scout-browser 4.82.1__py3-none-any.whl → 4.83__py3-none-any.whl

scout/server/blueprints/variant/templates/variant/acmg.html

@@ -29,22 +29,27 @@
     <form action="{{ url_for('variant.variant_acmg', institute_id=institute._id, case_name=case.display_name, variant_id=variant._id) }}" method="POST">
       <div class="card panel-default mt-3">
         <div class="card-body">
-          {% if not evaluation %}
-              <div class="mt-3 fixed-bottom bg-light border">
-                <div class="text-center">
-                  {% for option in ACMG_OPTIONS %}
-                    <a id="acmg-{{ option.code }}" class="btn acmg-preview">{{ option.label }}</a>
-                  {% endfor %}
-                </div>
-              </div>
-            <button class="btn btn-primary form-control">Submit</button>
-          {% else %}
-            <h4>
+          {% if evaluation %}
+             <h4>
               {{ evaluation.classification.label }}
               <span class="badge bg-info">{{ evaluation.classification.short }}</span>
             </h4>
             By {{ evaluation.user_name }} on {{ evaluation.created_at.date() }}
+            {% if edit %}
+              <br><br>
+              <button class="btn btn-primary form-control" data-bs-toggle="tooltip" title="Editing this classification will result in a new classification">Reclassify</button>
+            {% endif %}
+          {% elif not evaluation %}
+            <button class="btn btn-primary form-control">Submit</button>
           {% endif %}
+          <!-- classification preview in the footer-->
+          <div class="mt-3 fixed-bottom bg-light border">
+              <div class="text-center">
+                {% for option in ACMG_OPTIONS %}
+                  <a id="acmg-{{ option.code }}" class="btn acmg-preview">{{ option.label }}</a>
+                {% endfor %}
+              </div>
+          </div>
         </div>
       </div>
 
@@ -72,14 +77,14 @@
                         {{ criterion.short }}
                       </div>
                       <div class="form-check form-switch">
-                        <input type="checkbox" class="form-check-input" id="checkbox-{{ criterion_code }}" name="criteria" value="{{ criterion_code }}" {{ 'checked' if evaluation and criterion_code in evaluation.criteria }} {{ 'disabled' if evaluation }}>
+                        <input type="checkbox" class="form-check-input" id="checkbox-{{ criterion_code }}" name="criteria" value="{{ criterion_code }}" {{ 'checked' if evaluation and criterion_code in evaluation.criteria }} {{ 'disabled' if evaluation and edit is false}}>
                         <label class="form-check-label" for="checkbox-{{ criterion_code }}"></label>
                       </div>
                     </div>
                     <div id="comment-{{ criterion_code }}" class="{{ 'collapse' if not (comment or link or modifier) }} mt-2">
                       {% if criterion.documentation %}<div class="row"><span class="me-1 fw-light text-wrap">{{ criterion.documentation | safe}}</span></div>{% endif %}
                       <div class="row">
-                        <select {{ 'disabled' if evaluation }} id="modifier-{{ criterion_code }}" name="modifier-{{ criterion_code }}" class="form-control form-select">
+                        <select {{ 'disabled' if evaluation and edit is false}} id="modifier-{{ criterion_code }}" name="modifier-{{ criterion_code }}" class="form-control form-select">
                           <option value="" {% if not modifier %}selected{% endif %}>Strength modifier...</option>
                           {% for level in "Strong", "Moderate", "Supporting" %}
                             {% if(level != evidence) %}
@@ -89,10 +94,10 @@
                         </select>
                       </div>
                       <div class="row">
-                        <textarea {{ 'disabled' if evaluation }} class="form-control"
+                        <textarea {{ 'disabled' if evaluation and edit is false }} class="form-control"
                           name="comment-{{ criterion_code }}" rows="3" placeholder="Comment (optional)">{{ comment }}</textarea>
                       </div>
-                      <input type="url" {{ 'disabled' if evaluation }} class="form-control" name="link-{{ criterion_code }}"
+                      <input type="url" {{ 'disabled' if evaluation and edit is false }} class="form-control" name="link-{{ criterion_code }}"
                         placeholder="{{ link or 'Supporting link (optional)' }}" value="">
                     </div>
                   </div>
@@ -120,6 +125,11 @@
   {{ super() }}
 
   <script>
+
+    window.onload=function() {
+        update_classification();
+    }
+
     $(function () {
       $('[data-bs-toggle="tooltip"]').tooltip();
 
