scout-browser 4.100.2__py3-none-any.whl → 4.101.0__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 +20 -6
- scout/constants/file_types.py +1 -1
- scout/server/blueprints/cases/templates/cases/utils.html +1 -1
- scout/server/blueprints/clinvar/controllers.py +15 -21
- scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html +0 -2
- scout/server/blueprints/institutes/templates/overview/cases.html +7 -6
- scout/server/blueprints/panels/views.py +11 -2
- scout/server/blueprints/variants/templates/variants/cancer-variants.html +3 -3
- scout/server/blueprints/variants/templates/variants/indicators.html +18 -15
- scout/server/blueprints/variants/templates/variants/utils.html +1 -1
- {scout_browser-4.100.2.dist-info → scout_browser-4.101.0.dist-info}/METADATA +1 -1
- {scout_browser-4.100.2.dist-info → scout_browser-4.101.0.dist-info}/RECORD +15 -15
- {scout_browser-4.100.2.dist-info → scout_browser-4.101.0.dist-info}/WHEEL +0 -0
- {scout_browser-4.100.2.dist-info → scout_browser-4.101.0.dist-info}/entry_points.txt +0 -0
- {scout_browser-4.100.2.dist-info → scout_browser-4.101.0.dist-info}/licenses/LICENSE +0 -0
scout/adapter/mongo/case.py
CHANGED
@@ -6,7 +6,7 @@ import operator
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import re
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from collections import OrderedDict
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from copy import deepcopy
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from typing import Any, Dict, List, Optional
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from typing import Any, Dict, List, Optional, Tuple
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import pymongo
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from bson import ObjectId
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@@ -928,21 +928,35 @@ class CaseHandler(object):
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self.load_omics_variants(case_obj=case_obj, build=build, file_type=omics_file)
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def
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"""
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def get_load_type_categories(self, case_obj: dict) -> List[Tuple[str, str]]:
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"""Return an (ordered) list of tuples pairing variant type and category for loading.
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It is important for predictable variant collisions to retain the order specified in
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the file type map CLINICAL_ORDERED_FILE_TYPE_MAP. Hence the set operation is made in parallel
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with the list construction."""
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CLINICAL_ORDERED_FILE_TYPE_MAP = OrderedDict(
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(key, value)
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for key, value in ORDERED_FILE_TYPE_MAP.items()
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if value["variant_type"] != "research"
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)
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load_type_cat = []
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cat_seen = set()
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for file_name, vcf_dict in CLINICAL_ORDERED_FILE_TYPE_MAP.items():
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if not case_obj["vcf_files"].get(file_name):
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LOG.debug("didn't find {}, skipping".format(file_name))
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continue
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pair = (vcf_dict["variant_type"], vcf_dict["category"])
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if pair not in cat_seen:
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cat_seen.add(pair)
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load_type_cat.append(pair)
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return load_type_cat
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def _load_clinical_variants(self, case_obj: dict, build: str, update: bool = False):
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"""Load variants in the order specified by CLINICAL_ORDERED_FILE_TYPE_MAP."""
