{% extends "layout.html" %} {% from "cases/actionbar.html" import action_bar, research_modal, rerun_modal %} {% from "utils.html" import flash_messages, comments_panel, activity_panel %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} {% endblock %} {% block top_nav %} {{ super() }}
  • Institutes
  • {{ institute.display_name }}
  • {{ case.display_name }}
  • {% endblock %} {% block content %}
    {{ flash_messages() }}
    {{ variants_buttons() }}
    {{ related_causatives_list() }}
    {% set has_pedigree = case.madeline_info and case.individuals|length > 1 %}
    {{ individuals_table() }}
    {% if has_pedigree %}
    {{ pedigree_panel() }}
    {% endif %}
    {{ synopsis_panel() }}
    {{ candidates_list() }}
    {{ diagnosis_panel() }}
    {{ comments_panel(institute, case, current_user, comments) }}
    {{ phenotype_groups_panel() }}
    {{ phenotypes_panel() }}
    {{ genepanels_table() }}
    {{ hpo_genelist_panel() }}
    {{ activity_panel(events) }}
    {{ modal_synopsis() }} {{ rerun_modal(institute, case) }} {{ research_modal(institute, case) }}
    {% endblock %} {% macro variants_buttons() %}
    Clinical SNV and INDELs Clinical structural variants
    {% if case.is_research %}
    Research SNV and INDELs Research structural variants
    {% endif %} {% endmacro %} {% macro related_causatives_list() %}
    Matching causatives from other cases
    {% endmacro %} {% macro individuals_table() %}
    Individuals
    {% for ind in case.individuals %} {% endfor %}
    Sample Sex Phenotype Sequencing
    {{ ind.display_name }} {{ ind.sex_human }} {{ ind.phenotype_human }} {{ ind.analysis_type|upper }}
    {% endmacro %} {% macro pedigree_panel() %}
    Pedigree
    {{ case.madeline_info|safe }}
    {% endmacro %} {% macro synopsis_panel() %}
    Synopsis
    {{ case.synopsis|markdown if case.synopsis else 'Nothing written yet...' }}
    {% endmacro %} {% macro modal_synopsis() %}
    {% endmacro %} {% macro candidates_list() %}
    Causative variants
    Stong candidates
    {% for variant in suspects %} {% if variant._id %} {% else %} {% endif %} {% else %}
    No variants suspected yet
    {% endfor %}
    {{ variant.hgnc_symbols|join(', ') }} {% if variant.sanger_ordered %} Sanger ordered {% elif variant.manual_rank %} {{ variant.manual_rank }} {% endif %}
    {{ 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') }} {{ variant }} (not loaded)
    {% endmacro %} {% macro diagnosis_panel() %}
    Diagnosis phenotypes
    {{ diagnosis_form('phenotype') }}
    Diagnosis genes
    {{ diagnosis_form('gene') }}
    {% endmacro %} {% macro diagnosis_form(type) %}
    {% endmacro %} {% macro phenotype_groups_panel() %}
    Phenotype groups
    {% set url = 'http://compbio.charite.de/hpoweb/showterm?id=HP:0000018' %}
    Phenotype terms (HPO web)
    {% endmacro %} {% macro hpo_group_item(hpo_term) %}
  • {{ hpo_term.feature }} {{ hpo_term.phenotype_id }}
    {{ remove_form(url_for('cases.phenotypes', institute_id=institute._id, case_name=case.display_name, phenotype_id=hpo_term.phenotype_id, is_group='yes')) }}
  • {% endmacro %} {% macro phenotypes_panel() %}
    Added phenotypes
    {% endmacro %} {% macro hpo_item(hpo_term) %}
  • {{ hpo_term.feature }} {{ hpo_term.phenotype_id }}
  • {% endmacro %} {% macro remove_form(url, hidden_input=None, button_name=None, button_value=None) %}
    {% if hidden_input %} {% endif %}
    {% endmacro %} {% macro hpo_genelist_panel() %}
    HPO gene panel ({{ case.dynamic_gene_list|length }} genes)
    {% if case.dynamic_gene_list %} {% endif %}
    {% endmacro %} {% macro genepanels_table() %}
    Gene panels
    {% for panel in case.panels %} {% else %} {% endfor %}
    Panel Version Genes
    {{ panel.display_name|truncate(30, True) }} {% if panel.is_default %} Default {% endif %} {{ panel.version }} ({{ panel.updated_at.date() }}) {{ panel.nr_genes }}
    No panels linked to case
    {% endmacro %} {% block scripts %} {{ super() }} {% endblock %}