@@ -130,7 +140,6 @@
         } else {
           el.collapse('hide');
         }
-
         update_classification()
       });
 

scout/server/blueprints/variant/templates/variant/components.html

@@ -49,14 +49,19 @@
         {% endif %}
       </span>
     </div>
-    <small class="text-muted">
-      <form action="{{ url_for('variant.evaluation', evaluation_id=data._id) }}" method="POST">
+    <span>
+      <small class="text-muted">
       {{ data.user_name }} on {{ data.created_at.date() }}
       {% if current_variant %}
-        <button class="btn btn-xs btn-link">Delete</button>
+          <form action="{{ url_for('variant.evaluation', evaluation_id=data._id) }}" method="POST" style="display: inline-block;">
+            <button class="btn btn-xs btn-link" >Delete</button>
+          </form>
+          {% if data.criteria %}
+            <a class="btn btn-xs btn-link" href="{{ url_for('variant.evaluation', evaluation_id=data._id, edit=True) }}" data-bs-toggle="tooltip" title="Editing this classification will result in a new classification">Edit</a>
+          {% endif %}
       {% endif %}
-      </form>
-    </small>
+      </small>
+    </span>
   </li>
 {% endmacro %}
 
@@ -90,7 +95,7 @@
             {% endif %}
             </div>
           {% endfor %}
-          {% if config.SQLALCHEMY_DATABASE_URI %}
+          {% if config.chanjo_report %}
             <div class="d-flex flex-wrap ms-1">
               {% for gene in variant.genes %}
                 <a class="btn btn-sm btn-secondary text-white" rel="noopener noreferrer" target="_blank" href="{{ url_for('report.gene', gene_id=gene.hgnc_id, sample_id=variant.samples|map(attribute='sample_id')|list) }}">

scout/server/blueprints/variant/views.py

@@ -13,7 +13,7 @@ from flask import (
 from flask_login import current_user
 from markupsafe import Markup
 
-from scout.constants import ACMG_CRITERIA, ACMG_MAP
+from scout.constants import ACMG_CRITERIA, ACMG_MAP, ACMG_OPTIONS
 from scout.server.blueprints.variant.controllers import check_reset_variant_classification
 from scout.server.blueprints.variant.controllers import evaluation as evaluation_controller
 from scout.server.blueprints.variant.controllers import observations, str_variant_reviewer
@@ -308,7 +308,7 @@ def variant_update(institute_id, case_name, variant_id):
 @variant_bp.route("/evaluations/<evaluation_id>", methods=["GET", "POST"])
 @templated("variant/acmg.html")
 def evaluation(evaluation_id):
-    """Show or delete an ACMG evaluation."""
+    """Show, edit or delete an ACMG evaluation."""
 
     evaluation_obj = store.get_evaluation(evaluation_id)
     if evaluation_obj is None:
@@ -328,12 +328,15 @@ def evaluation(evaluation_id):
             flash("Cleared ACMG classification.", "info")
 
         return redirect(link)
+
     return dict(
         evaluation=evaluation_obj,
+        edit=bool(request.args.get("edit")),
         institute=evaluation_obj["institute"],
         case=evaluation_obj["case"],
         variant=evaluation_obj["variant"],
         CRITERIA=ACMG_CRITERIA,
+        ACMG_OPTIONS=ACMG_OPTIONS,
     )
 
 

scout/server/blueprints/variants/controllers.py

@@ -941,7 +941,6 @@ def parse_variant(
         variant_obj["end_chrom"] = variant_obj["chromosome"]
 
     # common motif count for STR variants
-
     variant_obj["str_mc"] = get_str_mc(variant_obj)
 
     # variant level links shown on variants page
@@ -970,7 +969,6 @@ def get_str_mc(variant_obj: dict) -> Optional[int]:
     from the variant FORMAT field, or as a number given in the ALT on the form
     '<STR123>'.
     """
-
     alt_mc = None
     if variant_obj["alternative"] == ".":
         return alt_mc
@@ -982,9 +980,9 @@ def get_str_mc(variant_obj: dict) -> Optional[int]:
     if alt_mc:
         return alt_mc
 
-    alt_num = NUM.match(variant_obj["alternative"])
+    alt_num = NUM.search(variant_obj["alternative"])
     if alt_num:
-        alt_mc = int(alt_num)
+        alt_mc = int(alt_num.group())
         return alt_mc
 
     return None
@@ -1998,7 +1996,7 @@ def activate_case(store, institute_obj, case_obj, current_user):
         store.update_status(institute_obj, case_obj, user_obj, "active", case_link)
 
 
-def reset_all_dimissed(store, institute_obj, case_obj):
+def reset_all_dismissed(store, institute_obj, case_obj):
     """Reset all dismissed variants for a case.
 
