filter.html

{% extends 'projectroles/project_base.html' %}
{% load projectroles_common_tags %}
{% load rules %}
{% load crispy_forms_tags %}
{% load static %}
{% load variants_tags %}

{% block navi_sub_project_extend %}
  <li class="breadcrumb-item"><a href="{% url "variants:case-list" project=project.sodar_uuid %}">Cases</a></li>
  {% if query_type == "case" %}
    <li class="breadcrumb-item"><a href="{% url "variants:case-detail" project=project.sodar_uuid case=object.sodar_uuid %}">{{ object.name }}</a></li>
    <li class="breadcrumb-item active">Filter</li>
  {%  else %}
    <li class="breadcrumb-item active">Joint Filtration</li>
  {% endif %}
{% endblock %}

{% block projectroles %}
  {% get_app_setting 'userprofile' 'enable_project_uuid_copy' user=request.user as enable_uuid_copy %}

{% block css %}
  {{ block.super }}
  <style type="text/css">
    .display-info-coordinates .detail-info-clinvar,
    .display-info-clinvar .detail-info-coordinates,
    .display-frequencies-exac .detail-frequencies-gnomad-exomes,
    .display-frequencies-exac .detail-frequencies-gnomad-genomes,
    .display-frequencies-exac .detail-frequencies-thousand-genomes,
    .display-frequencies-exac .detail-frequencies-inhouse,
    .display-frequencies-exac .detail-frequencies-mtdb,
    .display-frequencies-exac .detail-frequencies-helixmtdb,
    .display-frequencies-exac .detail-frequencies-mitomap,
    .display-frequencies-gnomad-exomes .detail-frequencies-exac,
    .display-frequencies-gnomad-exomes .detail-frequencies-gnomad-genomes,
    .display-frequencies-gnomad-exomes .detail-frequencies-thousand-genomes,
    .display-frequencies-gnomad-exomes .detail-frequencies-inhouse,
    .display-frequencies-gnomad-exomes .detail-frequencies-mtdb,
    .display-frequencies-gnomad-exomes .detail-frequencies-helixmtdb,
    .display-frequencies-gnomad-exomes .detail-frequencies-mitomap,
    .display-frequencies-gnomad-genomes .detail-frequencies-exac,
    .display-frequencies-gnomad-genomes .detail-frequencies-gnomad-exomes,
    .display-frequencies-gnomad-genomes .detail-frequencies-thousand-genomes,
    .display-frequencies-gnomad-genomes .detail-frequencies-inhouse,
    .display-frequencies-gnomad-genomes .detail-frequencies-mtdb,
    .display-frequencies-gnomad-genomes .detail-frequencies-helixmtdb,
    .display-frequencies-gnomad-genomes .detail-frequencies-mitomap,
    .display-frequencies-thousand-genomes .detail-frequencies-exac,
    .display-frequencies-thousand-genomes .detail-frequencies-gnomad-exomes,
    .display-frequencies-thousand-genomes .detail-frequencies-gnomad-genomes,
    .display-frequencies-thousand-genomes .detail-frequencies-inhouse,
    .display-frequencies-thousand-genomes .detail-frequencies-mtdb,
    .display-frequencies-thousand-genomes .detail-frequencies-helixmtdb,
    .display-frequencies-thousand-genomes .detail-frequencies-mitomap,
    .display-frequencies-inhouse .detail-frequencies-exac,
    .display-frequencies-inhouse .detail-frequencies-gnomad-exomes,
    .display-frequencies-inhouse .detail-frequencies-gnomad-genomes,
    .display-frequencies-inhouse .detail-frequencies-thousand-genomes,
    .display-frequencies-inhouse .detail-frequencies-mtdb,
    .display-frequencies-inhouse .detail-frequencies-helixmtdb,
    .display-frequencies-inhouse .detail-frequencies-mitomap,
    .display-frequencies-mtdb .detail-frequencies-exac,
    .display-frequencies-mtdb .detail-frequencies-gnomad-exomes,
    .display-frequencies-mtdb .detail-frequencies-gnomad-genomes,
    .display-frequencies-mtdb .detail-frequencies-thousand-genomes,
    .display-frequencies-mtdb .detail-frequencies-inhouse,
    .display-frequencies-mtdb .detail-frequencies-helixmtdb,
    .display-frequencies-mtdb .detail-frequencies-mitomap,
    .display-frequencies-helixmtdb .detail-frequencies-exac,
