scout-browser 4.100.2__tar.gz → 4.101.0__tar.gz

{scout_browser-4.100.2 → scout_browser-4.101.0}/CHANGELOG.md

@@ -4,6 +4,18 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+## [4.101]
+### Changed
+- Institutes are now sorted by ID on gene panels page (#5436)
+- Simplified visualization of previous ACMG and CCV classifications for a variant on variantS page (#5439 & #5440)
+- On ClinVar multistep submission form, skip fetching transcript versions for build 38 transcripts which are not MANE Select or MANE Plus Clinical (#5426)
+### Fixed
+- Malformatted table cell for analysis date on caseS page (#5438)
+- Remove "Add to ClinVar submission" button for pinned MEI variants as submission is not supported at the moment (#5442)
+- Clinical variant files could once again be read in arbitrary order on load (#5452)
+- Fix test_sanger_validation test to be run with a mock app instantiated (#5453)
+
+
 ## [4.100.2]
 ### Fixed
 - Keyerror 'ensembl_transcript_id' when loading transcripts from a pre-downloaded Ensembl transcripts file (#5435)

{scout_browser-4.100.2 → scout_browser-4.101.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scout-browser
-Version: 4.100.2
+Version: 4.101.0
 Summary: Clinical DNA variant visualizer and browser
 Project-URL: Repository, https://github.com/Clinical-Genomics/scout
 Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md

{scout_browser-4.100.2 → scout_browser-4.101.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "scout-browser"
-version = "4.100.2"
+version = "4.101.0"
 description = "Clinical DNA variant visualizer and browser"
 authors = [{name="Chiara Rasi", email="chiara.rasi@scilifelab.se"}, {name="Daniel Nilsson", email="daniel.nilsson@ki.se"}, {name="Robin Andeer", email="robin.andeer@gmail.com"}, {name="Mans Magnuson", email="monsunas@gmail.com"}]
 license = {text = "MIT License"}

{scout_browser-4.100.2 → scout_browser-4.101.0}/scout/adapter/mongo/case.py

@@ -6,7 +6,7 @@ import operator
 import re
 from collections import OrderedDict
 from copy import deepcopy
-from typing import Any, Dict, List, Optional
+from typing import Any, Dict, List, Optional, Tuple
 
 import pymongo
 from bson import ObjectId
@@ -928,21 +928,35 @@ class CaseHandler(object):
 
             self.load_omics_variants(case_obj=case_obj, build=build, file_type=omics_file)
 
-    def _load_clinical_variants(self, case_obj: dict, build: str, update: bool = False):
-        """Load variants in the order specified by CLINICAL_ORDERED_FILE_TYPE_MAP."""
+    def get_load_type_categories(self, case_obj: dict) -> List[Tuple[str, str]]:
+        """Return an (ordered) list of tuples pairing variant type and category for loading.
+
+        It is important for predictable variant collisions to retain the order specified in
+        the file type map CLINICAL_ORDERED_FILE_TYPE_MAP. Hence the set operation is made in parallel
+        with the list construction."""
+
         CLINICAL_ORDERED_FILE_TYPE_MAP = OrderedDict(
             (key, value)
             for key, value in ORDERED_FILE_TYPE_MAP.items()
             if value["variant_type"] != "research"
         )
-        load_type_cat = set()
+
+        load_type_cat = []
+        cat_seen = set()
         for file_name, vcf_dict in CLINICAL_ORDERED_FILE_TYPE_MAP.items():
             if not case_obj["vcf_files"].get(file_name):
                 LOG.debug("didn't find {}, skipping".format(file_name))
                 continue
-            load_type_cat.add((vcf_dict["variant_type"], vcf_dict["category"]))
+            pair = (vcf_dict["variant_type"], vcf_dict["category"])
+            if pair not in cat_seen:
+                cat_seen.add(pair)
+                load_type_cat.append(pair)
+        return load_type_cat
+
+    def _load_clinical_variants(self, case_obj: dict, build: str, update: bool = False):
+        """Load variants in the order specified by CLINICAL_ORDERED_FILE_TYPE_MAP."""
 
-        for variant_type, category in load_type_cat:
+        for variant_type, category in self.get_load_type_categories(case_obj):
             if update:
                 self.delete_variants(
                     case_id=case_obj["_id"],

{scout_browser-4.100.2 → scout_browser-4.101.0}/scout/constants/file_types.py

@@ -1,6 +1,6 @@
 from collections import OrderedDict
 
-# Variants in Scout will be loadedfor a case  in the same order as these ordered dictionaries
+# Variants in Scout will be loaded for a case in the same order as these ordered dictionaries
 ORDERED_FILE_TYPE_MAP = OrderedDict(
     [
         ("vcf_cancer", {"category": "cancer", "variant_type": "clinical"}),

{scout_browser-4.100.2 → scout_browser-4.101.0}/scout/server/blueprints/cases/templates/cases/utils.html