     Args:

scout/server/blueprints/variants/templates/variants/str-variants.html

@@ -93,7 +93,7 @@
             <td class="str-link">{{ str_locus_info(variant) }}</td>
 	          <td class="text-end">{{ variant.str_display_ru or variant.str_ru or variant.reference }}</td>
             <td class="text-end"><b><span data-bs-toggle="tooltip" title="{{ variant.alternative }}">{{ variant.str_mc }}</span></b></td>
-        <td class="text-end"><span data-bs-toggle="tooltip" title="{{ variant.reference }}">{{ variant.str_ref or "." }}</span></td>
+            <td class="text-end"><span data-bs-toggle="tooltip" title="{{ variant.reference }}">{{ variant.str_ref or "." }}</span></td>
             <td>{{ str_status(variant) }}</td>
             <td>{% for sample in variant.samples %}
                   {% if sample.genotype_call != "./." %}

scout/server/blueprints/variants/views.py

@@ -47,7 +47,7 @@ variants_bp = Blueprint(
 def reset_dismissed(institute_id, case_name):
     """Reset all dismissed variants for a case"""
     institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
-    controllers.reset_all_dimissed(store, institute_obj, case_obj)
+    controllers.reset_all_dismissed(store, institute_obj, case_obj)
     return redirect(request.referrer)
 
 

scout/server/config.py

@@ -75,10 +75,9 @@ ACCREDITATION_BADGE = "swedac-1926-iso17025.png"
 # Connection details for Scout REViewer service
 # SCOUT_REVIEWER_URL = "http://127.0.0.1:8000/reviewer"
 
-#
-# Cloud IGV tracks can be configured here to allow users to enable them on their IGV views.
-# A number of publicly-available tracks can be found here: https://trackhubregistry.org/
-# CLOUD_IGV_TRACKS = [
+# Custom IGV tracks can be configured here to allow users to enable them on their IGV views.
+# A number of publicly-available tracks can be found here: https://trackhubregistry.org/ or downloaded from
+# CUSTOM_IGV_TRACKS = [
 #    {
 #        "name": "public_tracks",
 #        "access": "public",
@@ -99,6 +98,19 @@ ACCREDITATION_BADGE = "swedac-1926-iso17025.png"
 #            },
 #        ],
 #    },
+#    {
+#        "name": "local_tracks",
+#        "access": "public",
+#        "tracks": [
+#            {
+#                "name": "MANE",
+#                "type": "annotation",
+#                "format": "bigbed",
+#                "build": "38",
+#                "url": "scout/resources/custom_igv_tracks/mane.bb",
+#            },
+#        ],
+#    },
 # ]
 
 # Chanjo-Report

scout/server/extensions/__init__.py

@@ -6,10 +6,11 @@ from flask_login import LoginManager
 from flask_mail import Mail
 
 from scout.adapter import MongoAdapter
-from scout.utils.cloud_resources import AlignTrackHandler
+from scout.utils.track_resources import AlignTrackHandler
 
 from .beacon_extension import Beacon
 from .bionano_extension import BioNanoAccessAPI
+from .chanjo_extension import ChanjoReport
 from .clinvar_extension import ClinVarApi
 from .gens_extension import GensViewer
 from .ldap_extension import LdapManager
@@ -33,5 +34,6 @@ phenopacketapi = PhenopacketAPI()
 rerunner = RerunnerService()
 matchmaker = MatchMaker()
 beacon = Beacon()
-cloud_tracks = AlignTrackHandler()
+config_igv_tracks = AlignTrackHandler()
 bionano_access = BioNanoAccessAPI()
+chanjo_report = ChanjoReport()

scout/server/extensions/beacon_extension.py

@@ -1,6 +1,7 @@
 """Scout supports integration with the Clinical Genomics SciLifeLab Beacon
    cgbeacon2: https://github.com/Clinical-Genomics/cgbeacon2
 """
+
 import datetime
 import logging
 