    .display-frequencies-helixmtdb .detail-frequencies-gnomad-exomes,
    .display-frequencies-helixmtdb .detail-frequencies-gnomad-genomes,
    .display-frequencies-helixmtdb .detail-frequencies-thousand-genomes,
    .display-frequencies-helixmtdb .detail-frequencies-inhouse,
    .display-frequencies-helixmtdb .detail-frequencies-mtdb,
    .display-frequencies-helixmtdb .detail-frequencies-mitomap,
    .display-frequencies-mitomap .detail-frequencies-exac,
    .display-frequencies-mitomap .detail-frequencies-gnomad-exomes,
    .display-frequencies-mitomap .detail-frequencies-gnomad-genomes,
    .display-frequencies-mitomap .detail-frequencies-thousand-genomes,
    .display-frequencies-mitomap .detail-frequencies-inhouse,
    .display-frequencies-mitomap .detail-frequencies-mtdb,
    .display-frequencies-mitomap .detail-frequencies-helixmtdb,
    .display-constraints-exac-pli .detail-constraints-exac-z-mis,
    .display-constraints-exac-pli .detail-constraints-exac-z-syn,
    .display-constraints-exac-pli .detail-constraints-gnomad-loeuf,
    .display-constraints-exac-pli .detail-constraints-gnomad-pli,
    .display-constraints-exac-pli .detail-constraints-gnomad-z-mis,
    .display-constraints-exac-pli .detail-constraints-gnomad-z-syn,
    .display-constraints-exac-z-mis .detail-constraints-exac-pli,
    .display-constraints-exac-z-mis .detail-constraints-exac-z-syn,
    .display-constraints-exac-z-mis .detail-constraints-gnomad-loeuf,
    .display-constraints-exac-z-mis .detail-constraints-gnomad-pli,
    .display-constraints-exac-z-mis .detail-constraints-gnomad-z-mis,
    .display-constraints-exac-z-mis .detail-constraints-gnomad-z-syn,
    .display-constraints-exac-z-syn .detail-constraints-exac-pli,
    .display-constraints-exac-z-syn .detail-constraints-exac-z-mis,
    .display-constraints-exac-z-syn .detail-constraints-gnomad-loeuf,
    .display-constraints-exac-z-syn .detail-constraints-gnomad-pli,
    .display-constraints-exac-z-syn .detail-constraints-gnomad-z-mis,
    .display-constraints-exac-z-syn .detail-constraints-gnomad-z-syn,
    .display-constraints-gnomad-loeuf .detail-constraints-gnomad-pli,
    .display-constraints-gnomad-loeuf .detail-constraints-gnomad-z-mis,
    .display-constraints-gnomad-loeuf .detail-constraints-gnomad-z-syn,
    .display-constraints-gnomad-loeuf .detail-constraints-exac-pli,
    .display-constraints-gnomad-loeuf .detail-constraints-exac-z-mis,
    .display-constraints-gnomad-loeuf .detail-constraints-exac-z-syn,
    .display-constraints-gnomad-pli .detail-constraints-gnomad-loeuf,
    .display-constraints-gnomad-pli .detail-constraints-gnomad-z-mis,
    .display-constraints-gnomad-pli .detail-constraints-gnomad-z-syn,
    .display-constraints-gnomad-pli .detail-constraints-exac-pli,
    .display-constraints-gnomad-pli .detail-constraints-exac-z-mis,
    .display-constraints-gnomad-pli .detail-constraints-exac-z-syn,
    .display-constraints-gnomad-z-mis .detail-constraints-gnomad-loeuf,
    .display-constraints-gnomad-z-mis .detail-constraints-gnomad-pli,
    .display-constraints-gnomad-z-mis .detail-constraints-gnomad-z-syn,
    .display-constraints-gnomad-z-mis .detail-constraints-exac-pli,
    .display-constraints-gnomad-z-mis .detail-constraints-exac-z-mis,
    .display-constraints-gnomad-z-mis .detail-constraints-exac-z-syn,
    .display-constraints-gnomad-z-syn .detail-constraints-gnomad-loeuf,
    .display-constraints-gnomad-z-syn .detail-constraints-gnomad-pli,
    .display-constraints-gnomad-z-syn .detail-constraints-gnomad-z-mis,
    .display-constraints-gnomad-z-syn .detail-constraints-exac-pli,
    .display-constraints-gnomad-z-syn .detail-constraints-exac-z-mis,
    .display-constraints-gnomad-z-syn .detail-constraints-exac-z-syn {
      display: none;
    }