@@ -627,7 +627,7 @@
                 (included in ClinVar submission)
             {% elif variant.category in ('cancer', 'cancer_sv') %}
                 <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>
-            {% else %}
+            {% elif variant.category in ('snv', 'sv') %}
                 <button type="submit" name="var_id" value="{{variant._id}}" class="btn btn-secondary btn-sm" style="float: right;">Add to ClinVar submission</button>
             {% endif %}
         </form>

{scout_browser-4.100.2 → scout_browser-4.101.0}/scout/server/blueprints/clinvar/controllers.py

@@ -40,33 +40,27 @@ def _get_var_tx_hgvs(case_obj: dict, variant_obj: dict) -> List[Tuple[str, str]]
         transcripts = gene.get("transcripts", [])
 
         for tx in transcripts:
-
             refseq_id = tx.get("refseq_id")
             coding_seq_name = tx.get("coding_sequence_name")
             if not (refseq_id and coding_seq_name):
                 continue  # Skip transcripts missing required fields
 
-            mane_select = tx.get("mane_select_transcript")
-            mane_plus_clinical = tx.get("mane_plus_clinical_transcript")
-
-            for refseq in tx.get("refseq_identifiers", []):
-                refseq_version = fetch_refseq_version(refseq)  # Adds version to a RefSeq ID
-                hgvs_simple = f"{refseq_version}:{coding_seq_name}"
-
-                refseq_is_mane_select = mane_select == refseq_version
-                refseq_is_mane_plus_clinical = mane_plus_clinical == refseq_version
-
-                # Transcript is validate only when conditions are met
-                validated = (
-                    validate_hgvs(build, hgvs_simple)
-                    if (case_has_build_37 or refseq_is_mane_select or refseq_is_mane_plus_clinical)
-                    else ""
-                )
-
-                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 ''}"
-
+            if case_has_build_37:
+                for refseq in tx.get("refseq_identifiers", []):
+                    refseq_version = fetch_refseq_version(refseq)
+                    hgvs_simple = f"{refseq_version}:{coding_seq_name}"
+                    validated = validate_hgvs(build, hgvs_simple)
+                    label = f"{hgvs_simple}{'_validated_' if validated else ''}"
+                    tx_hgvs_list.append((hgvs_simple, label))
+
+            else:  # build 38, collect only MANE Select or MANE Plus Clinical
+                mane_select = tx.get("mane_select_transcript")
+                mane_plus_clinical = tx.get("mane_plus_clinical_transcript")
+                if mane_select is None and mane_plus_clinical is None:
+                    continue
+                hgvs_simple = f"{mane_select or mane_plus_clinical}:{coding_seq_name}"
+                label = f"{hgvs_simple}{'_mane-select_' if mane_select else ''}{'_mane-plus-clinical_' if mane_plus_clinical else ''}"
                 tx_hgvs_list.append((hgvs_simple, label))
-
     return tx_hgvs_list
 
 

{scout_browser-4.100.2 → scout_browser-4.101.0}/scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html

@@ -154,8 +154,6 @@
                     {% endfor %}
                     </table>
 
-                    <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>
-
                     <br><br>
                     <!-- dbSNP identifier -->
                     {{variant_data.var_form.variations_ids.label(class="fw-bold, text-dark")}}

{scout_browser-4.100.2 → scout_browser-4.101.0}/scout/server/blueprints/institutes/templates/overview/cases.html

@@ -94,13 +94,14 @@
         <span class="badge bg-primary">migrated</span>
       {% endif %}
     </td>
-    <td class="d-flex justify-content-between align-items-center">
-      {{ case.analysis_date.date() }}
-      {% if case.rerun_requested %}
+    <td>
+      <div class="d-flex align-items-center justify-content-between">{{ case.analysis_date.date() }}
+        {% if case.rerun_requested %}
           <span class="badge bg-secondary">rerun pending</span>
-      {% elif case.is_rerun %}
-        <span class="badge bg-secondary">rerun</span>
-      {% endif %}
+        {% elif case.is_rerun %}
+          <span class="badge bg-secondary">rerun</span>
+        {% endif %}
+      </div>
     </td>
     <td>
       {% if case.is_research %}

{scout_browser-4.100.2 → scout_browser-4.101.0}/scout/server/blueprints/panels/views.py

@@ -3,7 +3,16 @@ import datetime
 import json
 import logging
 
-from flask import Blueprint, Response, flash, redirect, render_template, request, send_file, url_for
+from flask import (
+    Blueprint,
+    Response,
+    flash,
+    redirect,
+    render_template,
+    request,
+    send_file,
+    url_for,
+)
 from flask_login import current_user
 from markupsafe import escape
 
@@ -96,7 +105,7 @@ def panels():
 
         panel_groups.append((institute_obj, institute_panels))
     return dict(
-        panel_groups=panel_groups,
+        panel_groups=sorted(panel_groups, key=lambda x: x[0]["_id"]),
         panel_names=panel_names,
         panel_versions=panel_versions,
         institutes=institutes,

{scout_browser-4.100.2 → scout_browser-4.101.0}/scout/server/blueprints/variants/templates/variants/cancer-variants.html

