scout-browser 4.85__py3-none-any.whl → 4.86.1__py3-none-any.whl

scout/server/blueprints/dashboard/controllers.py

@@ -3,7 +3,7 @@ import logging
 from flask import flash, redirect, request, url_for
 from flask_login import current_user
 
-from scout.constants import CASE_SEARCH_TERMS
+from scout.constants import CASE_SEARCH_TERMS, CASE_TAGS
 from scout.server.extensions import store
 from scout.server.utils import user_institutes
 
@@ -139,8 +139,22 @@ def get_dashboard_info(adapter, data={}, institute_id=None, slice_query=None):
             "count": general_sliced_info["cohort_cases"],
             "percent": general_sliced_info["cohort_cases"] / total_sliced_cases,
         },
+        {
+            "title": "Case status tag",
+            "count": general_sliced_info["tagged_cases"],
+            "percent": general_sliced_info["tagged_cases"] / total_sliced_cases,
+        },
     ]
 
+    for stats_tag in CASE_TAGS.keys():
+        overview.append(
+            {
+                "title": CASE_TAGS[stats_tag]["label"] + " status tag",
+                "count": general_sliced_info[stats_tag + "_cases"],
+                "percent": general_sliced_info[stats_tag + "_cases"] / total_sliced_cases,
+            }
+        )
+
     data["overview"] = overview
 
     return data
@@ -149,6 +163,11 @@ def get_dashboard_info(adapter, data={}, institute_id=None, slice_query=None):
 def get_general_case_info(adapter, institute_id=None, slice_query=None):
     """Return general information about cases
 
+    Count e.g. cases with each kind of case tag, as well as cases that have phenotype, causatives or pinned variants
+    marked or are part of cohorts.
+
+    Gather pedigree information - single, duo, trio or many individuals in case.
+
     Args:
         adapter(adapter.MongoAdapter)
         institute_id(str)
@@ -168,15 +187,24 @@ def get_general_case_info(adapter, institute_id=None, slice_query=None):
         "suspects": 1,
         "cohorts": 1,
         "individuals": 1,
+        "tags": 1,
     }
     cases = adapter.cases(
         owner=institute_id, name_query=name_query, projection=CASE_GENERAL_INFO_PROJECTION
     )
 
-    phenotype_cases = 0
-    causative_cases = 0
-    pinned_cases = 0
-    cohort_cases = 0
+    case_counter_keys = [
+        "phenotype",
+        "causative",
+        "pinned",
+        "cohort",
+        "tagged",
+    ]
+    case_counter_keys.extend(CASE_TAGS.keys())
+
+    case_counter = {}
+    for counter in case_counter_keys:
+        case_counter[counter] = 0
 
     pedigree = {
         1: {"title": "Single", "count": 0},
@@ -191,13 +219,18 @@ def get_general_case_info(adapter, institute_id=None, slice_query=None):
     for total_cases, case in enumerate(cases, 1):
         case_ids.add(case["_id"])
         if case.get("phenotype_terms"):
-            phenotype_cases += 1
+            case_counter["phenotype"] += 1
         if case.get("causatives"):
-            causative_cases += 1
+            case_counter["causative"] += 1
         if case.get("suspects"):
-            pinned_cases += 1
+            case_counter["pinned"] += 1
         if case.get("cohorts"):
-            cohort_cases += 1
+            case_counter["cohort"] += 1
+        if case.get("tags"):
+            case_counter["tagged"] += 1
+            case_tags = case.get("tags")
+            for tag in case_tags:
+                case_counter[tag] += 1
 
         nr_individuals = len(case.get("individuals", []))
         if nr_individuals == 0:
@@ -208,12 +241,10 @@ def get_general_case_info(adapter, institute_id=None, slice_query=None):
             pedigree[nr_individuals]["count"] += 1
 
     general["total_cases"] = total_cases
-    general["phenotype_cases"] = phenotype_cases
-    general["causative_cases"] = causative_cases
-    general["pinned_cases"] = pinned_cases
-    general["cohort_cases"] = cohort_cases
     general["pedigree"] = pedigree
     general["case_ids"] = case_ids
+    for counter in case_counter_keys:
+        general[counter + "_cases"] = case_counter[counter]
 
