scout-browser 4.102.0__py3-none-any.whl → 4.103.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- scout/adapter/mongo/case.py +26 -122
- scout/adapter/mongo/clinvar.py +91 -25
- scout/adapter/mongo/event.py +0 -47
- scout/adapter/mongo/variant_loader.py +7 -3
- scout/build/variant/variant.py +1 -0
- scout/commands/load/variants.py +1 -1
- scout/commands/update/user.py +87 -49
- scout/constants/__init__.py +3 -0
- scout/constants/clinvar.py +10 -0
- scout/constants/variant_tags.py +18 -0
- scout/demo/NIST.trgt.stranger.vcf.gz +0 -0
- scout/demo/NIST.trgt.stranger.vcf.gz.tbi +0 -0
- scout/demo/__init__.py +1 -0
- scout/models/clinvar.py +86 -0
- scout/parse/variant/coordinates.py +5 -1
- scout/parse/variant/gene.py +5 -9
- scout/parse/variant/genotype.py +66 -42
- scout/parse/variant/variant.py +2 -0
- scout/server/app.py +71 -2
- scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html +2 -0
- scout/server/blueprints/cases/controllers.py +1 -1
- scout/server/blueprints/cases/templates/cases/case_report.html +19 -2
- scout/server/blueprints/cases/templates/cases/utils.html +8 -29
- scout/server/blueprints/clinvar/controllers.py +233 -53
- scout/server/blueprints/clinvar/form.py +38 -1
- scout/server/blueprints/clinvar/static/form_style.css +8 -1
- scout/server/blueprints/clinvar/templates/clinvar/clinvar_onc_submissions.html +200 -0
- scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html +3 -2
- scout/server/blueprints/clinvar/templates/clinvar/components.html +198 -0
- scout/server/blueprints/clinvar/templates/clinvar/multistep_add_onc_variant.html +187 -0
- scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html +9 -348
- scout/server/blueprints/clinvar/templates/clinvar/scripts.html +193 -0
- scout/server/blueprints/clinvar/views.py +90 -13
- scout/server/blueprints/institutes/controllers.py +44 -5
- scout/server/blueprints/institutes/forms.py +1 -0
- scout/server/blueprints/institutes/templates/overview/gene_variants.html +15 -6
- scout/server/blueprints/institutes/templates/overview/institute_sidebar.html +28 -2
- scout/server/blueprints/institutes/templates/overview/utils.html +1 -1
- scout/server/blueprints/institutes/views.py +17 -4
- scout/server/blueprints/mme/templates/mme/mme_submissions.html +2 -2
- scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html +2 -2
- scout/server/blueprints/variant/controllers.py +1 -1
- scout/server/blueprints/variant/templates/variant/cancer-variant.html +2 -1
- scout/server/blueprints/variant/templates/variant/components.html +0 -1
- scout/server/blueprints/variant/templates/variant/sv-variant.html +2 -1
- scout/server/blueprints/variant/templates/variant/variant.html +2 -2
- scout/server/blueprints/variant/templates/variant/variant_details.html +32 -24
- scout/server/blueprints/variants/templates/variants/cancer-variants.html +5 -3
- scout/server/blueprints/variants/templates/variants/str-variants.html +4 -1
- scout/server/blueprints/variants/templates/variants/sv-variants.html +3 -3
- scout/server/blueprints/variants/templates/variants/utils.html +4 -0
- scout/server/blueprints/variants/templates/variants/variants.html +4 -4
- scout/server/extensions/clinvar_extension.py +2 -2
- scout/server/templates/layout.html +1 -1
- {scout_browser-4.102.0.dist-info → scout_browser-4.103.0.dist-info}/METADATA +1 -1
- {scout_browser-4.102.0.dist-info → scout_browser-4.103.0.dist-info}/RECORD +59 -53
- {scout_browser-4.102.0.dist-info → scout_browser-4.103.0.dist-info}/WHEEL +0 -0
- {scout_browser-4.102.0.dist-info → scout_browser-4.103.0.dist-info}/entry_points.txt +0 -0
- {scout_browser-4.102.0.dist-info → scout_browser-4.103.0.dist-info}/licenses/LICENSE +0 -0
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{% extends "bootstrap_global.html" %}
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{% from "clinvar/components.html" import condition_identifiers, hgvs_choices, observations %}
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{% block css %}
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{{ super() }}
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<link rel="stylesheet" href="{{ url_for('clinvar.static', filename='form_style.css') }}"
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<link rel="stylesheet" href="{{ url_for('clinvar.static', filename='form_style.css') }}"/>
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<link href="https://cdn.jsdelivr.net/npm/select2@4.0.13/dist/css/select2.min.css" rel="stylesheet" integrity="sha512-nMNlpuaDPrqlEls3IX/Q56H36qvBASwb3ipuo3MxeWbsQB1881ox0cRv7UPTgBlriqoynt35KjEwgGUeUXIPnw==" crossorigin="anonymous" referrerpolicy="no-referrer"/>
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<link href="https://cdn.jsdelivr.net/npm/select2-bootstrap-5-theme@1.2.0/dist/select2-bootstrap-5-theme.min.css" rel="stylesheet" />
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{% endblock %}
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<div class="col-md-10">
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<form id="clinVarAdd" method="POST" action="{{ url_for('clinvar.clinvar_save', institute_id=institute._id, case_name=case.display_name) }}" id="{{variant_data.var_id}}_form">
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<!-- progressbar -->
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<ul id="progressbar">
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<ul id="progressbar" class="steps-7">
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<li class="active">Start</li>
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<li>Assertion Criteria</li>
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<li>Variant Details</li>
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<li>Inheritance Model</li>
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<li>Germline Classification</li>
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<li>Associated conditions</li>
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<li>Observation Data</li>
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</ul>
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<!-- fieldsets -->
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<fieldset data-step="1">
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<br>
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{% if var_category == 'snv' %}
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<br><br>
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{{ variant_data.var_form.tx_hgvs.label(class="fw-bold, text-dark") }}
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<span class="text-danger" data-bs-toggle='tooltip' title="If you do not provide any HGVS expression, chromosome coordinates will be used to describe this variant instead (automatic). HGVS expressions were validated using VariantValidator"><strong>?</strong></span>
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<span class="badge bg-primary float-end"><a class="text-white" href="https://variantvalidator.org/service/validate/" target="_blank" rel="noopener">VariantValidator</a></span>