scout/server/extensions/chanjo_extension.py

@@ -0,0 +1,58 @@
+"""
+    Generate coverage reports using chanjo and chanjo-report. Documentation under -> `docs/admin-guide/chanjo_coverage_integration.md`
+"""
+
+import logging
+
+from flask import current_app, request
+from flask_babel import Babel
+from markupsafe import Markup
+
+LOG = logging.getLogger(__name__)
+try:
+    from chanjo_report.server.app import configure_template_filters
+    from chanjo_report.server.blueprints import report_bp
+    from chanjo_report.server.extensions import api as chanjo_api
+except ImportError as error:
+    chanjo_api = None
+    report_bp = None
+    configure_template_filters = None
+    LOG.warning("chanjo-report is not properly installed! %s.", error)
+
+
+class ChanjoReport:
+    """Interfaces with chanjo-report. Creates the /reports endpoints in scout domain. Use Babel to set report language."""
+
+    def init_app(self, app):
+        if not chanjo_api:
+            raise ImportError(
+                "An SQL db path was given, but chanjo-report could not be registered."
+            )
+
+        def get_locale():
+            """Determine locale to use for translations."""
+            accept_languages = current_app.config.get("ACCEPT_LANGUAGES", ["en"])
+
+            # first check request args
+            session_language = Markup.escape(request.args.get("lang"))
+            if session_language in accept_languages:
+                current_app.logger.info("using session language: %s", session_language)
+                return session_language
+
+            # language can be forced in config
+            user_language = current_app.config.get("REPORT_LANGUAGE")
+            if user_language:
+                return user_language
+
+            # try to guess the language from the user accept header that
+            # the browser transmits.  We support de/fr/en in this example.
+            # The best match wins.
+            return request.accept_languages.best_match(accept_languages)
+
+        babel = Babel(app)
+        babel.init_app(app, locale_selector=get_locale)
+        chanjo_api.init_app(app)
+        configure_template_filters(app)
+        app.register_blueprint(report_bp, url_prefix="/reports")
+        app.config["chanjo_report"] = True
+        app.config["SQLALCHEMY_TRACK_MODIFICATIONS"] = True if app.debug else False

scout/server/extensions/phenopacket_extension.py

@@ -3,6 +3,7 @@ Extension to Scout for Phenopacket integration (http://phenopackets.org).
 Write and read JSON Phenopackets, and interact with phenopacket-api backend
 (https://github.com/squeezeday/phenopacket-api).
 """
+
 import json as json_lib
 import logging
 

scout/server/static/bs_styles.css

@@ -351,6 +351,24 @@ body {
 }
 /* end of sidebar-related stuff */
 
+/* Closed submenu icon - general case */
+.text-body[aria-expanded="false"] .collapse-icon::after {
+  content: " \f0d7";
+  font-family: "Font Awesome 5 Free", ui-monospace;
+  font-weight: 900;
+  display: inline;
+  text-align: left;
+}
+/* Opened submenu icon - general case */
+.text-body[aria-expanded="true"] .collapse-icon::after {
+  content: " \f0da";
+  font-family: "Font Awesome 5 Free", ui-monospace;
+  font-weight: 900;
+  display: inline;
+  text-align: left;
+}
+/* end of sidebar-related stuff */
+
 option {
   width: 100%;
 }

scout/server/utils.py

@@ -206,12 +206,26 @@ def user_institutes(store, login_user):
     return institutes
 
 
+def case_has_mtdna_report(case_obj: dict):
+    """Display mtDNA report on the case sidebar only for some specific cases."""
+    if case_obj.get("track", "rare") == "cancer":
+        return
+    for ind in case_obj.get("individuals", []):
+        if ind.get("analysis_type") == "wts":
+            continue
+        case_obj["mtdna_report"] = True
+        return
+
+
 def case_has_chanjo_coverage(case_obj: dict):
     """Set case_obj["chanjo_coverage"] to True if there is an instance of chanjo available and case has coverage stats in chanjo."""
 
-    chanjo_instance: bool = bool(current_app.config.get("SQLALCHEMY_DATABASE_URI"))
+    chanjo_instance: bool = bool(current_app.config.get("chanjo_report"))
     if case_obj.get("track", "rare") != "cancer" and chanjo_instance:
-        case_obj["chanjo_coverage"] = True
+        for ind in case_obj.get("individuals", []):
+            if ind.get("analysis_type") != "wts":
+                case_obj["chanjo_coverage"] = True
+                return
 
 
 def case_has_chanjo2_coverage(case_obj: dict):

