifier|truncate(20,True)) }}
        {% endif %}
      {% endfor %}

      {% if not display_genes %}
          {{ "" if display_genes.append( variant.simple_id|truncate(40,True) ) }}
      {% endif %}

      {{ display_genes|join(", ") }}

    {% elif variant.category == "outlier" %}
      {{ variant.sub_category|upper }} - {% if variant.genes %}
        {% for gene in variant.genes %}
           {% if gene.hgnc_symbol %}
             {{ gene.hgnc_symbol }}
           {% else %}
             {{gene.hgnc_id}}
           {% endif %}
        {% endfor %} {% else %}
          {{ variant.gene_name_orig }}{% endif %} - {% if variant.sub_category == "splicing" %}
          {{ variant.delta_psi }}&Delta;&psi;  {{ variant.potential_impact }} - fs {{ variant.causes_frameshift }}
        {% elif variant.sub_category == "expression" %}
          {{ variant.l2fc }}{% if variant.l2fc > 0 %}&uarr;{% elif variant.l2fc < 0 %}&darr;{% endif %}
        {% elif variant.sub_category == "methylation" %}
          {{ variant.compare_label }} {{ variant.cpg_label.split("_")[0] }}
        {% endif %}
    {% else %} <!-- structural variants -->
      {{ variant.sub_category|upper }}({{ variant.chromosome }}{{ variant.cytoband_start }}-{{ variant.end_chrom }}{{ variant.cytoband_end }})
    {% endif %}
  {% endif %}

{% endmacro %}

{% macro pretty_link_variant(variant, case) %}
{# Returns human readable links to the corresponding variant page #}

  {% if variant.category in ("mei", "snv") %}
    <a href='{{ url_for('variant.variant',
                   institute_id=variant.institute,
                   case_name=case.display_name,
                   variant_id=variant._id) }}' target='_blank'>
  {% elif variant.category == "str" %}
    <a href='{{ url_for('variant.variant',
                   institute_id=variant.institute,
                   case_name=case.display_name,
                   variant_id=variant._id) }}'
       data-bs-toggle='tooltip'
       title='{{ variant.alternative | replace("<", " ") | replace(">", "")}}'
       target='_blank'>
  {% elif variant.category == "cancer" %}
    <a href='{{ url_for('variant.cancer_variant',
                   institute_id=variant.institute,
                   case_name=case.display_name,
                   variant_id=variant._id) }}' target='_blank'>
  {% elif variant.category == "outlier" %}
    <a href='{{ url_for('omics_variants.outliers',
       institute_id=variant.institute, case_name=case.display_name) }}' target='_blank'>
  {% else %} <!-- structural variants -->
    <a href='{{ url_for('variant.sv_variant',
                              institute_id=variant.institute,
                              case_name=case.display_name,
                              variant_id=variant._id) }}' target='_blank'>
  {% endif %}
  {{ pretty_variant(variant) }}
  </a>
{% endmacro %}

{% macro variant_validation_badge(variant) %}
  {% if variant.validation == 'True positive' %}
    <span class="badge bg-success">Validated</span>
  {% elif variant.validation == 'False positive' %}
    <span class="badge bg-danger">Validated</span>
  {% elif variant.sanger_ordered %}
    <span class="badge bg-secondary">Verification ordered</span>
  {% endif %}
{% endmacro %}

{% macro tumor_allele_freq(variant) %}
  {% if variant.tumor %}
    {{ allele_div(variant.tumor, "Tumor") }}
  {% endif %}
  {% if variant.normal %}
    {{ allele_div(variant.normal, "Normal") }}
  {% endif %}
{% endmacro %}


{% macro causatives_list(causatives, partial_causatives, evaluated_variants, institute, case, manual_rank_options, cancer_tier_options) %}
  {% set already_displayed_variant_ids = [] %}
  <div class="card mt-3">
     <div data-bs-toggle='tooltip' title="Displays all variants that have been marked causative for this case">
      <div class="d-flex align-items-center">
        <h6><span class="fa fa-medkit ms-3 mt-2"></span>
          {% if case.track == 'cancer' %}
            Clinically significant
          {% else %}
            Causative variants ({{causatives|length + partial_causatives|length}})
          {% endif %}
        </h6>
        {% if not case.causatives|length and not case.partial_causatives|length %}
        <span class="text-muted ms-3 mt-2">
          <h6>No causative variants</h6>
        </span>
        {% endif %}
      </div>
    </div>
    <div class="mb-3" style="max-height:300px; overflow-y: scroll;">
      <ul class="list-group">
        {% for variant in causatives %}
          <li class="list-group-item list-group-item-action">
            {% if variant._id %}
              {% do already_displayed_variant_ids.append( variant._id ) %}
              <div class="row">
                <div class="col">
                   <i class="far fa-check-circle"></i>
                  {{ pretty_link_variant(variant, case) }}
                  {{ variant_validation_badge(variant) }}
                  {{ clinical_assessments_badge(variant) }}
                  {{ tumor_allele_freq(variant) }}
                </div>
                <div class="col-auto" style="width:fit-content;">
                  {{ remove_form(url_for('cases.mark_causative',
                                         institute_id=institute._id,
                                         case_name=case.display_name,
                                         variant_id=variant._id,
                                         partial_causative=False),
                                 button_name='action', button_value='DELETE') }}
                </div>
              </div>
            {% else %} <!-- no variant._id -->
              {{ variant }} <small class="text-muted">(not loaded)</small>
            {% endif %}
          </li>
        {% endfor %}
        <!-- End of causative variants -->