     return general
 

scout/server/blueprints/dashboard/static/charts.js

@@ -15,12 +15,16 @@ function analysisTypeData(analysis_types) {
     "bkgColors": {
       "WES": "#46bfbd",
       "WGS": "#fdb45c",
-      "PANEL": "#44449B"
+      "PANEL": "#44449B",
+			"PANEL-UMI": "#949fb1",
+			"WTS": "#f7464A"
     },
     "hoverColors": {
       "WES": "#5ad3d1",
       "WGS": "#ffc870",
-      "PANEL": "#353578"
+      "PANEL": "#353578",
+			"PANEL-UMI": "#a8b3c5",
+			"WTS": "#ff5a5e"
     }
   };
   var bkg = [];
@@ -77,7 +81,7 @@ function casesType(cases) {
   var bkg = [];
   var hover = [];
   labels.forEach(function (item, index) {
-    bkg.push(bkgColors[index]);
+		bkg.push(bkgColors[index]);
     hover.push(hoverColors[index]);
   });
   var chart_data = {
@@ -129,52 +133,58 @@ function casesDetailed(overview, all_cases) {
   var bkg = [];
   var hover = [];
   labels.forEach(function (item, index) {
-    bkg.push(bkgColors[index]);
+		ncol = bkgColors.length;
+    bkg.push(bkgColors[index % ncol]);
   });
   var chart_data = {
-    type: "horizontalBar",
+    type: "bar",
     data: {
       labels: labels,
       datasets: [{
         data: overview.map(function (overview) {
           return overview.count * 100 / all_cases;
         }),
+				label: "Case percentage",
         backgroundColor: bkg,
         hoverBackgroundColor: hover
       }]
     },
     options: {
-      tooltips: {
-        callbacks: {
-          label: function label(tooltipItems) {
-            return Math.round(Number(tooltipItems.value) * all_cases / 100);
-          }
-        }
-      },
-      scales: {
-        xAxes: [{
-          ticks: {
-            min: 0,
-            max: 100,
-            callback: function callback(value) {
-              return value + "%";
-            }
-          },
-          scaleLabel: {
-            display: true,
-            labelString: "Case percentage",
-            fontSize: 20
-          }
-        }],
-        yAxes: [{
-          ticks: {
-            fontSize: 20
-          }
-        }]
-      },
-      legend: {
-        display: false
-      }
+			indexAxis: 'y',
+			tooltips: {
+				callbacks: {
+					label: function label(tooltipItems) {
+						return Math.round(Number(tooltipItems.value) * all_cases / 100);
+					}
+				}
+			},
+			scales: {
+				x: {
+					ticks: {
+						min: 0,
+						max: 100,
+						callback: function callback(value) {
+							return value + "%";
+						}
+					},
+					title: {
+						display: true,
+						text: "Case percentage",
+						font: 20
+					}
+				},
+				y: {
+					ticks: {
+						fontSize: 20
+					}
+				}
+			},
+			plugins:
+				{
+					legend: {
+						display: false
+					}
+				}
     }
   };
   return chart_data;

scout/server/blueprints/dashboard/templates/dashboard/dashboard_general.html

@@ -108,7 +108,7 @@
 {% endmacro %}
 
 {% macro cases_stats_panels() %}
-<div class="mt-3" id="cases">
+<div class="mt-3 mb-1" id="cases">
   <div class="row">
     <div class="col-md-8">
         <canvas id="cases-bar-horiz" height="80"></canvas>
@@ -129,7 +129,7 @@
 
 {% block scripts %}
   {{ super() }}
-  <script src="https://cdnjs.cloudflare.com/ajax/libs/Chart.js/2.8.0/Chart.bundle.min.js" integrity="sha512-60KwWtZOhzgr840mc57MV8JqDZHAws3w61mhK45KsYHmhyNFJKmfg4M7/s2Jsn4PgtQ4Uhr9xItS+HCbGTIRYQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
+  <script src="https://cdn.jsdelivr.net/npm/chart.js@4.4.3/dist/chart.umd.min.js" integrity="sha512-NqRhTU0DQNHNUO0pTx6zPLJ11YhOqj4MRcvv0+amxJk+re07ykGhFuhMmrQpfTRAUx8nQ4EcMuX/m8cz2K8vIQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
   <script src="{{ url_for('dashboard.static', filename='charts.js') }}"></script>
   <script type="text/javascript">
 

scout/server/blueprints/institutes/forms.py

@@ -17,6 +17,7 @@ from scout.constants import CASE_SEARCH_TERMS, PHENOTYPE_GROUPS
 from scout.models.case import STATUS
 