scout/utils/acmg.py

@@ -190,27 +190,40 @@ def get_acmg(acmg_terms):
     bs_terms = []
     # Collection of terms with supporting Benign evidence
     bp_terms = []
+
+    suffix_map = {
+        "_Strong": {"P": ps_terms, "B": bs_terms},
+        "_Moderate": {"P": pm_terms},
+        "_Supporting": {"P": pp_terms, "B": bp_terms},
+    }
+
+    prefix_map = {
+        "PS": ps_terms,
+        "PM": pm_terms,
+        "PP": pp_terms,
+        "BS": bs_terms,
+        "BP": bp_terms,
+    }
+
     for term in acmg_terms:
-        if term.endswith("_Strong"):
-            ps_terms.append(term)
-        elif term.endswith("_Moderate"):
-            pm_terms.append(term)
-        elif term.endswith("_Supporting"):
-            pp_terms.append(term)
-        elif term.startswith("PVS"):
-            pvs = True
-        elif term.startswith("PS"):
-            ps_terms.append(term)
-        elif term.startswith("PM"):
-            pm_terms.append(term)
-        elif term.startswith("PP"):
-            pp_terms.append(term)
-        elif term.startswith("BA"):
-            ba = True
-        elif term.startswith("BS"):
-            bs_terms.append(term)
-        elif term.startswith("BP"):
-            bp_terms.append(term)
+        for suffix, prefix_dict in suffix_map.items():
+            if term.endswith(suffix):
+                for prefix, term_list in prefix_dict.items():
+                    if term.startswith(prefix):
+                        term_list.append(term)
+                        break
+                break
+        else:
+            # Do we match any of the two standalone terms
+            if term.startswith("PVS"):
+                pvs = True
+            elif term.startswith("BA"):
+                ba = True
+            else:  # Check remaining prefixes if no suffix match or standalone criteria match
+                for prefix, term_list in prefix_map.items():
+                    if term.startswith(prefix):
+                        term_list.append(term)
+                        break
 
     # We need to start by checking for Pathogenecity
     pathogenic = is_pathogenic(pvs, ps_terms, pm_terms, pp_terms)

scout/utils/track_resources.py

@@ -0,0 +1,70 @@
+# coding=UTF-8
+import logging
+import re
+from os.path import abspath, exists, isabs
+
+LOG = logging.getLogger(__name__)
+
+REQUIRED_FIELDS = ["name", "type", "url"]
+TRACK_KEYS = ["name", "type", "format", "url", "indexURL"]
+URL_PATTERN = re.compile("https?://")
+
+from typing import List
+
+
+class AlignTrackHandler:
+    """Class collecting external IGV tracks stored in the cloud"""
+
+    def init_app(self, app):
+        self.tracks = self.set_custom_tracks(
+            app.config.get("CUSTOM_IGV_TRACKS") or app.config.get("CLOUD_IGV_TRACKS")
+        )
+
+    def track_template(self, track_info: dict) -> dict:
+        """Provides the template for a VCF track object"""
+        track = {}
+
+        for key in TRACK_KEYS:
+            if key in track_info:
+                track[key] = track_info[key]
+
+        # Save track only of it contains the minimal required keys
+        if all(track.get(key) for key in REQUIRED_FIELDS):
+            return track
+        else:
+            raise FileNotFoundError(
+                f"One or more custom tracks specified in the config file could not be used, Please provide all required keys:{REQUIRED_FIELDS}"
+            )
+
+    def set_local_track_path(self, path: str) -> str:
+        """Returns the complete path to a local igv track file"""
+        if exists(path) and isabs(path):
+            return path
+        elif exists(path):
+            return abspath(path)
+        else:
+            raise FileNotFoundError(f"Could not verify path to IGV track:{path}")
+
+    def set_custom_tracks(self, track_dictionaries: List[dict]) -> dict:
+        """Return a list of IGV tracks collected from the config settings
+
+        Args:
+            track_dictionaries: a list of cloud bucket dictionaries containing IGV tracks, can be public or private
+        """
+        custom_tracks = {"37": [], "38": []}
+        # Loop over the bucket list and collect all public tracks
+        for track_category in track_dictionaries:
+            for track in track_category.get("tracks", []):
+                build = track.get("build")
+                if build not in ["37", "38"]:
+                    LOG.warning(
+                        "One or more IGV public tracks could not be used, Please provide a genome build ('37', '38') for it."
+                    )
+                    continue
+                track_obj = self.track_template(track)
+
+                if not URL_PATTERN.search(track_obj["url"]):  # It's a local file
+                    track_obj["url"] = self.set_local_track_path(track_obj["url"])
+
+                custom_tracks[build].append(track_obj)
+        return custom_tracks

{scout_browser-4.82.1.dist-info → scout_browser-4.83.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.82.1
+Version: 4.83
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson