scout-browser 4.88.1__py3-none-any.whl → 4.89__py3-none-any.whl

scout/server/blueprints/login/views.py

@@ -47,16 +47,20 @@ def load_user(user_id):
 @public_endpoint
 def login():
     """Login a user if they have access."""
-    if "next" in request.args:
-        session["next_url"] = request.args["next"]
+
+    if current_app.config.get("USERS_ACTIVITY_LOG_PATH"):
+        if request.form.get("consent_checkbox") is None and "consent_given" not in session:
+            flash(
+                "Logging user activity is a requirement for using this site and accessing your account. Without consent to activity logging, you will not be able to log in into Scout.",
+                "warning",
+            )
+            return redirect(url_for("public.index"))
+        session["consent_given"] = True
 
     user_id = None
     user_mail = None
 
-    if (
-        current_app.config.get("LDAP_HOST", current_app.config.get("LDAP_SERVER"))
-        and request.method == "POST"
-    ):
+    if current_app.config.get("LDAP_HOST", current_app.config.get("LDAP_SERVER")):
         ldap_authorized = controllers.ldap_authorized(
             request.form.get("ldap_user"), request.form.get("ldap_password")
         )
@@ -66,20 +70,19 @@ def login():
             flash("User not authorized by LDAP server", "warning")
             return redirect(url_for("public.index"))
 
-    if current_app.config.get("GOOGLE"):
+    elif current_app.config.get("GOOGLE"):
         if session.get("email"):
             user_mail = session["email"]
             session.pop("email", None)
         else:
-            LOG.info("Google Login!")
             redirect_uri = url_for(".authorized", _external=True)
             try:
                 return oauth_client.google.authorize_redirect(redirect_uri)
             except Exception as ex:
                 flash("An error has occurred while logging in user using Google OAuth")
 
-    if request.args.get("email"):  # log in against Scout database
-        user_mail = request.args.get("email")
+    elif request.form.get("email"):  # log in against Scout database
+        user_mail = request.form["email"]
         LOG.info("Validating user %s email %s against Scout database", user_id, user_mail)
 
     user_obj = store.user(email=user_mail, user_id=user_id)
@@ -101,6 +104,7 @@ def login():
 @public_endpoint
 def authorized():
     """Google auth callback function"""
+
     token = oauth_client.google.authorize_access_token()
     google_user = oauth_client.google.parse_id_token(token, None)
     session["email"] = google_user.get("email").lower()
@@ -116,6 +120,7 @@ def logout():
     session.pop("email", None)
     session.pop("name", None)
     session.pop("locale", None)
+    session.pop("consent_given", None)
     flash("you logged out", "success")
     return redirect(url_for("public.index"))
 
@@ -130,7 +135,6 @@ def users():
 def perform_login(user_dict):
     if login_user(user_dict, remember=True):
         flash("you logged in as: {}".format(user_dict.name), "success")
-        next_url = session.pop("next_url", None)
-        return redirect(request.args.get("next") or next_url or url_for("cases.index"))
+        return redirect(url_for("cases.index"))
     flash("sorry, you could not log in", "warning")
     return redirect(url_for("public.index"))

scout/server/blueprints/panels/controllers.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 import datetime as dt
 import logging
+import re
 
 from flask import flash, redirect
 from flask_login import current_user
@@ -309,9 +310,11 @@ def downloaded_panel_name(panel_obj, format) -> str:
     Returns:
         a string describing the panel
     """
+    sanitized_panel_id = re.sub(r"[^a-zA-Z_\-]+", "", panel_obj["panel_name"])
+
     return "_".join(
         [
-            panel_obj["panel_name"],
+            sanitized_panel_id,
             str(panel_obj["version"]),
             dt.datetime.now().strftime(DATE_DAY_FORMATTER),
             f"scout.{format}",

scout/server/blueprints/panels/templates/panels/panel.html

@@ -76,7 +76,7 @@
       </li>
       <li class="list-group-item">
         <label for="date">Date</label>
-        <span class="float-end" id="date">{{ panel.date.date() }}</span>
+        <span class="float-end" id="date">{{panel._id.generation_time.strftime('%Y-%m-%d')}} {% if panel.hidden %} deleted:{{ panel.date.date()}} {% endif %}</span>
       </li>
       <li class="list-group-item">
           <label for="mainainer">Maintainers</label>