        <!-- Partial causative variants -->
        {% for variant_phenotypes in partial_causatives %}
          {% set variant = variant_phenotypes.variant %}
          <div class="list-group-item list-group-item-action">
            {% if variant._id %}
              {% do already_displayed_variant_ids.append(variant._id) %}
              <div class="row">
                <div class="col">
                  <i class="far fa-check-circle"></i>
                  {{ pretty_link_variant(variant, case) }} (partial causative)
                </div>
                <div class="col-2" style="width:fit-content;">
                  {{ remove_form(url_for('cases.mark_causative',
                                         institute_id=institute._id,
                                         case_name=case.display_name,
                                         variant_id=variant._id,
                                         partial_causative=True),
                                 button_name='action', button_value='DELETE') }}
                </div>
              </div>
              <div class="row">
                <div class="col-4">
                  <i class="far fa-check-circle" style="color:transparent; background-color:transparent"></i>
                  Diagnoses
                </div>
                <div class="col-8">
                  {% for term in variant_phenotypes.disease_terms %}
                    {% if 'OMIM' in term %}
                      <a class="btn btn-xs btn-secondary text-white" target="_blank" href="http://omim.org/entry/{{term|replace('OMIM:','')}}">
                        {{term}}
                      </a>
                    {% elif 'ORPHA' in term %}
                      <a class="btn btn-xs btn-secondary text-white" target="_blank" href="https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert={{term}}">
                        {{term}}
                      </a>
                    {% endif %}
                  {% else %}
                    N/A
                  {% endfor %}
                </div>
              </div>
              <div class="row">
                <div class="col-4">
                   <i class="far fa-check-circle" style="color:transparent; background-color:transparent"></i>
                  HPO terms
                </div>
                <div class="col-8">
                  {% for hpo in variant_phenotypes.hpo_terms %}
                    <a target="_blank" href="https://hpo.jax.org/browse/term/{{hpo.phenotype_id}}">
                      <span class="badge badge-sm bg-info">{{hpo.phenotype_id}}</span>
                    </a>
                  {% else %}
                    N/A
                  {% endfor %}
                </div>
              </div>

            {% else %}
              {{ variant }} <small class="text-muted">(not loaded)</small>
            {% endif %}
          </div>
        {% endfor %}
        <!-- end of partial causative variants -->

        <!-- variants with cancer tier I or II -->
        {% if case.track == 'cancer' %}
          {% set exp_tiers =  ['1A', '1B', '2C', '2D'] %}
          {% set exp_acmg =  ['pathogenic', 'likely_pathogenic'] %}
          {% for variant in evaluated_variants %}
            {% if variant._id %}
              <!-- set acmg classification -->
              {% if variant.cancer_tier in exp_tiers or (variant.acmg_classification and variant.acmg_classification.code in exp_acmg) %}
                {% if variant._id not in already_displayed_variant_ids %}
                  {% do already_displayed_variant_ids.append(variant._id) %}
                  <li class="list-group-item list-group-item-action">
                    <div class="d-flex align-items-center">
                      <div class="col">
                        {{ pretty_link_variant(variant, case) }}
                        {{ variant_validation_badge(variant) }}
                      </div>
                        {{ clinical_assessments_badge(variant) }}
                        {{ tumor_allele_freq(variant) }}
                      <div class="col-1">
                        <!-- remove classification placeholder -->
                      </div>
                    </div>
                  </li>

                {% endif %}
              {% endif %}
            {% else %} <!-- no variant._id -->
              {{ variant }} <small class="text-muted">(not loaded)</small>
            {% endif %}

          {% endfor %}
        {% endif %}
        <!-- end of cancer tier variants -->
      </ul>
    </div> <!--end of card body div-->
  </div> <!--end of card div--->
{% endmacro %}