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{% with messages = get_flashed_messages() %}
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{% if messages %}
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{% for message in messages %}
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<span class="ml-3">{{ message }}</span><br>
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{% endfor %}
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{% endif %}
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{% endwith %}
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<table style="width:100%; table-layout: auto; border-collapse: collapse;">
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<caption></caption>
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<tr><th></th></tr>
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{% for item_row in variant_data.var_form.tx_hgvs | batch(3) %}
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<tr>
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{% for item in item_row %}
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{% set ns = namespace(label='', validated=false, mane_select=false, mane_plus_clinical=false) %}
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{% if "_validated_" in item.label.text %}
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{% set ns.validated = true %}
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{% endif %}
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{% if "_mane-select_" in item.label.text %}
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{% set ns.mane_select = true %}
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{% endif %}
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{% if "_mane-plus-clinical_" in item.label.text %}
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{% set ns.mane_plus_clinical = true %}
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{% endif %}
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{% set ns.label = item.label.text | replace("_validated_", "") | replace("_mane-select_", "") %}
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<td style="width: 3%; text-align: right; vertical-align: baseline;">
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<input type="radio" name="tx_hgvs" value="{{ ns.label }}"
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{% if ns.mane_select %}checked{% endif %}>
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</td>
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<td style="width: 30%; text-align: left; ">
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<p class="text-dark"
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{% if ns.label|length > 50 %}
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data-bs-toggle="tooltip" title="{{ns.label}}">{{ ns.label|truncate(25,true,'..') }}
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{% else %}
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>{{ ns.label }}
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{% endif %}
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{% if ns.mane_select %}
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<span class='badge bg-dark'>MANE SELECT</span>
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{% endif %}
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{% if ns.mane_plus_clinical %}
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<span class='badge bg-dark'>MANE PLUS CLINICAL</span>
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{% endif %}
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{% if ns.validated %}
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<em class="fa fa-check text-success" aria-hidden="true" data-bs-toggle="tooltip" title="Verified by VariantValidator"></em>
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{% endif %}
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</p>
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</td>
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{% endfor %}
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</tr>
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{% endfor %}
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</table>
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{{hgvs_choices(variant_data.var_form.tx_hgvs)}}
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<br><br>
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<!-- dbSNP identifier -->
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{{variant_data.var_form.variations_ids.label(class="fw-bold, text-dark")}}
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<legend class="text-dark">Associated Conditions</legend>
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<h3 class="fs-subtitle">The condition for which the variant is interpreted. Examples available at <a href="https://www.ncbi.nlm.nih.gov/clinvar/docs/spreadsheet/#condition" target="_blank" rel="noopener">ClinVar</a></h3>
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<div class="col-6" id="clinvar_condition_container">
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{{variant_data.var_form.condition_type.label(class="fw-bold, text-dark")}}<span class="text-danger" data-bs-toggle='tooltip' title="Required field."><strong>*</strong></span>
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<select class="form-control, btn-secondary" name="condition_type" id="condition_type">
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{% for dbtype, _ in variant_data.var_form.condition_type.choices %}
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<option value="{{dbtype}}">{{dbtype}}</option>
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{% endfor %}
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</select>
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<br><br>
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{{variant_data.var_form.conditions.label(class="fw-bold, text-dark")}} <span class="text-danger" data-bs-toggle='tooltip' title="Required field. Include data from ONE DATABASE TYPE ONLY (i.e. only OMIM terms, only HPO terms etc). If multiple conditions are submitted for a variant, this indicates that the variant was interpreted for the combination of conditions in the same individual(s). i.e. this variant causes both condition A and condition B in the same individual. This scenario is most common for a new disease or syndrome that does not yet have a name and is described by several clinical features. If you want to indicate that the variant has been interpreted for more than one condition, please submit these as separate records."><strong>*?</strong></span>
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<select class="select2" id="condition_tags" name="conditions" multiple="true" style="width:100%;">
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{% if variant_data.var_form.omim_terms.choices %}
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{% for term, _ in variant_data.var_form.omim_terms.choices %}
