{% extends "layout.html" %} {% from "cases/collapsible_actionbar.html" import action_bar, research_modal, reanalysis_modal, solve_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 hpo_item, cohort_panel, diagnosis_phenotypes, phenotype_groups_panel, add_phenotype_terms_panel, hpo_panel %} {% from "cases/gene_panel.html" import genepanels_table, hpo_genelist_panel %} {% from "cases/clinvar.html" import clinvar_vars %} {% 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, causatives, collaborators, current_user, report_types, has_rna_tracks) }} {{ case_page() }}
{% endblock %} {% macro case_page() %}

Case: {{case.display_name}} {{case._id}}
Status: {{case.status}}


Set:
{% if case.status != 'archived' %} {% else %} {% endif %} {% if case.status != 'solved' %} {% else %} {% endif %}
{{ variants_buttons() }}
Safe variant matching: {% if institute.gene_panels_matching %} on {% else %} off {% endif %}
{% if other_causatives|length > 0%}
{{ matching_causatives(other_causatives, institute, case) }}
{% endif %} {% if default_other_causatives|length > 0%}
{{ matching_causatives(default_other_causatives, institute, case, default=True) }}
{% endif %} {% if managed_variants|length > 0%}
{{ matching_managed_variants(managed_variants, institute, case) }}
{% endif %} {% if default_managed_variants|length > 0%}
{{ matching_managed_variants(default_managed_variants, institute, case, default=True) }}
{% 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.clinvar_variants or case.suspects %}
{{ clinvar_vars(institute, case, suspects) }}
{% endif %}
{% if case.track == 'cancer' %}
{{ cancer_individuals_table(case, institute, tissue_types, gens_info) }}
{% else %}
1 else "12"}}">{{ individuals_table(case, institute, tissue_types, display_rerunner, gens_info) }}
{% if case.madeline_info and case.individuals|length > 1 %}
{{ pedigree_panel(case) }}
{% endif %} {% endif %}
{{ synopsis_panel() }}
{{ comments_panel(institute, case, current_user, comments) }}
{{ insert_multi_image_panel() }}
{{ custom_image_panels() }}
 Phenotypes & diagnoses
{{ hpo_panel(case, institute, config) }}
{{ hpo_genelist_panel(case, institute, config) }}
{% if not case.track == 'cancer' %}
 Diagnoses (OMIM)
{{ diagnosis_phenotypes(case, institute, omim_terms) }}
{% endif %}
 Groups & cohorts
{{ group_panel() }}
{{ cohort_panel(case, institute, cohort_tags) }}
{{ phenotype_groups_panel(case, institute, hpo_groups) }}
{{ genepanels_table(case, institute) }}
{{activity_panel(events)}}
{{ modal_synopsis() }} {{ solve_modal(institute, case) }} {{ research_modal(institute, case) }} {{ reanalysis_modal(institute, case) }} {{ beacon_modal(institute, case) }} {{ matchmaker_modal(institute, case, suspects, mme_nodes) }}
{% endmacro %} {% macro variants_buttons() %}
{% if case.vcf_files.vcf_snv %} Clinical {% if case.track=="cancer" %}germline {% endif %}SNV and INDELs {% endif %} {% if case.vcf_files.vcf_sv %} Clinical {% if case.track=="cancer" %}germline {% endif %}structural variants {% endif %} {% if case.vcf_files.vcf_mei %} Clinical Mobile Element Insertion variants {% endif %} {% if case.vcf_files.vcf_str %} Clinical STR variants {% endif %} {% if case.smn_tsv %} SMN CN {% endif %} {% if case.individuals|rejectattr('bionano_access', 'undefined')|rejectattr('bionano_access', 'none')|list|length > 0 %} BioNano FSHD {% endif %} {% if case.vcf_files.vcf_cancer %} Clinical {% if case.track=="cancer" %}somatic {% endif %}SNV and INDELs {% endif %} {% if case.vcf_files.vcf_cancer_sv %} Clinical {% if case.track=="cancer" %}somatic {% endif %}structural variants {% endif %} {% if case.vcf_files.vcf_fusion %} Clinical fusion variants {% endif %}
{% if case.is_research %}
{% if case.vcf_files.vcf_snv_research %} Research {% if case.track=="cancer" %}germline {% endif %}SNV and INDELs {% endif %} {% if case.vcf_files.vcf_sv_research %} Research {% if case.track=="cancer" %}germline {% endif %}structural variants {% endif %} {% if case.vcf_files.vcf_mei_research %} Research Mobile Element Insertion variants {% endif %} {% if case.vcf_files.vcf_cancer_research %} Research somatic SNV and INDELs {% endif %} {% if case.vcf_files.vcf_cancer_sv_research %} Research somatic structural variants {% endif %} {% if case.vcf_files.vcf_fusion_research %} Research fusion variants {% endif %}
{% endif %}
{% endmacro %} {% macro synopsis_panel() %}
 Synopsis
{{ case.synopsis|markdown if case.synopsis else 'Nothing written yet...' }}
{% endmacro %} {% macro group_panel() %}
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 %} {% endfor %}
{% endfor %} {% endif %}
{% endmacro %} {% macro modal_add_to_group(group_id, case_group, label) %}
{% endmacro %} {% set chromograph = namespace(available=false) %} {% macro insert_multi_image_panel() %}
{% for i in case.individuals %} {% if i.chromograph_images and (i.chromograph_images.coverage or i.chromograph_images.autozygous or i.chromograph_images.upd_sites) %} {% set chromograph.available = true %}
Chromograph images {{i.display_name}} (legend)
{% endif %} {% endfor %}
{% endmacro %} {% macro custom_image_panels() %} {% if case.custom_images %} {% for section_name in case.custom_images %}
{% for image in case.custom_images[section_name] %}
{{ image.title }}
{% endfor %}
{% endfor %} {% endif %} {% endmacro %} {% macro add_modal_panel(id_tag, display_name) %} {% endmacro %} {% macro modal_synopsis() %}
{% endmacro %} {% macro remove_form(url, hidden_input=None, button_name=None, button_value=None) %}
{% if hidden_input %} {% endif %}
{% endmacro %} {% block scripts %} {{ super() }} {% endblock %}