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for variant_type, category in
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for variant_type, category in self.get_load_type_categories(case_obj):
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if update:
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self.delete_variants(
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case_id=case_obj["_id"],
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scout/constants/file_types.py
CHANGED
@@ -1,6 +1,6 @@
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from collections import OrderedDict
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# Variants in Scout will be
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# Variants in Scout will be loaded for a case in the same order as these ordered dictionaries
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ORDERED_FILE_TYPE_MAP = OrderedDict(
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[
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("vcf_cancer", {"category": "cancer", "variant_type": "clinical"}),
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@@ -627,7 +627,7 @@
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(included in ClinVar submission)
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{% elif variant.category in ('cancer', 'cancer_sv') %}
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<button data-bs-toggle='tooltip' data-bs-placement="bottom" title="Submission of somatic variants from Scout is temporarily suspended. We are working to harmonize submissions with changes introduced by ClinVar for this variant category." disabled >Add to ClinVar submission</button>
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{%
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{% elif variant.category in ('snv', 'sv') %}
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<button type="submit" name="var_id" value="{{variant._id}}" class="btn btn-secondary btn-sm" style="float: right;">Add to ClinVar submission</button>
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{% endif %}
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</form>
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@@ -40,33 +40,27 @@ def _get_var_tx_hgvs(case_obj: dict, variant_obj: dict) -> List[Tuple[str, str]]
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transcripts = gene.get("transcripts", [])
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for tx in transcripts:
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-
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refseq_id = tx.get("refseq_id")
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coding_seq_name = tx.get("coding_sequence_name")
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if not (refseq_id and coding_seq_name):
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continue # Skip transcripts missing required fields
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)
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label = f"{hgvs_simple}{'_validated_' if validated else ''}{'_mane-select_' if refseq_is_mane_select else ''}{'_mane-plus-clinical_' if refseq_is_mane_plus_clinical else ''}"
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if case_has_build_37:
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for refseq in tx.get("refseq_identifiers", []):
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refseq_version = fetch_refseq_version(refseq)
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hgvs_simple = f"{refseq_version}:{coding_seq_name}"
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validated = validate_hgvs(build, hgvs_simple)
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label = f"{hgvs_simple}{'_validated_' if validated else ''}"
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tx_hgvs_list.append((hgvs_simple, label))
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else: # build 38, collect only MANE Select or MANE Plus Clinical
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mane_select = tx.get("mane_select_transcript")
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mane_plus_clinical = tx.get("mane_plus_clinical_transcript")
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if mane_select is None and mane_plus_clinical is None:
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continue
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hgvs_simple = f"{mane_select or mane_plus_clinical}:{coding_seq_name}"
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label = f"{hgvs_simple}{'_mane-select_' if mane_select else ''}{'_mane-plus-clinical_' if mane_plus_clinical else ''}"
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tx_hgvs_list.append((hgvs_simple, label))
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return tx_hgvs_list
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@@ -154,8 +154,6 @@
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{% endfor %}
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</table>
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<span class="text-danger">HGVS validation is performed only for variants in build GRCh37 or MANE Select and MANE Plus Clinical transcripts. For any other available HGVS present in this list, manual validation can be performed using the VariantValidator link above.</span>
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-
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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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<span class="badge bg-primary">migrated</span>
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{% endif %}
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</td>
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<td
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{{ case.analysis_date.date() }}
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<td>
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<div class="d-flex align-items-center justify-content-between">{{ case.analysis_date.date() }}
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{% if case.rerun_requested %}
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<span class="badge bg-secondary">rerun pending</span>
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{% elif case.is_rerun %}