    .varfish-variant-table th {
      text-align: center;
    }

    .variant-row-positive { background-color: {% get_row_bgcolor "pathogenic" %}; }
    .variant-row-uncertain { background-color: {% get_row_bgcolor "uncertain" %}; }
    .variant-row-negative { background-color: {% get_row_bgcolor "benign" %}; }
    .variant-row-wip { background-color: {% get_row_bgcolor "wip" %}; }

    .warning-conflict .hidden { display: none; }

    .compact-form-groups .form-group {
      margin-bottom: 0;
    }
  </style>
{% endblock %}

  <div class="row sodar-pr-content-title pb-2">
    {# Project menu dropdown, only visible if browser width < X and sidebar is hidden #}
    {% include 'projectroles/_project_menu_btn.html' %}

    <h2 class="sodar-pr-content-title">
      {% if query_type == "case" %}
        Filter Variants for Case
        <small class="text-muted">{{ object.name }}</small>
      {% else %}
        {% if cohort %}
          Joint Filtration for Cohort
          <small class="text-muted">{{ cohort.name }}</small>
        {% else %}
          Joint Filtration for Project
          <small class="text-muted">{{ project.title }}</small>
        {% endif %}
      {% endif %}
    </h2>

    {# Project copy uuid #}
    {% if enable_uuid_copy %}
      {% if query_type == "case" %}
        <a role="submit" class="btn btn-link mr-2 sodar-pr-btn-title sodar-pr-btn-copy-uuid sodar-copy-btn"
           id="sodar-pr-btn-copy-uuid"
           data-clipboard-text="{{ object.sodar_uuid }}"
           title="Copy UUID to clipboard" data-toggle="tooltip" data-placement="top">
          <i class="fa fa-clipboard text-muted" aria-hidden="true"></i>
        </a>
      {% else %}
        {% if not cohort %}
          <a role="submit" class="btn btn-link mr-2 sodar-pr-btn-title sodar-pr-btn-copy-uuid sodar-copy-btn"
             id="sodar-pr-btn-copy-uuid"
             data-clipboard-text="{{ project.sodar_uuid }}"
             title="Copy UUID to clipboard" data-toggle="tooltip" data-placement="top">
            <i class="fa fa-clipboard text-muted" aria-hidden="true"></i>
          </a>
        {% endif %}
      {% endif %}
    {% endif %}

    {% include "variants/_case_filter_buttons.html" %}
  </div>

  <div class="container-fluid sodar-page-container pt-3">
    <div class="alert alert-secondary small p-2">
      <i class="fa fa-info-circle"></i>
      This is the variant filtration form.
      You can use the form controls below to adjust your filter criteria.
      <strong>Click the <span class="badge badge-primary"><i class="fa fa-refresh"></i> Filter &amp; Display</span> when you are ready!</strong>
      The results of your previous query will be loaded automatically if there are any.
    </div>

    {% include "variants/_filter_form.html" %}
  </div>

  <!-- table to fill when query finished -->
  <div id="resultsTable" data-loaded="false">
  </div>

{% endblock projectroles %}

{% block javascript %}
  {{ block.super }}
  {% include 'variants/scripts.html' %}
  <script type="text/javascript" src="{% static 'js/panelapp.js' %}"></script>
{% endblock javascript %}