{% extends "minibase.html" %}
{% block body %}

<h1>GPSEA cohort analysis</h1>
<div id="cohort-summary">
  <p>
    Successfully loaded {{ cohort | count | pluralize('individual') }}.

    {# Sex #}
    {{ cohort.count_males() | was_were }} recorded as male,
    {{ cohort.count_females() }} as female,
    and {{ cohort.count_unknown_sex() }} as unknown sex.

    {# Vital status #}
    {% if cohort | count == cohort.count_unknown_vital_status() %}
    No information about individuals' vital status was reported.
    {% else %}
    {{ cohort.count_alive() | was_were }} reported to be alive at the time of last encounter,
    {{ cohort.count_deceased() | was_were }} deceased,
    and vital status was unreported for {{ cohort.count_unknown_vital_status() | pluralize('individual')}}.
    {% endif %}

    {# Disease and age at last encounter #}
    {{ cohort.count_with_disease_onset() | pluralize('individual')}} had disease onset information
    and {{ cohort.count_with_age_of_last_encounter() }} had information about the age of last encounter.
  </p>
</div>

{# Genotype & Phenotype #}
<div class="cards">
  {# HPO terms #}
  <div id="hpo" class="card">
    <h2>HPO terms</h2>
    {% set distinct_hpos = cohort.count_distinct_hpo_terms() %}
    {% if distinct_hpos > 0 %}
    <table>
      The cohort included {{ distinct_hpos | pluralize('distinct HPO term') }}.
      <caption>
        {% if distinct_hpos > top_phenotype_count %}
        Top {{top_phenotype_count}} most common HPO terms.
        {% endif %}
        {% if n_has_onset_info %} {# Optional onset info #}
        {{ n_has_onset_info }} had onset information for at least 20% of individuals.
        {% endif %}
      </caption>
      <tbody>
        <tr class="strng">
          <th><em>n</em></th>
          <th>HPO Term</th>
        </tr>

        {% for count in hpo_counts %}
        <tr>
          <td>{{ count['count'] }}</td>
          <td><a href="https://hpo.jax.org/browse/term/{{ count['term_id'] }}">{{ count['label'] }}</a>
          </td>
        </tr>
        {% endfor %}
      </tbody>
    </table>
    {% else %}
    No HPO terms were provided.
    {% endif %}
    {# The table is inconsistent. Skip it for now!
    {% if n_has_onset_info > 0 %}
    <h3>Top {{top_var_count}} HPO Terms</h3>
    <p>
      A total of {{ cohort.count_distinct_hpo_terms() }} HPO terms were used to annotated the cohort.
    </p>
    <table>
      <tbody>
        <tr class="strng">
          <th>HPO</th>
          <th>Count</th>
        </tr>
        {% for onset_info in has_onset_information %}
        <tr>
          <td>{{ onset_info.display_label }}</td>
          <td>{{ onset_info.count }}</td>
        </tr>
        {% endfor %}
      </tbody>
    </table>
    {% endif %}
    #}
  </div>

  {# Measurements #}
  <div id="measurements" class="card">
    <h2>Measurements</h2>
    {% set distinct_measurements = cohort.count_distinct_measurements() %}
    {% if distinct_measurements > 0 %}
    The cohort included {{ distinct_measurements | pluralize('measurement') }}.
    <table>
      {% if distinct_measurements > top_phenotype_count %}
      <caption></caption>
      Top {{ top_phenotype_count }} most common measurements.
      </caption>
      {% endif %}
      <tbody>
        <tr class="strng">
          <th><em>n</em></th>
          <th>Measurement</th>
          <th>ID</th>
        </tr>

        {% for count in measurement_counts %}
        <tr>
          <td>{{ count['count'] }}</td>
          <td>{{ count['label'] }}</td>
          <td>{{ count['term_id'] }}</td>
        </tr>
        {% endfor %}
      </tbody>
    </table>
    {% else %}
    No data regarding measurement assays were provided.
    {% endif %}
  </div>

  {# The most common diseases #}
  <div id="diseases" class="card">
    <h2>Diseases</h2>
    {% set distinct_diseases = cohort.count_distinct_diseases() %}
    {% if distinct_diseases > 0 %}
    The cohort members were diagnosed with {{ distinct_diseases | pluralize('disease') }}.
    <table>
      {% if distinct_diseases > top_phenotype_count %}
      <caption>
        Top {{ top_phenotype_count }} most common diseases.
      </caption>
      {% endif %}

      <tbody>
        <tr class="strng">
          <th><em>n</em></th>
          <th>Disease</th>
        </tr>
        {% for count in disease_counts %}
        <tr>
          <td>{{ count['count'] }}</td>
          <td><a href="https://hpo.jax.org/browse/disease/{{ count['term_id'] }}">{{ count['label'] }}</a>
          </td>
        </tr>
        {% endfor %}
      </tbody>
    </table>
    {% else %}
    No diagnoses were provided.
    {% endif %}
  </div>

  {# Genotype #}
  {# The most common variants #}
  <div class="card">
    <h2>Variants</h2>
    <p>
      A total of {{ cohort.all_variant_infos() | count | pluralize('unique variant') }}
      were identified in the cohort. Variants were annotated with respect to {{ transcript_id }}.
    </p>
    <table>
      <caption>
        <h3>Top {{top_var_count}} variants</h3>
      </caption>
      <tbody>
        <tr class="strng">
          <th><em>n</em></th>
          <th>Variant key</th>
          <th>HGVS</th>
          <th>Variant Class</th>
        </tr>
        {% for count in var_counts %}
        <tr>
          <td>{{ count['count'] }}</td>
          <td>{{ count['key'] }}</td>
          <td>{{ count['hgvsc'] }} ({{ count['hgvsp'] }})</td>
          <td>{{ count['effects'] }}</td>
        </tr>
        {% endfor %}
      </tbody>
    </table>
  </div>

  {# The most common variant effects #}
  <div class="card">
    {% if has_transcript %}
    <h2>Variant effects</h2>
    <p>
      The effects were predicted for {{ transcript_id }}
    </p>
    <table>
      <tbody>
        <tr class="strng">
          <th>Variant effect</th>
          <th>Count</th>
        </tr>
        {% for effect in variant_effects %}
        <tr>
          <td>{{ effect['effect'] }}</td>
          <td>{{ effect['count'] }} ({{ effect['percent'] }}%)</td>
        </tr>
        {% endfor %}
      </tbody>
    </table>
    {% else %}
    <p>Call this function with transcript to see table with variant effect counts.</p>
    {% endif %}
  </div>
</div>
{% endblock %}