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<span class="badge bg-secondary">rerun</span>
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{% endif %}
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</div>
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</td>
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<td>
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{% if case.is_research %}
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import json
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import logging
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from flask import
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from flask import (
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Blueprint,
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Response,
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flash,
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redirect,
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render_template,
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request,
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send_file,
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url_for,
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)
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from flask_login import current_user
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from markupsafe import escape
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panel_groups.append((institute_obj, institute_panels))
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return dict(
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panel_groups=panel_groups,
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panel_groups=sorted(panel_groups, key=lambda x: x[0]["_id"]),
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panel_names=panel_names,
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panel_versions=panel_versions,
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institutes=institutes,
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{% from "variants/components.html" import allele_cell, external_scripts, external_stylesheets, gene_cell, frequency_cell_general, observed_cell_general, variant_funct_anno_cell %}
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{% from "variants/utils.html" import cancer_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell %}
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{% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge,
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{% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, group_assessments_badge, matching_manual_rank, other_tiered_variants, research_assessments_badge %}
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{% block title %}
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{{ variant_type|capitalize }} somatic variants
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</a>
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</td>
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<td>
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{{ evaluations_badge(variant) }}
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{{ evaluations_badge(variant.evaluations) }}
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{{ dismissals_badge(variant) }}
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{{ matching_manual_rank(variant) }}
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{{ research_assessments_badge(variant) }}
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{{ comments_badge(case, institute, variant) }}
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{{ causative_badge(variant, case) }}
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{{ other_tiered_variants(variant) }}
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{{
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{{ evaluations_badge(variant.ccv_evaluations) }}
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</td>
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<td>{{ rank_cell(variant) }}</td>
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<td>{{ cadd_cell(variant) }}</td>
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{% endif %}
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{% endmacro %}
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{% macro evaluations_badge(
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{% if
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{% macro evaluations_badge(evaluations) %}
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{% if evaluations %}
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{% set classification_counts = {} %}
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{% for evaluation in evaluations %}
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{% set c = evaluation.classification if evaluation.classification is defined else evaluation.ccv_classification %}
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{% if c %}
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{% set short = c.short %}
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{% set label = c.label %}
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{% set current = classification_counts.get(short, {'count': 0, 'label': label}) %}
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{% set _ = classification_counts.update({short: {
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'count': current.count + 1,
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'label': label
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}}) %}
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{% endif %}
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{% endfor %}
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{% endif %}
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{% endmacro %}
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{%
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title="Previously classified as {{ evaluation.ccv_classification.label }}">
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{{ evaluation.ccv_classification.short }}
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{% for short, data in classification_counts.items() | sort(attribute='1.count', reverse=true) %}