@@ -2,7 +2,7 @@
 
 {% from "variants/components.html" import allele_cell, external_scripts, external_stylesheets, gene_cell, frequency_cell_general, observed_cell_general, variant_funct_anno_cell %}
 {% 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 %}
-{% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, ccv_evaluations_badge, group_assessments_badge, matching_manual_rank, other_tiered_variants, research_assessments_badge %}
+{% 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 %}
 
 {% block title %}
   {{ variant_type|capitalize }} somatic variants
@@ -101,7 +101,7 @@
               </a>
             </td>
             <td>
-              {{ evaluations_badge(variant) }}
+              {{ evaluations_badge(variant.evaluations) }}
               {{ dismissals_badge(variant) }}
               {{ matching_manual_rank(variant) }}
               {{ research_assessments_badge(variant) }}
@@ -110,7 +110,7 @@
               {{ comments_badge(case, institute, variant) }}
               {{ causative_badge(variant, case) }}
               {{ other_tiered_variants(variant) }}
-              {{ ccv_evaluations_badge(variant) }}
+              {{ evaluations_badge(variant.ccv_evaluations) }}
             </td>
             <td>{{ rank_cell(variant) }}</td>
             <td>{{ cadd_cell(variant) }}</td>

{scout_browser-4.100.2 → scout_browser-4.101.0}/scout/server/blueprints/variants/templates/variants/indicators.html

@@ -61,23 +61,26 @@
   {% endif %}
 {% endmacro %}
 
-{% macro evaluations_badge(variant) %}
-  {% if variant.evaluations %}
-    {% for evaluation in (variant.evaluations or []) %}
-      <span class="badge bg-secondary" style="margin-left:1px" data-bs-toggle="tooltip" data-bs-placement="right"
-        title="Previously classified as {{ evaluation.classification.label }}">
-        {{ evaluation.classification.short }}
-      </span>
+{% macro evaluations_badge(evaluations) %}
+  {% if evaluations %}
+    {% set classification_counts = {} %}
+    {% for evaluation in evaluations %}
+      {% set c = evaluation.classification if evaluation.classification is defined else evaluation.ccv_classification %}
+      {% if c %}
+        {% set short = c.short %}
+        {% set label = c.label %}
+        {% set current = classification_counts.get(short, {'count': 0, 'label': label}) %}
+        {% set _ = classification_counts.update({short: {
+          'count': current.count + 1,
+          'label': label
+        }}) %}
+      {% endif %}
     {% endfor %}
-  {% endif %}
-{% endmacro %}
 
-{% macro ccv_evaluations_badge(variant) %}
-  {% if variant.ccv_evaluations %}
-    {% for evaluation in (variant.ccv_evaluations or []) %}
-      <span class="badge bg-secondary" style="margin-left:1px" data-bs-toggle="tooltip" data-bs-placement="right"
-        title="Previously classified as {{ evaluation.ccv_classification.label }}">
-        {{ evaluation.ccv_classification.short }}
+    {% for short, data in classification_counts.items() | sort(attribute='1.count', reverse=true) %}
+      <span class="badge bg-secondary ms-1" data-bs-toggle="tooltip" data-bs-placement="right"
+            title="Previously classified as {{ data.label }} ({{ data.count }} times)">
+        {{ short }} ×{{ data.count }}
       </span>
     {% endfor %}
   {% endif %}

{scout_browser-4.100.2 → scout_browser-4.101.0}/scout/server/blueprints/variants/templates/variants/utils.html

@@ -1118,7 +1118,7 @@
 
   {{ variant.variant_rank }}</a>&nbsp;
 
-  {{ evaluations_badge(variant) }}
+  {{ evaluations_badge(variant.evaluations) }}
   {{ research_assessments_badge(variant) }}
   {{ clinical_assessments_badge(variant) }}
   {{ group_assessments_badge(variant) }}

{scout_browser-4.100.2 → scout_browser-4.101.0}/tests/adapter/mongo/test_load_adapter_case.py

@@ -48,3 +48,13 @@ def test_load_case_empty_vcf(real_panel_database, parsed_case, empty_sv_clinical
 
     ## THEN assert that the empty VCF was used
     assert existing_case["vcf_files"]["vcf_sv"] == empty_sv_clinical_file
+
+
+def test_get_load_order(adapter, cancer_case_obj):
+    ### GIVEN a database adapter and a parsed case
+
+    ### WHEN determining variant load order
+    load_type_cat = adapter.get_load_type_categories(cancer_case_obj)
+
+    ### THEN cancer SNVs are taken before cancer SVs
+    assert load_type_cat == [("clinical", "cancer"), ("clinical", "cancer_sv")]

{scout_browser-4.100.2 → scout_browser-4.101.0}/tests/adapter/mongo/test_sanger_validation.py

@@ -90,7 +90,7 @@ def test_case_sanger_and_verified_variants(adapter, institute_obj, case_obj, use
 
 
 def test_get_sanger_unevaluated(
-    real_populated_database, variant_objs, institute_obj, case_obj, user_obj
+    mock_app, real_populated_database, variant_objs, institute_obj, case_obj, user_obj
 ):
     """Test get all sanger ordered but not evaluated for an institute"""