{% extends "layout_bs4.html" %} {% from "cases/collapsible_actionbar.html" import action_bar, research_modal, rerun_modal %} {% from "utils.html" import comments_panel, activity_panel, pedigree_panel %} {% from "cases/utils.html" import causatives_list, suspects_list, remove_form, matching_causatives, matching_managed_variants, beacon_modal, matchmaker_modal %} {% from "cases/individuals_table.html" import cancer_individuals_table, individuals_table %} {% from "cases/phenotype.html" import cohort_panel, diagnosis_phenotypes, diagnosis_genes, phenotype_groups_panel, phenotype_terms_panel, phenotypes_panel %} {% from "cases/gene_panel.html" import genepanels_table, hpo_genelist_panel %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} {% endblock %} {% block css %} {{ super() }} {% endblock %} {% block top_nav %} {{ super() }} {% endblock %} {% block content_main %}
{{ action_bar(institute, case, collaborators, current_user) }} {{ case_page() }}
{% endblock %} {% macro case_page() %}

Case: {{case.display_name}}

Status: {{case.status}}
Internal ID: {{case._id}}

{{ variants_buttons() }}
{% if other_causatives|length > 0%}
{{ matching_causatives(other_causatives, institute, case) }}
{% endif %} {% if managed_variants|length > 0%}
{{ matching_managed_variants(managed_variants, institute, case) }}
{% endif %}
{{ causatives_list(causatives, partial_causatives, evaluated_variants, institute, case, manual_rank_options, cancer_tier_options) }}
{{ suspects_list(suspects, institute, case, manual_rank_options, cancer_tier_options) }}
{% if case.track == 'cancer' %}
{{ cancer_individuals_table(case, institute, tissue_types) }}
{% else %}
{{ individuals_table(case, institute, tissue_types) }}
{% endif %}
{{ insert_multi_image_panel() }}
{% if case.track != 'cancer' %} {% if case.madeline_info and case.individuals|length > 1 %} {{ pedigree_panel(case) }} {% else %}

No pedigree picture available.

{% endif %} {% endif %} {{ group_panel() }}
{{ synopsis_panel() }} {{ comments_panel(institute, case, current_user, comments) }}
{% if not case.track == 'cancer' %}
 Diagnoses
{{ diagnosis_phenotypes(case, institute, omim_terms) }}
{{ diagnosis_genes(case, institute) }}
{% endif %}
{{ cohort_panel(case, institute, cohort_tags) }}
{{ phenotype_groups_panel(case, institute, hpo_groups) }}
{{ phenotype_terms_panel(case, institute) }}
{{ phenotypes_panel(case, institute, config) }}
{{ genepanels_table(case, institute) }}
{{ hpo_genelist_panel(case, institute, config) }}
{% if case.clinvar_variants %}
{{ clinvar_panel() }}
{% endif %}
{{activity_panel(events)}}
{{ modal_synopsis() }} {{ rerun_modal(institute, case) }} {{ research_modal(institute, case) }} {{ beacon_modal(case) }} {{ matchmaker_modal(institute, case, mme_nodes) }}
{% endmacro %} {% macro variants_buttons() %}
{% if case.vcf_files.vcf_snv %} Clinical SNV and INDELs {% endif %} {% if case.vcf_files.vcf_sv %} Clinical structural variants {% endif %} {% if case.vcf_files.vcf_str %} Clinical STR variants {% endif %} {% if case.smn_tsv %} SMN CN {% endif %} {% if case.vcf_files.vcf_cancer %} Clinical SNV and INDELs {% endif %} {% if case.vcf_files.vcf_cancer_sv %} Clinical structural variants {% endif %} {% if gens_info.display %} View CN profile {% endif %}
{% if case.is_research%}
{% if case.track=="cancer" %} Research SNV and INDELs Research structural variants {% else %} Research SNV and INDELs Research structural variants {% endif %}
{% endif %} {% endmacro %} {% macro synopsis_panel() %}
 Synopsis
{{ case.synopsis|markdown if case.synopsis else 'Nothing written yet...' }}
{% endmacro %} {% macro group_panel() %}
Group connected cases ({{case_groups|length}} groups) New group
{% if case_groups %} {% for group_id, case_group in case_groups.items() %} {% if loop.index > 1 %}
{% endif %} {{ modal_add_to_group(group_id, case_group, case_group_label[group_id]) }}
{% for grouped_case in case_group %} {{ grouped_case.display_name }} {% endfor %}
{% endfor %} {% endif %}
{% endmacro %} {% macro modal_add_to_group(group_id, case_group, label) %}
{% endmacro %} {% macro insert_multi_image_panel() %} {% for i in case.individuals %} {% if i.chromograph_images %} {% if i.chromograph_images.coverage or i.chromograph_images.autozygous or i.chromograph_images.upd_sites %} {{ add_collapsable_panel(i.individual_id, i.display_name) }} {% endif %} {% endif %} {% endfor %} {% endmacro %} {% macro add_collapsable_panel(id_tag, display_name) %}
Images {{display_name}} >
{% endmacro %} {% macro modal_synopsis() %}
{% endmacro %} {% macro clinvar_panel() %}
Variants in ClinVar submissions
{% endmacro %} {% macro remove_form(url, hidden_input=None, button_name=None, button_value=None) %}
{% if hidden_input %} {% endif %}
{% endmacro %} {% block scripts %} {{ super() }} {% endblock %}