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<span class="badge bg-secondary ms-1" data-bs-toggle="tooltip" data-bs-placement="right"
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title="Previously classified as {{ data.label }} ({{ data.count }} times)">
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{{ short }} ×{{ data.count }}
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</span>
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{% endfor %}
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{% endif %}
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{{ variant.variant_rank }}</a>
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{{ evaluations_badge(variant) }}
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{{ evaluations_badge(variant.evaluations) }}
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{{ research_assessments_badge(variant) }}
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{{ clinical_assessments_badge(variant) }}
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{{ group_assessments_badge(variant) }}
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Metadata-Version: 2.4
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Name: scout-browser
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Version: 4.
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Version: 4.101.0
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Summary: Clinical DNA variant visualizer and browser
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Project-URL: Repository, https://github.com/Clinical-Genomics/scout
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Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md
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scout/adapter/mongo/__init__.py,sha256=NdHYCUXWUAuX5cUS3-6HCws2hW9uoGep8i0SC-oJd3k,31
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scout/adapter/mongo/acmg.py,sha256=v2Zuw-6APVmcnBnNXa18WJEu2vj5GUhZNiKMkruJsBI,4170
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scout/adapter/mongo/base.py,sha256=iIa2AjGNztKHcZzolY0T6r7Oh0guj6R1putztp4OTNY,4427
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scout/adapter/mongo/case.py,sha256=
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scout/adapter/mongo/case.py,sha256=Cqb_uWbW5gnAoOMoJVK9LYeCrJEE-M3fgI97-3t6gbc,66613
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scout/adapter/mongo/case_events.py,sha256=slHR4XJF9vRuEbuInJKMMAImLF8m7tHWVfGP42fbXr0,26859
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scout/adapter/mongo/case_group.py,sha256=tG8DuO0rNYepV4k0yCGPqssODErc0HMsAypg3mfhcV0,1575
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scout/adapter/mongo/ccv.py,sha256=VIz-Yqzm-1UVPDKvZkBllO4BOKXzvKCXcQUjTtZCHTI,4165
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scout/constants/clinvar.py,sha256=nr7KhwMIO_7taNQokRJlpgZfenMlKsdPIMpdOx3TwKY,5594
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scout/constants/clnsig.py,sha256=anWIOuj_qLcDl4UsRQ50W6qlv7UaHTUbSdHOkAzL0No,1594
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scout/constants/disease_parsing.py,sha256=M9_OgsN88oXwKH_XpxdDma0zuWPRoHFQjL19tzojBPo,686
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scout/constants/file_types.py,sha256=
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scout/constants/file_types.py,sha256=3N3TReXVkhxbpvYupsENVFAHEGQyZ1S7efP7wZEqs44,2890
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scout/constants/filters.py,sha256=ZgVGt6No5D7PiN1o1wWDm3E5SCRk7YLya87_4QtIMPs,979
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scout/constants/gene_tags.py,sha256=yBrMu9qXyYaQ13l3XMakooyd2ZtPXm1XgpSSH_bC-5U,4513
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scout/constants/igv_tracks.py,sha256=584SdO6qJHAcfCxHJQaM4YAnzu4M_uviJIUg6gt_jok,4675
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scout/server/blueprints/cases/templates/cases/institutes_sidebar.html,sha256=u0oPGHJ0ipZ1LkjHkbwlWfkUWc1h6XH1nh3tkbX17z0,4546
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scout/server/blueprints/cases/templates/cases/matchmaker.html,sha256=kPYnmcZJ1gmx_guW52H7baT9Sw4WE0VJmLGF6N7Z3iA,13639
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scout/server/blueprints/cases/templates/cases/phenotype.html,sha256=7vz5XPUExD6vc-wdijLKnPzaOFm9mQxOZ_ITAL3y7U8,16420
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scout/server/blueprints/cases/templates/cases/utils.html,sha256=
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scout/server/blueprints/cases/templates/cases/utils.html,sha256=Jpt5uwH7IHisdd1DvxjGodFaZ9e1g3JlANpkkQ3P6kA,36973
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scout/server/blueprints/clinvar/__init__.py,sha256=BV3aH2AbiA2WWrUEMbGd0H9MefFd2eTsRE9ShywbzpI,30
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scout/server/blueprints/clinvar/controllers.py,sha256=
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scout/server/blueprints/clinvar/controllers.py,sha256=cqThe0iM7ltT_uF3S0bj6642DrOW5OJiWAUM-w5lShk,24972
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scout/server/blueprints/clinvar/form.py,sha256=2h42YJzaOtsdEglxqt7F1i2ncjSU_IHNt-m4QOJytK4,5148
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scout/server/blueprints/clinvar/static/form_style.css,sha256=Tro2w0Su9st2ZRpt8PjF7qXYet-0n6Eyol4oh94JafU,4073
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scout/server/blueprints/clinvar/templates/clinvar/clinvar_howto.html,sha256=phFsRl6Hv94sy4GueBN0MXYbQsW6qmR1NoH-3Iwt2zs,4852
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scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html,sha256=XvS6WR7xPy3KNB9q9sWzAsXf2QAjkxGeMaJlx6BkeVE,18694
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scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html,sha256=
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scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html,sha256=ilDxkFUUDMy6Qzcby2BKJ21zmpI1HYI1ZC4HmrGYLpk,32953
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scout/server/blueprints/dashboard/__init__.py,sha256=9YTjGeFexyEbl4P-gs7j8VEjyhnVwHZFfz57eTtod1M,69
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scout/server/blueprints/dashboard/controllers.py,sha256=x6EWKROskF4iyZ5_hAgL7CWp1X3CXHp-7v0JVsDHKZU,9612
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scout/server/blueprints/dashboard/forms.py,sha256=vbdkujKZxVjiZw2inNhysN3yYMPCdMPbqvKV88DamwI,501