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<option value="{{term}}" selected>{{term}}</option>
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{% endfor %}
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{% elif variant_data.var_form.orpha_terms.choices %}
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{% for term, _ in variant_data.var_form.orpha_terms.choices %}
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<option value="{{term}}" selected>{{term}}</option>
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{% endfor %}
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{% elif variant_data.var_form.hpo_terms.choices %}
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{% for term, _ in variant_data.var_form.hpo_terms.choices %}
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<option value="{{term}}" selected>{{term}}</option>
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{% endfor %}
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{% endif %}
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</select>
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<div class="mt-3">
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{{variant_data.var_form.multiple_condition_explanation.label(class="fw-bold, text-dark")}} <span class="text-danger" data-bs-toggle='tooltip' title="Required if you provide more than one condition ID."><strong>?</strong></span>
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<select name="multiple_condition_explanation" id="multiple_condition_explanation" class="form-control, btn-secondary">
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<option selected value>-</option>
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{% for choice, _ in variant_data.var_form.multiple_condition_explanation.choices %}
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<option value="{{choice}}">{{choice}}</option>
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{% endfor %}
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</select>
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</div>
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</div>
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<div class="col-6">
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{{ variant_data.var_form.omim_terms.label(class="fw-bold, text-dark" )}}<br>
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<ul class="list-group">
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{% for term in variant_data.var_form.omim_terms %}
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<li class="list-group-item">{{ term.label }}</li>
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{% else %}
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<span class="text-dark">N/A</span>
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{% endfor %}
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</ul>
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{{variant_data.var_form.orpha_terms.label(class="fw-bold, text-dark")}}<br>
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<ul class="list-group">
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{% for term in variant_data.var_form.orpha_terms %}
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<li class="list-group-item">{{ term.label }}</li>
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{% else %}
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<span class="text-dark">N/A</span>
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{% endfor %}
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</ul>
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{{variant_data.var_form.hpo_terms.label(class="fw-bold, text-dark")}}<br>
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{% for term in variant_data.var_form.hpo_terms %}
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<li class="list-group-item">{{ term.label }}</li>
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{% else %}
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N/A
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</ul>
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{% endfor %}
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</div>
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{{ condition_identifiers(variant_data.var_form) }}
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<input type="button" name="previous" class="previous action-button-previous" value="Previous"/>
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<input type="button" name="next" class="next action-button" value="Next"/>
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<legend class="text-dark">Observation Data</legend>
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<h3 class="fs-subtitle">Information provided by filling in these fields will be used to create the CaseData.csv file. Observations from at least one individuals are required.</h3>
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{% for cdata in variant_data.cdata_forms %}
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{{cdata.linking_id(class="fw-bold, text-dark")}} <!-- hidden field -->
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<div class="row">
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{{ cdata.include_ind.label(class="fw-bold, text-dark") }}
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{{ cdata.include_ind() }}
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</div>
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{{ cdata.individual_id.label(class="fw-bold, text-dark") }}
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{{ cdata.individual_id(class="form-control, bg-white", readonly=true) }}
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{{ cdata.affected_status.label(class="fw-bold, text-dark") }}
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{{ cdata.affected_status(class="form-control, btn-secondary") }}
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{{ cdata.allele_of_origin.label(class="fw-bold, text-dark") }}
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{{ cdata.collection_method.label(class="fw-bold, text-dark") }}
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{{ cdata.collection_method(class="form-control, btn-secondary") }}
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<input type="button" name="previous" class="previous action-button-previous" value="Previous"/>
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<input type="submit" name="submit" class="submit action-button" value="Add to submission"/>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery-easing/1.4.1/jquery.easing.min.js" integrity="sha512-0QbL0ph8Tc8g5bLhfVzSqxe9GERORsKhIn1IrpxDAgUsbBGz/V7iSav2zzW325XGd1OMLdL4UiqRJj702IeqnQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.14.0-beta3/js/bootstrap-select.min.js" integrity="sha512-yrOmjPdp8qH8hgLfWpSFhC/+R9Cj9USL8uJxYIveJZGAiedxyIxwNw4RsLDlcjNlIRR4kkHaDHSmNHAkxFTmgg==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
