{% import "bootstrap/wtf.html" as wtf %} {% extends "layout.html" %} {% from "overview/institute_sidebar.html" import institute_actionbar %} {% from "overview/utils.html" import analysis_type %} {% block title %} {{ super() }} - {{ institute.display_name }} - Cases {% endblock %} {% block top_nav %} {{ super() }} {% endblock %} {% macro search_form() %}
{{ form.search_type.label(class="control-label") }} {{ form.search_type(class="form-control") }}
{{ form.search(class="btn btn-primary form-control") }}
{{ form.search_limit.label(class="control-label") }} {{ form.search_limit(class="form-control") }}
{{ form.skip_assigned(class="form-check-input") }} {{ form.skip_assigned.label(class="form-check-label") }}
{{ form.is_research(class="form-check-input") }} {{ form.is_research.label(class="form-check-label") }}
{{ form.has_rna(class="form-check-input") }} {{ form.has_rna.label(class="form-check-label") }}
{{ form.clinvar_submitted(class="form-check-input") }} {{ form.clinvar_submitted.label(class="form-check-label") }}
{{ form.validation_ordered(class="form-check-input") }} {{ form.validation_ordered.label(class="form-check-label") }}
{% endmacro %} {% macro cases_table(group_name, cases) %} {% if sort_order == 'asc' %} {% set sort_option = 'desc'%} {% else %} {% set sort_option = 'asc'%} {% endif %}
{% for case in cases %} {{ case_row(case) }} {% else %} {% endfor %}
{{ group_name|capitalize }} cases ({{cases|length}}/{{status_ncases[group_name] or 0}}) Status Analysis date Link Default panel Seq Track Share
No cases found with this query.
{% endmacro %} {% macro case_row(case) %} {{ case.display_name }} {% if case.individuals|length > 1 %} {% for item in case.individuals %} {% if case.track == "cancer" %} {% else %} {% endif %} {% endfor %} {% endif %} {% for user in case.assignees %} {{ user.name }} {% endfor %} {% if case.needs_check %} decipher {% endif %} {{ case.status }} {% if case.is_migrated %} migrated {% endif %} {{ case.analysis_date.date() }} {% if case.rerun_requested %} rerun pending {% elif case.is_rerun %} rerun {% endif %} {% if case.is_research %} {% if case.vcf_files.vcf_snv %} Research SNV and INDELs {% elif case.vcf_files.vcf_cancer %} Clinical Somatic Variants {% endif %} {% else %} {% if case.vcf_files.vcf_snv %} Clinical SNV and INDELs {% elif case.vcf_files.vcf_cancer %} Clinical Somatic Variants {% elif case.vcf_files.vcf_cancer_sv %} Clinical Somatic Structural Variants {% elif case.vcf_files.vcf_fusion %} Clinical Fusion Variants {% elif case.individuals|rejectattr('bionano_access', 'undefined')|rejectattr('bionano_access', 'none')|list|length > 0 %} Optical Genome Mapping BioNano FSHD {% endif %} {% endif %} {{ default_gene_panel(institute, case) }} {{ analysis_type(case.analysis_types) }} {{ case.display_track }} {% if case.clinvar_variants %} {% endif %} {% if case.mme_submission %} {% endif %} {% if case.beacon %} {% endif %} {% endmacro %} {% block content_main %}
{{ institute_actionbar(institute) }}
{{ search_form() }}
{% if sanger_unevaluated %} {% endif %}
{% set ordered_statuses = ['prioritized', 'inactive', 'active', 'archived', 'solved', 'ignored'] -%} {% for status in ordered_statuses %} {% for group_name, case_group in cases %} {% if status == group_name %}
{{ cases_table(group_name, case_group) }}
{% endif %} {% endfor %} {% endfor %}
{% endblock %} {% block scripts %} {{ super() }} {% endblock %} {% macro default_gene_panel(institute, case) %} {% set count = namespace(count=0, displayed=0) %} {% for panel in case.panels if panel.is_default %} {% set count.count = count.count + 1 %} {% if count.count < 3 %} {{ panel.panel_name }} {% set count.displayed = count.displayed + 1 %} {% else %} ... {% endif %} {% endfor %} {% if case.panels|length > count.displayed %} + {{ case.panels|length - count.displayed }} {% endif %} {% endmacro %}