{% macro allele_div(allele, type) %}
  {% if 'alt_freq' in allele %}
    <div class="col-1.5" data-bs-toggle="tooltip" data-bs-placement="top" title="{{ type }} alternative AF ">
      <div style="padding: 0 15px">{{ allele.alt_freq|round(4) }}</div>
    </div>
  {% endif %}
{% endmacro %}

{% macro suspects_list(suspects, institute, case, manual_rank_options, cancer_tier_options) %}
  <div class="card mt-3">
    <div class="d-flex align-items-center" data-bs-toggle='tooltip' title="Displays all variants that have been pinned or included in a ClinVar submission for this case">
      <h6><span class="fa fa-map-pin ms-3 mt-2"></span>&nbsp;Variants pinned ({{suspects|length}}) or included in a ClinVar submission({{ case.clinvar_variants.items()|length }})</h6>
    </div>
    <div class="mb-3" style="max-height:300px; overflow-y: scroll;">
    <ul class="list-group">
      {% if not suspects|length %}
        <span class="text-muted ms-3 mt-2">
          <h6>No pinned variants</h6>
        </span>
      {% endif %}
      {% for variant in suspects %}
        <li class="list-group-item">
          {% if variant._id %}
            <div class="row">
              <div class="col">
                <div class="row">
                  <div class="col">
                    {{ pretty_link_variant(variant, case)}}
                    {{ clinical_assessments_badge(variant) }}
                    {{ variant_validation_badge(variant) }}
                    {{ tumor_allele_freq(variant) }}
                    {% if variant.mosaic_tags %}
                      <span class="badge bg-info">mosaic</span>
                    {% endif %}
                  </div>
                </div>
              </div>
              <div class="col-auto">
              <form action="{{ url_for('cases.mark_validation',
                                         institute_id=variant.institute,
                                         case_name=case.display_name,
                                         variant_id=variant._id) }}"
                      method="POST" accept-charset="utf-8">
                  <select class="form-control form-control-sm" onchange="this.form.submit()" name="type">
                    {% for type in ('Not validated', 'True positive', 'False positive') %}
                      <option value="{{ type }}" {% if type == variant.validation %}selected{% endif %}>{{ type }}</option>
                    {% endfor %}
                  </select>
                </form>
              </div>
              <div class="col">{{ clinvar_var_status(variant, case, institute) }}</div>
            <div class="col-auto" style="width: fit-content;">
              {{ remove_form(url_for('cases.pin_variant',
                                     institute_id=institute._id,
                                     case_name=case.display_name,
                                     variant_id=variant._id),
                             button_name='action', button_value='DELETE') }}
            </div>
          </div>
          {% else %}
            {{ variant }} <small class="text-muted">(not loaded)</small>
          {% endif %}
        </li>
      {% endfor %}
    </ul>
      {{ clinvar_vars_summary(case, institute) }}
      </div>
  </div>
{% endmacro %}

{% macro clinvar_var_status(variant, case, institute) %}
    {% if case.clinvar_variants and variant._id in case.clinvar_variants.keys() %}
      <span class="badge rounded-pill bg-dark" data-bs-toggle="tooltip" title="Variant included in a germline ClinVar submission"><em class="fas fa-database"></em></span>
    {% elif case.onco_clinvar_variants and variant._id in case.onco_clinvar_variants %}
      <span class="badge rounded-pill bg-dark" data-bs-toggle="tooltip" title="Variant included in an oncogenic ClinVar submission"><em class="fas fa-database"></em></span>
    {% elif variant._id and variant.category in ["snv", "sv"] %}
        <form id="clinvar_submit" class="d-flex justify-content-center" action="{{ url_for('clinvar.clinvar_add_variant', institute_id=institute._id, case_name=case.display_name) }}" method="POST">
          <button type="submit" name="var_id" value="{{variant._id}}" class="btn btn-secondary btn-sm" style="float: right;">Add to ClinVar submission</button>
        </form>
    {% elif variant.category in ('cancer') %}
        <form id="clinvar_onc_submit" class="d-flex justify-content-center" action="{{ url_for('clinvar.clinvar_add_onc_variant', institute_id=institute._id, case_name=case.display_name) }}" method="POST">
          <button type="submit" name="var_id" value="{{variant._id}}" class="btn btn-secondary btn-sm" style="float: right;">Add to ClinVar submission</button>
        </form>
    {% endif %}
{% endmacro %}