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<script src="https://cdn.jsdelivr.net/npm/select2@4.0.13/dist/js/select2.min.js" integrity="sha512-2ImtlRlf2VVmiGZsjm9bEyhjGW4dU7B6TNwh/hx/iSByxNENtj3WVE6o/9Lj4TJeVXPi4bnOIMXFIJJAeufa0A==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
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384
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// Enable tooltips
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var tooltipTriggerList = [].slice.call(document.querySelectorAll('[data-bs-toggle="tooltip"]'))
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var tooltipList = tooltipTriggerList.map(function (tooltipTriggerEl) {
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return new bootstrap.Tooltip(tooltipTriggerEl)
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388
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})
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389
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-
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390
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// Validates fields for conditions associated to a variant
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391
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function validateConditions(){
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392
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393
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if ($("#condition_tags option:selected").length == 0) {
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394
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alert("Please provide at least one condition ID");
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395
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return false;
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396
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}
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225
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{% include "clinvar/scripts.html" %}
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397
226
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398
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399
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alert("When multiple condition IDs are provided then an option for 'Explanation for multiple conditions' must be provided");
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400
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return false;
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401
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}
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402
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403
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if ($("#condition_tags option:selected").length == 1 && $("#multiple_condition_explanation option:selected").text() !== "-") {
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404
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alert("Please deselect the selected option in 'Explanation for multiple conditions' since only one condition ID was provided.");
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405
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return false;
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406
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}
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407
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-
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408
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// Make sure that provided conditions are numbers, except when condition type is MeSH or MedGen
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409
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var selectedConditionsValues = $('#condition_tags').val();
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410
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-
for (let i = 0; i < selectedConditionsValues.length; i++) {
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411
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if (isNaN(selectedConditionsValues[i]) && !['Mesh', 'MedGen'].includes($('#condition_type').val())){
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412
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-
alert(`Condition ID "${selectedConditionsValues[i]}" has an invalid format.`);
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413
|
-
return false;
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414
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-
}
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415
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-
}
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416
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417
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return true;
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418
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}
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419
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420
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var current_fs, next_fs, previous_fs; //fieldsets
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421
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var left, opacity, scale; //fieldset properties which we will animate
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422
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var animating; //flag to prevent quick multi-click glitches
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423
|
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424
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$(".next").click(function(){
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425
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if(animating) return false;
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426
|
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animating = true;
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427
|
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428
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current_fs = $(this).parent();
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429
|
-
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430
|
-
// run the validations on the input for the current step
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431
|
-
var validationPassed = true;
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432
|
-
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433
|
-
if(current_fs.data('step') == 6){
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434
|
-
validationPassed = validateConditions();
|
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435
|
-
}
|
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436
|
-
|
|
437
|
-
// check to see if the validator for the specific step we are on passed or not.