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scout/server/blueprints/institutes/static/select2_darktheme.css,sha256=Nq_va597W_e5y-52B4ClwSJzACq0WFbPU8SIp3DtKIo,1818
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scout/server/blueprints/institutes/static/timeline_styles.css,sha256=Vq48ffIidpQmDQhAzfW47O9mGQZEWdlbMtOE8AK-ZEU,2122
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scout/server/blueprints/institutes/static/variants_list_scripts.js,sha256=R4rqoCXzVs9RLqXLK851n0mFgN4xytHxSCaRm0egk5M,377
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scout/server/blueprints/institutes/templates/overview/cases.html,sha256=
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scout/server/blueprints/institutes/templates/overview/cases.html,sha256=R6pzv4EVqe6x69tP94ROITy_I-zi96ITCblMRjtUs70,12926
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scout/server/blueprints/institutes/templates/overview/causatives.html,sha256=192pgqUSXQF4qhC933qsYtTwvmlqDctxwHcArERkHc8,1619
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scout/server/blueprints/institutes/templates/overview/filters.html,sha256=SXvimbFNKfhoh8lpSfnMCTLMb4QghZRxT6W5PteGj68,3519
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scout/server/blueprints/institutes/templates/overview/gene_variants.html,sha256=EyhBZEdMZQBaJWR_FDeabuWXRSd4Xcqh0teaxVyNvAE,8442
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scout/server/blueprints/panels/__init__.py,sha256=usxBF0O7zNX1d9jt-8DRoFZwcfHHS96Gv87LDr1AgG4,53
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scout/server/blueprints/panels/controllers.py,sha256=_LXiayDyGcyRQ3Hw13fD8zVYFQ1jIIXUMQ49WsimrZ8,12618
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scout/server/blueprints/panels/forms.py,sha256=DYlhYpnpv7ehf9JlY3HRFwy-TZ5QDHB0RIRaNTAW1jQ,696
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scout/server/blueprints/panels/views.py,sha256=DUnrUWIIxqe6bOpSN1G_6dSysPpIRGq3jJDSF4FfKkA,15844
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scout/server/blueprints/panels/templates/panels/gene-edit.html,sha256=KqdUdu93707upLxh31Bwxgd1w4kH-WHtVilSNmAqiRo,3627
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scout/server/blueprints/panels/templates/panels/panel.html,sha256=t7OE23uwlSyE4puT0OFWm9xPirnVvSsuIQ23E0MLbI0,17113
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scout/server/blueprints/panels/templates/panels/panel_pdf_case_hits.html,sha256=uzfZJiMNQiTa_6u4uMuIbK3VXIs-8Rw-MjKujFttZG8,3438
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scout/server/blueprints/variants/views.py,sha256=0HI1SsL6gMP2-XSxq232cw6ECT13LVpdfxkI6QyRthk,28642
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scout/server/blueprints/variants/static/form_scripts.js,sha256=o3GCboaesA9Sm1HgejS_yQwt0I-NTkvcl56jiBdLqZs,8319
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scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html,sha256=QlGmUEdUQ7gCq7tMMUFAlGqqC9jFB78Q0h6tSp3QUas,7271
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scout/server/blueprints/variants/templates/variants/cancer-variants.html,sha256=
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scout/server/blueprints/variants/templates/variants/cancer-variants.html,sha256=iEL4InO43JGwZP0QDC5VA-4LcZtIadm8d1FFI8mFb-M,9689
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scout/server/blueprints/variants/templates/variants/components.html,sha256=Oa3MU0DokDDeTx8eD_EQXop5UmjTFHv7SdZUlpCBl04,19150
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scout/server/blueprints/variants/templates/variants/fusion-variants.html,sha256=XGaLgWobzeFHwyQLXr_Yq9THssf8tGU91VbFKdGOFBg,4801
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scout/server/blueprints/variants/templates/variants/indicators.html,sha256=
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scout/server/blueprints/variants/templates/variants/indicators.html,sha256=5IPiNgEB_JmYpvD6_Mpx9wd1gmKpsVnTm-HKfuBsKXg,5081
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scout/server/blueprints/variants/templates/variants/mei-variants.html,sha256=E5nkN7I5PtfizYKf3wuhm0xLf4rdgvDmC6EI2x1WQZA,6093
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scout/server/blueprints/variants/templates/variants/str-variants.html,sha256=n424D8xV76bCKDSFzzIsWfFAoU2dAYE-PPZyTtQeMdM,10924
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scout/server/blueprints/variants/templates/variants/sv-variants.html,sha256=-0eLlk1txdnPB5Y69sVxhL9ji9FDuUM8pXjMkR8jdGI,6703
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scout/server/blueprints/variants/templates/variants/utils.html,sha256=
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scout/server/blueprints/variants/templates/variants/utils.html,sha256=g6nvYsYwhlXP7ubT1mEX0zU9cAXIZ8KJWHvTFzMCxNI,52919
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scout/server/blueprints/variants/templates/variants/variants.html,sha256=oqJdyiIVwhZKnOGDfx07dPlRduIUvN5r0JmmK4hYExQ,8450
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scout/server/extensions/__init__.py,sha256=s6qkGSFNRi_tP7yoeoXB5UarvLHidaK1Yw2Pae7Py90,1366
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scout/server/extensions/beacon_extension.py,sha256=W2dHjTWbWXLnQN3dCOzXlGX8VxSYejT_UUlEF-elh14,9901
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scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
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scout/utils/scout_requests.py,sha256=6R8boknrfwlmrRQ2txD81lfVtqUK_iabywEiVyIiZfQ,12685
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scout/utils/track_resources.py,sha256=eUjSEe-Ff8BIb4BHPC_COkJocQO2PaWueiPz1GAuiwY,2614
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scout_browser-4.101.0.dist-info/METADATA,sha256=Mk2AmmUzaWO6IslzOG_LTXNcBp8qK6l3O7CQO_23fHw,15527
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scout_browser-4.101.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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scout_browser-4.101.0.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
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scout_browser-4.101.0.dist-info/licenses/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
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scout_browser-4.101.0.dist-info/RECORD,,
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