 CASE_SEARCH_KEY = [(value["prefix"], value["label"]) for key, value in CASE_SEARCH_TERMS.items()]
+CATEGORY_CHOICES = [("snv", "SNV"), ("sv", "SV")]
 
 
 class NonValidatingSelectField(SelectField):
@@ -142,6 +143,7 @@ class GeneVariantFiltersForm(FlaskForm):
     """Base FiltersForm for SNVs"""
 
     variant_type = SelectMultipleField(choices=[("clinical", "clinical"), ("research", "research")])
+    category = SelectMultipleField(choices=CATEGORY_CHOICES)
     hgnc_symbols = TagListField(
         "HGNC Symbols (comma-separated, case sensitive)", validators=[validators.InputRequired()]
     )

scout/server/blueprints/institutes/templates/overview/cases.html

@@ -113,19 +113,21 @@
 {% macro case_row(case) %}
   <tr class="{% if case.status == 'solved' %}causative{% endif %}">
     <td>
-      <a href="{{ url_for('cases.case', institute_id=case.owner, case_name=case.display_name) }}">
+      <a class="me-2"
+         {% if case.individuals|length == 1 %} data-bs-toggle="tooltip" title="{{case.individuals[0].display_name}}" {% endif %}
+         href="{{ url_for('cases.case', institute_id=case.owner, case_name=case.display_name) }}">
         {{ case.display_name }}
       </a>
       {% if case.individuals|length > 1 %}
-      <span class="badge bg-primary">
-        {% for item in case.individuals %}
+        {% for sample in case.individuals %}
+          <span class="badge {{'bg-danger' if sample.phenotype == 2 else 'bg-primary'}}" style="margin:-3px !important;" data-bs-toggle="tooltip" title="{{sample.display_name}}">
           {% if case.track == "cancer" %}
             <span class="fa fa-vial"></span>
           {% else %} <!-- rare disease case -->
             <span class="fa fa-user"></span>
           {% endif %}
+          </span>
         {% endfor %}
-      </span>
       {% endif %}
       {% for user in case.assignees %}
         <span class="badge bg-secondary">{{ user.name }}</span>

scout/server/blueprints/institutes/templates/overview/gene_variants.html

@@ -1,5 +1,5 @@
 {% extends "layout.html" %}
-{% from "variants/components.html" import gene_cell, frequency_cell_general %}
+{% from "variants/components.html" import frequency_cell_general, variant_funct_anno_cell, variant_gene_symbols_cell, variant_region_anno_cell %}
 {% from "utils.html" import comments_table %}
 {% from "overview/institute_sidebar.html" import institute_actionbar %}
 {% from "variants/utils.html" import pagination_footer, pagination_hidden_div %}
@@ -39,12 +39,12 @@
 <thead>
         <tr>
           <th scope="col">Case : Score</th>
+          <th scope="col">Var</th>
           <th scope="col">Gene</th>
           <th scope="col">Pop Freq</th>
           <th scope="col">CADD</th>
           <th scope="col">Region</th>
           <th scope="col">Function</th>
-          <th scope="col">HGVS</th>
         </tr>
 </thead>
 <tbody>
@@ -55,20 +55,12 @@
         <tr>
       {% endif %}
             <td class="align-middle">{{ cell_rank(variant) }}</td>
-            <td class="align-middle">{{ gene_cell(variant) }}</td>
+            <td class="align-middle">{{ pretty_link_no_gene(variant) }} </td>
+            <td class="align-middle">{{ variant_gene_symbols_cell(variant) }}</td>
             <td class="align-middle">{{ frequency_cell_general(variant) }}</td>
             <td class="align-middle">{{ cell_cadd(variant) }}</td>
-            <td class="align-middle">
-              {% for annotation in variant.region_annotations %}
-                <div>{{ annotation }}</div>
-              {% endfor %}
-            </td>
-            <td class="align-middle">
-              {% for annotation in variant.functional_annotations %}
-                <div>{{ annotation }}</div>
-              {% endfor %}
-            </td>
-            <td class="align-middle"> {{ (variant.hgvs or '')|url_decode  }}</td>
+            <td class="align-middle">{{ variant_region_anno_cell(variant) }}</td>
+            <td class="align-middle">{{ variant_funct_anno_cell(variant) }}</td>
           </tr>
         {% endfor %}
         {% if form.hgnc_symbols.data == [] %}
@@ -80,7 +72,10 @@
         {% elif variants == [] %}
         <tr>
           <td colspan=7>
-            No variants matching your query in genes: {{form.hgnc_symbols.data|join(", ")}}
+            No variants matching your query in genes: {{form.hgnc_symbols.data|join(", ")}}.
+            {% if "research" not in form.variant_type.data %}
+              Consider a lower rank score threshold or including research variants.
+            {% endif %}
           </td>
         </tr>
         {% endif %}
@@ -92,12 +87,26 @@
 </form>
 {% endmacro %}
 