|
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438
|
-
if(validationPassed == false){
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439
|
-
// do not proceed
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440
|
-
animating = false;
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441
|
-
return;
|
|
442
|
-
}
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443
|
-
|
|
444
|
-
next_fs = $(this).parent().next();
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445
|
-
|
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446
|
-
//activate next step on progressbar using the index of next_fs
|
|
447
|
-
$("#progressbar li").eq($("fieldset").index(next_fs)).addClass("active");
|
|
448
|
-
|
|
449
|
-
//show the next fieldset
|
|
450
|
-
next_fs.show();
|
|
451
|
-
//hide the current fieldset with style
|
|
452
|
-
current_fs.animate({opacity: 0}, {
|
|
453
|
-
step: function(now, mx) {
|
|
454
|
-
//as the opacity of current_fs reduces to 0 - stored in "now"
|
|
455
|
-
//1. scale current_fs down to 80%
|
|
456
|
-
scale = 1 - (1 - now) * 0.2;
|
|
457
|
-
//2. bring next_fs from the right(50%)
|
|
458
|
-
left = (now * 50)+"%";
|
|
459
|
-
//3. increase opacity of next_fs to 1 as it moves in
|
|
460
|
-
opacity = 1 - now;
|
|
461
|
-
current_fs.css({
|
|
462
|
-
'transform': 'scale('+scale+')',
|
|
463
|
-
'position': 'absolute'
|
|
464
|
-
});
|
|
465
|
-
next_fs.css({'left': left, 'opacity': opacity});
|
|
466
|
-
},
|
|
467
|
-
duration: 800,
|
|
468
|
-
complete: function(){
|
|
469
|
-
current_fs.hide();
|
|
470
|
-
animating = false;
|
|
471
|
-
},
|
|
472
|
-
//this comes from the custom easing plugin
|
|
473
|
-
easing: 'easeInOutBack'
|
|
474
|
-
});
|
|
475
|
-
});
|
|
476
|
-
|
|
477
|
-
$(".previous").click(function(){
|
|
478
|
-
if(animating) return false;
|
|
479
|
-
animating = true;
|
|
480
|
-
|
|
481
|
-
current_fs = $(this).parent();
|
|
482
|
-
previous_fs = $(this).parent().prev();
|
|
483
|
-
|
|
484
|
-
//de-activate current step on progressbar
|
|
485
|
-
$("#progressbar li").eq($("fieldset").index(current_fs)).removeClass("active");
|
|
486
|
-
|
|
487
|
-
//show the previous fieldset
|
|
488
|
-
previous_fs.show();
|
|
489
|
-
//hide the current fieldset with style
|
|
490
|
-
current_fs.animate({opacity: 0}, {
|
|
491
|
-
step: function(now, mx) {
|
|
492
|
-
//as the opacity of current_fs reduces to 0 - stored in "now"
|
|
493
|
-
//1. scale previous_fs from 80% to 100%
|
|
494
|
-
scale = 0.8 + (1 - now) * 0.2;
|
|
495
|
-
//2. take current_fs to the right(50%) - from 0%
|
|
496
|
-
left = ((1-now) * 50)+"%";
|
|
497
|
-
//3. increase opacity of previous_fs to 1 as it moves in
|
|
498
|
-
opacity = 1 - now;
|
|
499
|
-
current_fs.css({'left': left});
|
|
500
|
-
previous_fs.css({'transform': 'scale('+scale+')', 'opacity': opacity});
|
|
501
|
-
},
|
|
502
|
-
duration: 800,
|
|
503
|
-
complete: function(){
|
|
504
|
-
current_fs.hide();
|
|
505
|
-
animating = false;
|
|
506
|
-
},
|
|
507
|
-
//this comes from the custom easing plugin
|
|
508
|
-
easing: 'easeInOutBack'
|
|
509
|
-
});
|
|
510
|
-
});
|
|
227
|
+
<script>
|
|
511
228
|
|
|
512
229
|
//Function definition for keeping the tooltip updated for each Assertion method database option
|
|
513
230
|
function updateTooltip(){
|
|
@@ -542,62 +259,6 @@ $(function () {
|
|
|
542
259
|
})
|
|
543
260
|
});
|
|
544
261
|
|
|
545
|
-
|
|
546
|
-
var conditionsPlaceHolders = {"OMIM": "e.g. 100800, ..", "HPO": "e.g. 0002839, ..", "MedGen": "e.g. C0001080, ..", "MeSh": "e.g. D000130, ..", "MONDO": "e.g. 0007947, ..", "Orphanet": "e.g. 155, .."};
|
|
547
|
-
|
|
548
|
-
// Populate condition list
|
|
549
|
-
$('#condition_tags').select2({
|
|
550
|
-
tags: true,
|
|
551
|
-
theme: 'bootstrap-5',
|
|
552
|
-
tokenSeparators: [','],
|
|
553
|
-
allowClear: true,
|
|
554
|
-
});
|
|
555
|
-
|
|
556
|
-
// Set selected condition type on page load
|
|
557
|
-
window.onload = function() {
|
|
558
|
-
const selectedCondId = document.getElementById('condition_type');
|
|
559
|
-
{% if variant_data.var_form.omim_terms.choices %}
|
|
560
|
-
selectedCondId.options.selectedIndex = 4;
|
|
561
|
-
{% elif variant_data.var_form.orpha_terms.choices %}
|
|
562
|
-
selectedCondId.options.selectedIndex = 5;
|
|
563
|
-
{% elif variant_data.var_form.hpo_terms.choices %}
|
|
564
|
-
selectedCondId.options.selectedIndex = 0;
|
|
565
|
-
{% endif %}
|
|
566
|
-
};
|
|
567
|
-
|
|
568
|
-
// reset and modify conditions field's placeholder when condition ID type changes
|
|
569
|
-
$(function(){
|
|
570
|
-
$("#condition_type").change(function(){
|
|
571
|
-
$('#condition_tags')[0].options.length = 0; // reset conditions multiselect
|
|
572
|
-
|
|
573
|
-
// Change placeholder
|
|
574
|
-
selectedCondId = $("#condition_type option:selected").text();
|
|
575
|
-
$('#condition_tags').select2({
|
|
576
|
-
placeholder: conditionsPlaceHolders[selectedCondId],
|
|
577
|
-
theme: 'bootstrap-5',
|
|
578
|
-
tags: true,
|
|
579
|
-
tokenSeparators: [','],
|
|
580
|
-
allowClear: true,
|
|
581
|
-
});
|
|
582
|
-
|
|
583
|
-
// repopulate option values according to the selected condition ID
|
|
584
|
-
choices = {};
|
|
585
|
-
if ($('#condition_type').val() == 'OMIM'){
|
|
586
|
-
choices = {{ variant_data.var_form.omim_terms.choices|tuple_list_to_dict(0,1)|safe}};
|
|
587
|
-
}
|
|
588
|
-
if ($('#condition_type').val() == 'Orphanet'){
|
|
589
|
-
choices = {{ variant_data.var_form.orpha_terms.choices|tuple_list_to_dict(0,1)|safe }};
|
|
590
|
-
}
|
|
591
|
-
if ($('#condition_type').val() == 'HPO'){
|
|
592
|
-
choices = {{ variant_data.var_form.hpo_terms.choices|tuple_list_to_dict(0,1)|safe }};
|
|
593
|
-
}
|
|
594
|
-
for (var key in choices) {
|
|
595
|
-
var newOption = new Option(key, key, true, true);
|
|
596
|
-
$('#condition_tags').append(newOption).trigger('change');
|
|
597
|
-
}
|
|
598
|
-
});
|
|
599
|
-
});
|
|
600
|
-
|
|
601
262
|
// Modify variant classification options based on selected assertion_method_cit (ACMG-based or not)
|
|
602
263
|
$(function(){
|
|
603
264
|
$("#assertion_method_cit_db, #assertion_method_cit_id").change(function(){
|
|
@@ -0,0 +1,193 @@
|
|
|
1
|
+
<script>
|
|
2
|
+
|
|
3
|
+
// Enable tooltips
|
|
4
|
+
var tooltipTriggerList = [].slice.call(document.querySelectorAll('[data-bs-toggle="tooltip"]'))
|
|
5
|
+
var tooltipList = tooltipTriggerList.map(function (tooltipTriggerEl) {
|
|
6
|
+
return new bootstrap.Tooltip(tooltipTriggerEl)
|
|
7
|
+
})
|
|
8
|
+
|
|
9
|
+
var current_fs, next_fs, previous_fs; //fieldsets
|
|
10
|
+
var left, opacity, scale; //fieldset properties which we will animate
|
|
11
|
+
var animating; //flag to prevent quick multi-click glitches
|
|
12
|
+
|
|
13
|
+
$(".next").click(function(){
|
|
14
|
+
if(animating) return false;
|
|
15
|
+
animating = true;
|
|
16
|
+
|
|
17
|
+
current_fs = $(this).parent();
|
|
18
|
+
|
|
19
|
+
// run the validations on the input for the current step
|
|
20
|
+
var validationPassed = true;
|
|
21
|
+
|
|
22
|
+
{% if variant_data.var_obj.category == "snv" %}
|
|
23
|
+
if(current_fs.data('step') == 6){
|
|
24
|
+
validationPassed = validateConditions();
|
|
25
|
+
}
|
|
26
|
+
{% elif variant_data.var_obj.category == "cancer" %}
|
|
27
|
+
if(current_fs.data('step') == 4){
|
|
28
|
+
validationPassed = validateConditions();
|
|
29
|
+
}
|
|
30
|
+
{% endif %}
|
|
31
|
+
|
|
32
|
+
// check to see if the validator for the specific step we are on passed or not.