{% macro clinvar_vars_summary(case, institute) %}
  {% if case.clinvar_variants %}
    <div class="card-footer d-flex justify-content-center pb-0" style="background-color:inherit;">
        <a href="{{url_for('clinvar.clinvar_germline_submissions', institute_id=institute._id)}}"
           class="btn btn-secondary btn-sm text-white mx-3" target="_blank" rel="noopener noreferrer">View ClinVar submissions <i class="fas fa-arrow-circle-right"></i></a>
    </div>
  {% elif case.onco_clinvar_variants %}
    <div class="card-footer d-flex justify-content-center pb-0" style="background-color:inherit;">
        <a href="{{url_for('clinvar.clinvar_onc_submissions', institute_id=institute._id)}}"
           class="btn btn-secondary btn-sm text-white mx-3" target="_blank" rel="noopener noreferrer">View ClinVar submissions <i class="fas fa-arrow-circle-right"></i></a>
    </div>
  {% endif %}
{% endmacro %}

{% macro matching_causatives(other_causatives, institute, case, default=False) %}
    <div data-bs-toggle='tooltip' class="panel-heading" title="If there are any variants in this case
      matching a causative in another case for this institute. {% if default %}Variants in default panels for the case only.{% endif %}">
      <strong><a data-bs-toggle="collapse" href="#matchingCausatives{% if default %}Default{% endif %}" class="text-body" aria-expanded="false"><span class="collapse-icon me-1"></span>Matching causatives {% if default %}in case default panels{% endif %}({{other_causatives|length}})</a></strong>
    </div>
    <ul class="list-group collapse" id="matchingCausatives{% if default %}Default{% endif %}">
      {% for variant in other_causatives %}
        <li class="list-group-item">
          {{ pretty_link_variant(variant, case)}}
        </li>
      {% else %}
        <li class="list-group-item">No matching causative variants.</li>
      {% endfor %}
    </ul>
{% endmacro %}

{% macro matching_managed_variants(managed_variants, institute, case, default=False) %}
    <div data-bs-toggle='tooltip' class="panel-heading" title="Any variants in this case
      that have been marked as managed. {% if default %}Variants in default panels for the case only.{% endif %}">
      <strong><a data-bs-toggle="collapse" class="text-body" href="#matchingManaged{% if default %}Default{% endif %}" aria-expanded="false"><span class="collapse-icon me-1"></span>Managed variants {% if default %}in case default panels{% endif %}({{managed_variants|length}})</a></strong>
    </div>
    <ul class="list-group">
      {% for variant in managed_variants %}
        <li class="list-group-item collapse" id="matchingManaged{% if default %}Default{% endif %}">
           {{ pretty_link_variant(variant, case)}}
        </li>
      {% else %}
        <li class="list-group-item">No managed variants.</li>
      {% endfor %}
    </ul>
{% endmacro %}


{% macro remove_form(url, hidden_input=None, button_name=None, button_value=None) %}
  <form action="{{ url }}" method="POST">
    {% if hidden_input %}
      <input type="hidden"
             name="{{ hidden_input[0] }}"
             value="{{ hidden_input[1] }}">
    {% endif %}
    <div class="pull-end">
      <button class="btn btn-sm"
              name="{{ button_name if button_name }}"
              value="{{ button_value if button_value }}"
              type="submit">
        <i class="fa fa-times text-danger"></i>
      </button>
    </div>
  </form>
{% endmacro %}

{% macro sex_table_cell_content(ind) %}
  {% if ind.sex_human in ['female','male'] %}
    {% if ind.sex_human == 'female' %}
      F
    {% elif ind.sex_human == 'male' %}
      M
    {% else %}
      {{ind.sex_human}}
    {% endif %}
  {% endif %}
  {% if ind.confirmed_sex %}
    <i class="fa fa-check"></i>
  {% else %}
    <span class="fa fa-exclamation-circle text-danger" data-bs-toggle='tooltip' title="Sex is not confirmed."></span>
  {% endif %}
{% endmacro %}

{% macro filter_audits(audits, edit=none) %}
<table id="audit-table" class="table table-sm" style="background-color: transparent">
  <thead>
    <tr>
      <th>Filters marked audited for case</th>
    </tr>
  </thead>
  <tbody>
  {% set audit_query = namespace() %}
  {% for audit in audits %}
  {% set audit_query = audit.link|url_args %}
    <tr>
      <td class="d-flex align-items-center"><strong>{{ audit.subject }} ({{audit_query.variant_type if audit_query.variant_type else "type unavailable -"}} {{ audit_query.category if audit_query.category else "category unavailable"}})</strong>&nbspwas marked checked by {{ audit.user_name }} on {{audit.created_at.strftime('%Y-%m-%d')}}.
      {% if edit is true %}
        <a href="{{ url_for('variants.unaudit_filter', audit_id=audit._id) }}" class="btn btn-link btn-sm" type="submit" data-bs-toggle='tooltip' title="Un-audit filter"><i class="fa fa-times text-danger"></i></a>
      {% endif %}
      </td>
    </tr>
  {%  endfor %}
  </tbody>
</table>
{% endmacro %}