-{% macro cell_rank(variant) %}
-    <a
-       href="{{ url_for('variant.variant', institute_id=variant.institute,
+
+{% macro pretty_link_no_gene(variant) %}
+  {% if variant.category == "sv" %}
+    <a href="{{ url_for('variant.sv_variant', institute_id=variant.institute,
             case_name=variant.case_display_name, variant_id=variant._id) }}" target="_blank">
-      {{ variant.case_display_name}}
-    </a>
+       {% if hgvs in variant %}
+        {{ variant.hgvs }}
+       {% else %}
+        {{ variant.sub_category|upper }}({{ variant.chromosome }}{{ variant.cytoband_start }}-{{ variant.end_chrom }}{{ variant.cytoband_end }})
+       {% endif %}
+  {% else %}
+    <a href="{{ url_for('variant.variant', institute_id=variant.institute,
+            case_name=variant.case_display_name, variant_id=variant._id) }}" target="_blank">
+    {{ (variant.hgvs or '')|url_decode }}
+  {% endif %}
+  </a>
+{% endmacro %}
+
+{% macro cell_rank(variant) %}
+   {{ variant.case_display_name }}
     :
     <span class="badge bg-info">{{ variant.rank_score|int }}</span>
 {% endmacro %}
@@ -123,29 +132,33 @@
           {{ form.hgnc_symbols.label(class="control-label") }}
           {{ form.hgnc_symbols(class="form-control") }}
         </div>
-        <div class="col col-md-3">
-          <label class="control-label">Rank Score ></label>
+        <div class="col col-md-1">
+          <label class="control-label" for="rank_score">Rank Score</label>
           <input type="number" class="form-control" id="rank_score" name="rank_score" min="5" value={{form.rank_score.data}}>
         </div>
-        <div class="col col-md-3">
+        <div class="col col-md-2">
           {{ form.variant_type.label(class="control-label") }}
           {{ form.variant_type(class="form-control", class="selectpicker", data_style="btn-secondary") }}
         </div>
+        <div class="col col-md-2">
+          {{ form.category.label(class="control-label") }}
+          {{ form.category(class="form-control", class="selectpicker", data_style="btn-secondary") }}
+        </div>
       </div>
       <div class="row">
-        <div class="col-md-3">
+        <div class="col-md-6">
           {{ form.phenotype_terms.label(class="control-label") }}
           {{ form.phenotype_terms(class="form-control") }}
         </div>
-        <div class="col-md-3">
+        <div class="col-md-2">
           {{ form.phenotype_groups.label(class="control-label") }}
           {{ form.phenotype_groups(class="form-control") }}
         </div>
-        <div class="col-md-3">
+        <div class="col-md-2">
           {{ form.cohorts.label(class="control-label") }}
           {{ form.cohorts(class="form-control") }}
         </div>
-        <div class="col-md-3">
+        <div class="col-md-2">
           {{ form.similar_case.label(class="control-label") }}
           {{ form.similar_case(class="form-control") }}
         </div>

scout/server/blueprints/institutes/templates/overview/institute_sidebar.html

@@ -31,7 +31,7 @@
       <a href="{{ url_for('overview.gene_variants', institute_id=institute._id) }}" class="bg-dark list-group-item list-group-item-action flex-column align-items-start h-100">
           <div class="d-flex w-100 justify-content-start align-items-center">
               <span class="fa fa-search me-3"></span>
-              <span class="menu-collapsed">Search SNVs and INDELs</span>
+              <span class="menu-collapsed">Search SNVs & SVs</span>
           </div>
       </a>
 

scout/server/blueprints/institutes/views.py

@@ -2,16 +2,7 @@
 import json
 import logging
 
-from flask import (
-    Blueprint,
-    current_app,
-    flash,
-    jsonify,
-    redirect,
-    render_template,
-    request,
-    url_for,
-)
+from flask import Blueprint, flash, jsonify, redirect, render_template, request
 from flask_login import current_user
 from pymongo import DESCENDING
 
@@ -138,11 +129,13 @@ def gene_variants(institute_id):
         form = GeneVariantFiltersForm(request.args)
     else:  # POST
         form = GeneVariantFiltersForm(request.form)
+
         if form.variant_type.data == []:
             form.variant_type.data = ["clinical"]
-
         variant_type = form.data.get("variant_type")
 
+        category = form.data.get("category") or ["snv", "sv"]
+
         update_form_hgnc_symbols(store=store, case_obj=None, form=form)
 