|
|
33
|
+
if(validationPassed == false){
|
|
34
|
+
// do not proceed
|
|
35
|
+
animating = false;
|
|
36
|
+
return;
|
|
37
|
+
}
|
|
38
|
+
|
|
39
|
+
next_fs = $(this).parent().next();
|
|
40
|
+
|
|
41
|
+
//activate next step on progressbar using the index of next_fs
|
|
42
|
+
$("#progressbar li").eq($("fieldset").index(next_fs)).addClass("active");
|
|
43
|
+
|
|
44
|
+
//show the next fieldset
|
|
45
|
+
next_fs.show();
|
|
46
|
+
//hide the current fieldset with style
|
|
47
|
+
current_fs.animate({opacity: 0}, {
|
|
48
|
+
step: function(now, mx) {
|
|
49
|
+
//as the opacity of current_fs reduces to 0 - stored in "now"
|
|
50
|
+
//1. scale current_fs down to 80%
|
|
51
|
+
scale = 1 - (1 - now) * 0.2;
|
|
52
|
+
//2. bring next_fs from the right(50%)
|
|
53
|
+
left = (now * 50)+"%";
|
|
54
|
+
//3. increase opacity of next_fs to 1 as it moves in
|
|
55
|
+
opacity = 1 - now;
|
|
56
|
+
current_fs.css({
|
|
57
|
+
'transform': 'scale('+scale+')',
|
|
58
|
+
'position': 'absolute'
|
|
59
|
+
});
|
|
60
|
+
next_fs.css({'left': left, 'opacity': opacity});
|
|
61
|
+
},
|
|
62
|
+
duration: 800,
|
|
63
|
+
complete: function(){
|
|
64
|
+
current_fs.hide();
|
|
65
|
+
animating = false;
|
|
66
|
+
},
|
|
67
|
+
//this comes from the custom easing plugin
|
|
68
|
+
easing: 'easeInOutBack'
|
|
69
|
+
});
|
|
70
|
+
});
|
|
71
|
+
|
|
72
|
+
$(".previous").click(function(){
|
|
73
|
+
if(animating) return false;
|
|
74
|
+
animating = true;
|
|
75
|
+
|
|
76
|
+
current_fs = $(this).parent();
|
|
77
|
+
previous_fs = $(this).parent().prev();
|
|
78
|
+
|
|
79
|
+
//de-activate current step on progressbar
|
|
80
|
+
$("#progressbar li").eq($("fieldset").index(current_fs)).removeClass("active");
|
|
81
|
+
|
|
82
|
+
//show the previous fieldset
|
|
83
|
+
previous_fs.show();
|
|
84
|
+
//hide the current fieldset with style
|
|
85
|
+
current_fs.animate({opacity: 0}, {
|
|
86
|
+
step: function(now, mx) {
|
|
87
|
+
//as the opacity of current_fs reduces to 0 - stored in "now"
|
|
88
|
+
//1. scale previous_fs from 80% to 100%
|
|
89
|
+
scale = 0.8 + (1 - now) * 0.2;
|
|
90
|
+
//2. take current_fs to the right(50%) - from 0%
|
|
91
|
+
left = ((1-now) * 50)+"%";
|
|
92
|
+
//3. increase opacity of previous_fs to 1 as it moves in
|
|
93
|
+
opacity = 1 - now;
|
|
94
|
+
current_fs.css({'left': left});
|
|
95
|
+
previous_fs.css({'transform': 'scale('+scale+')', 'opacity': opacity});
|
|
96
|
+
},
|
|
97
|
+
duration: 800,
|
|
98
|
+
complete: function(){
|
|
99
|
+
current_fs.hide();
|
|
100
|
+
animating = false;
|
|
101
|
+
},
|
|
102
|
+
//this comes from the custom easing plugin
|
|
103
|
+
easing: 'easeInOutBack'
|
|
104
|
+
});
|
|
105
|
+
});
|
|
106
|
+
|
|
107
|
+
// Conditions-asociated code
|
|
108
|
+
|
|
109
|
+
var conditionsPlaceHolders = {"OMIM": "e.g. 100800, ..", "HPO": "e.g. 0002839, ..", "HP": "e.g. 0002839, .." , "MedGen": "e.g. C0001080, ..", "MeSh": "e.g. D000130, ..", "MONDO": "e.g. 0007947, ..", "Orphanet": "e.g. 155, .."};
|
|
110
|
+
|
|
111
|
+
// Set selected condition type on page load
|
|
112
|
+
window.onload = function() {
|
|
113
|
+
const selectedCondId = document.getElementById('condition_type');
|
|
114
|
+
{% if variant_data.var_form.omim_terms.choices %}
|
|
115
|
+
selectedCondId.options.selectedIndex = 4;
|
|
116
|
+
{% elif variant_data.var_form.orpha_terms.choices %}
|
|
117
|
+
selectedCondId.options.selectedIndex = 5;
|
|
118
|
+
{% elif variant_data.var_form.hpo_terms.choices %}
|
|
119
|
+
selectedCondId.options.selectedIndex = 0;
|
|
120
|
+
{% endif %}
|
|
121
|
+
};
|
|
122
|
+
|
|
123
|
+
// Populate condition list
|
|
124
|
+
$('#condition_tags').select2({
|
|
125
|
+
tags: true,
|
|
126
|
+
theme: 'bootstrap-5',
|
|
127
|
+
tokenSeparators: [','],
|
|
128
|
+
allowClear: true,
|
|
129
|
+
});
|
|
130
|
+
|
|
131
|
+
// reset and modify conditions field's placeholder when condition ID type changes
|
|
132
|
+
$(function(){
|
|
133
|
+
$("#condition_type").change(function(){
|
|
134
|
+
$('#condition_tags')[0].options.length = 0; // reset conditions multiselect
|
|
135
|
+
|
|
136
|
+
// Change placeholder
|
|
137
|
+
selectedCondId = $("#condition_type option:selected").text();
|
|
138
|
+
$('#condition_tags').select2({
|
|
139
|
+
placeholder: conditionsPlaceHolders[selectedCondId],
|
|
140
|
+
theme: 'bootstrap-5',
|
|
141
|
+
tags: true,
|
|
142
|
+
tokenSeparators: [','],
|
|
143
|
+
allowClear: true,
|
|
144
|
+
});
|
|
145
|
+
|
|
146
|
+
// repopulate option values according to the selected condition ID
|
|
147
|
+
choices = {};
|
|
148
|
+
if ($('#condition_type').val() == 'OMIM'){
|
|
149
|
+
choices = {{ variant_data.var_form.omim_terms.choices|tuple_list_to_dict(0,1)|safe}};
|
|
150
|
+
}
|
|
151
|
+
if ($('#condition_type').val() == 'Orphanet'){
|
|
152
|
+
choices = {{ variant_data.var_form.orpha_terms.choices|tuple_list_to_dict(0,1)|safe }};
|
|
153
|
+
}
|
|
154
|
+
if ($('#condition_type').val() == 'HPO' || $('#condition_type').val() == 'HP'){
|
|
155
|
+
choices = {{ variant_data.var_form.hpo_terms.choices|tuple_list_to_dict(0,1)|safe }};
|
|
156
|
+
}
|
|
157
|
+
for (var key in choices) {
|
|
158
|
+
var newOption = new Option(key, key, true, true);
|
|
159
|
+
$('#condition_tags').append(newOption).trigger('change');
|
|
160
|
+
}
|
|
161
|
+
});
|
|
162
|
+
});
|
|
163
|
+
|
|
164
|
+
// Validates fields for conditions associated to a variant
|
|
165
|
+
function validateConditions(){
|
|
166
|
+
|
|
167
|
+
if ($("#condition_tags option:selected").length == 0) {
|
|
168
|
+
alert("Please provide at least one condition ID");
|
|
169
|
+
return false;
|
|
170
|
+
}
|
|
171
|
+
|
|
172
|
+
if ($("#condition_tags option:selected").length > 1 && $("#multiple_condition_explanation option:selected").text() === "-") {
|
|
173
|
+
alert("When multiple condition IDs are provided then an option for 'Explanation for multiple conditions' must be provided");
|
|
174
|
+
return false;
|
|
175
|
+
}
|
|
176
|
+
|
|
177
|
+
if ($("#condition_tags option:selected").length == 1 && $("#multiple_condition_explanation option:selected").text() !== "-") {
|
|
178
|
+
alert("Please deselect the selected option in 'Explanation for multiple conditions' since only one condition ID was provided.");
|
|
179
|
+
return false;
|
|
180
|
+
}
|
|
181
|
+
|
|
182
|
+
// Make sure that provided conditions are numbers, except when condition type is MeSH or MedGen
|
|
183
|
+
var selectedConditionsValues = $('#condition_tags').val();
|
|
184
|
+
for (let i = 0; i < selectedConditionsValues.length; i++) {
|
|
185
|
+
if (isNaN(selectedConditionsValues[i]) && !['Mesh', 'MedGen'].includes($('#condition_type').val())){
|
|
186
|
+
alert(`Condition ID "${selectedConditionsValues[i]}" has an invalid format.`);
|
|
187
|
+
return false;
|
|
188
|
+
}
|
|
189
|
+
}
|
|
190
|
+
|
|
191
|
+
return true;
|
|
192
|
+
}
|
|
193
|
+
</script>
|