         # If no valid gene is provided, redirect to form
@@ -153,7 +146,7 @@ def gene_variants(institute_id):
         variants_query = store.build_variant_query(
             query=form.data,
             institute_ids=[inst["_id"] for inst in user_institutes(store, current_user)],
-            category="snv",
+            category=category,
             variant_type=variant_type,
         )  # This is the actual query dictionary, not the cursor with results
 

scout/server/blueprints/omics_variants/__init__.py

@@ -0,0 +1 @@
+from .views import omics_variants_bp

scout/server/blueprints/omics_variants/controllers.py

@@ -0,0 +1,122 @@
+from flask import Response
+from pymongo.cursor import CursorType
+from werkzeug.datastructures import Headers
+
+from scout.adapter import MongoAdapter
+from scout.constants import EXPORTED_VARIANTS_LIMIT
+from scout.server.blueprints.variant.utils import update_variant_case_panels
+from scout.server.blueprints.variants.utils import update_case_panels
+from scout.server.utils import case_has_alignments, case_has_mt_alignments, case_has_rna_tracks
+
+
+def outliers(
+    store: MongoAdapter,
+    institute_obj: dict,
+    case_obj: dict,
+    omics_variants_query: CursorType,
+    variant_count: int,
+    page: int = 1,
+    per_page: int = 50,
+):
+    """Pre-process list of outlier omics variants."""
+    skip_count = per_page * max(page - 1, 0)
+
+    more_variants = variant_count > (skip_count + per_page)
+    variants = []
+
+    update_case_panels(store, case_obj)
+
+    case_has_alignments(case_obj)
+    case_has_mt_alignments(case_obj)
+    case_has_rna_tracks(case_obj)
+
+    for variant_obj in omics_variants_query.skip(skip_count).limit(per_page):
+        parsed_variant = decorate_omics_variant(
+            store,
+            institute_obj,
+            case_obj,
+            variant_obj,
+        )
+
+        variants.append(parsed_variant)
+
+    return {"variants": variants, "more_variants": more_variants}
+
+
+def decorate_omics_variant(
+    store: MongoAdapter, institute_obj: dict, case_obj: dict, omics_variant_obj: dict
+):
+    """Decorate each variant with a limited selection of variant obj level information for display on variantS page."""
+
+    omics_variant_obj["comments"] = store.events(
+        institute_obj,
+        case=case_obj,
+        variant_id=omics_variant_obj["omics_variant_id"],
+        comments=True,
+    )
+
+    update_variant_case_panels(case_obj, omics_variant_obj)
+
+    return omics_variant_obj
+
+
+def download_omics_variants(case_obj: dict, variant_objs: CursorType):
+    """Download omics variants in a csv file."""
+
+    def generate(header, lines):
+        yield header + "\n"
+        for line in lines:
+            yield line + "\n"
+
+    DOCUMENT_HEADER = [
+        "Gene",
+        "Gene annotation",
+        "Category",
+        "Sub-category",
+        "Potential impact",
+        "Delta PSI",
+        "L2FC",
+        "P-value",
+        "Fold-change",
+        "Samples/Individuals",
+        "Position",
+    ]
+
+    export_lines = []
+    for variant in variant_objs.limit(EXPORTED_VARIANTS_LIMIT):
+        variant_genes: str = (
+            f'"{", ".join(variant.get("hgnc_symbols", variant.get("hgnc_ids", variant.get("gene_name_orig"))))}"'
+        )
+        gene_anno = variant["gene_type"]
+        category = variant["category"]
+        sub_category = variant["sub_category"]
+
+        if sub_category == "splicing":
+            delta_psi = variant["delta_psi"]
+            l2fc = "N/A"
+            potential_impact = f"{variant['potential_impact']} - fs {variant['causes_frameshift']}"
+            fold_change = "N/A"
+        else:
+            delta_psi = "N/A"
+            l2fc = variant["l2fc"]
+            potential_impact = "N/A"
+            fold_change = variant["fold_change"]
+        p_value = "%.3e" % variant["p_value"]
+        samples = f'"{", ".join([sample["display_name"] for sample in variant.get("samples")])}"'
+        position = f"{variant['chromosome']}:{variant['position']}-{variant['end']}"
+
+        variant_line = f"{variant_genes},{gene_anno},{category},{sub_category},{potential_impact},{delta_psi},{l2fc},{p_value},{fold_change},{samples},{position}"
+        export_lines.append(variant_line)
+
+    headers = Headers()
+    headers.add(
+        "Content-Disposition",
+        "attachment",
+        filename=str(case_obj["display_name"]) + "-filtered-omics_variants.csv",
+    )
+    # return a csv with the exported variants
+    return Response(
+        generate(",".join(DOCUMENT_HEADER), export_lines),
+        mimetype="text/csv",
+        headers=headers,
+    )