scout/server/blueprints/panels/templates/panels/panels.html

@@ -109,7 +109,7 @@
           </div>
           <div class="col-sm-3 text-center">
               <input type="text" name="new_panel_name" class="form-control" placeholder="Panel ID" required
-                pattern="^[a-zA-Z0-9_-]*$" title="Only alphanumeric characters (A-Z+a-z+0-9), hyphens, and underscores allowed.">
+                pattern="[A-Za-z0-9_\-]+" title="Only alphanumeric characters (A-Z+a-z+0-9), hyphens, and underscores allowed.">
             </div>
             <div class="col-sm-4 text-center">
               <input type="text" name="display_name" class="form-control" placeholder="Full name">
@@ -150,8 +150,8 @@
         <table class="table table-striped" id="panelTable" style="table-layout: fixed;">
         <thead>
           <tr>
-            <th style="width: 30%">Name</th>
-            <th>Version</th>
+            <th style="width: 20%">Name</th>
+            <th style="width: 20%">Version</th>
             <th>Number of genes</th>
             <th>History</th>
             <th></th>
@@ -170,10 +170,10 @@
                 <span class="badge bg-danger" data-bs-toggle="tooltip" title="This panel was removed">Removed</span>
               {% endif %}
             </td>
-            <td>{{ panel.version }} ({{ panel.date.date()}})</td>
+            <td>{{ panel.version }} ({{panel._id.generation_time.strftime('%Y-%m-%d')}} {% if panel.hidden %} deleted:{{ panel.date.date()}} {% endif %})</td>
             <td><span class="badge rounded-pill bg-secondary">{{ panel.genes|length}}</span></td>
             <td><button id="{{panel._id}}" type="button" data-bs-toggle="collapse" href="#paneldiv_{{panel._id}}" aria-expanded="false" aria-controls="paneldiv_{{panel._id}}" class="btn btn-primary btn-xs"><span class="fa fa-search-plus"></span></button><br>{{ history_view(panel._id, panel.panel_name) }}</td>
-            <td><button id="{{panel._id}}" type="button" data-bs-toggle="collapse" href="#modifydiv_{{panel._id}}" aria-expanded="false" aria-controls="modifydiv_{{panel._id}}" class="btn btn-warning btn-xs"><span class="fa fa-pen-square"></span></button><br>{{ history_view(panel._id, panel.panel_name) }}</td>
+            <td><button id="{{panel._id}}" type="button" data-bs-toggle="collapse" href="#modifydiv_{{panel._id}}" aria-expanded="false" aria-controls="modifydiv_{{panel._id}}" class="btn btn-warning btn-xs"><span class="fa fa-pen-square"></span></button></td>
             <td>
               {% if panel.hidden %}
                 <form action="{{ url_for('panels.panel_restore', panel_id=panel._id) }}" method="POST">

scout/server/blueprints/public/templates/public/index.html

@@ -20,12 +20,12 @@
         </a>
       </p>
     {% else %}
-      {% if config.GOOGLE %}
-        <a class="btn btn-primary btn-lg text-white" href="{{ url_for('login.login') }}" role="button">
-          Login with Google
-        </a>
-      {% elif config.LDAP_HOST or config.LDAP_SERVER %}
-        <form class="row" method="POST" action="{{ url_for('login.login') }}">
+      <form class="row" method="POST" action="{{ url_for('login.login') }}">
+        {% if config.GOOGLE %}
+          <button name="googleLogin" class="btn btn-primary btn-lg text-white" href="{{ url_for('login.login') }}" type="submit">
+            Login with Google
+          </button>
+        {% elif config.LDAP_HOST or config.LDAP_SERVER %}
           <div class="col-5">
           <input type="text" name="ldap_user" class="form-control" placeholder="user email/id" required>
           </div>
@@ -35,9 +35,7 @@
           <div class="col-2">
             <button type="submit" class="btn btn-primary form-control text-white">Login</button>
           </div>
-        </form>
         {% else %}
-        <form action="{{ url_for('login.login') }}">
           <div class="row">
             <div class="col-8">
               <input type="text" placeholder="email" class="form-control" name="email">
@@ -46,8 +44,18 @@
               <button type="submit" class="btn btn-primary form-control text-white">Login</button>
             </div>
           </div>
-        </form>
-      {% endif %}
+        {% endif %}
+        <!-- Consent Banner -->
+        {% if config.USERS_ACTIVITY_LOG_PATH %}
+          <div class="row mt-3 ms-0 alert-warning" style="text-align: center; padding: 20px;">
+            <p>To ensure security and improve functionality, we log user activity, including interactions and navigation. This helps us enhance performance and maintain platform safety.
+              By checking the box, you agree that your activity will be logged, which is required to use this portal and log in.</p>
+              <label>
+                <input type="checkbox" name="consent_checkbox"> I agree to my activity being logged
+              </label>
+          </div>
+        {% endif %}
+    </form>
     {% endif %}
   </div>
   <div class="container bg-light rounded-3 py-4">

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

@@ -273,7 +273,6 @@
           {% if gene.decipher_link %}
             <a href="{{ gene.decipher_link }}" class="btn btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank">Decipher</a>
           {% endif %}
-          <a href="http://tools.genes.toronto.edu/" class="btn btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank">SPANR</a>
           <a href="{{ gene.reactome_link }}" class="btn btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank">Reactome</a>
           <a href="{{ gene.expression_atlas_link }}" class="btn btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank">Expr. Atlas</a>
           <a href="{{ gene.clingen_link }}" class="btn btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank">ClinGen</a>

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

@@ -50,7 +50,7 @@
               {% if gene.common and gene.disease_terms %}
                 {% for disease_term in gene.disease_terms %}
                   {% if disease_term.source == 'ORPHA' %}
-                    <tr data-bs-toggle="tooltip" title="Some ORPHA disorders are phenotypic umbrella terms for multiple genetic entities. The inheritance models are in this case a set derived from all those entities, not necessarily the inheritance mode known for this gene.">
+                    <tr data-bs-toggle="tooltip" title="Some ORPHA disorders are phenotypic umbrella terms for multiple genetic entities. The inheritance models are in this case a set derived from all those entities, not necessarily modes of inheritance known for this gene. ORPHA inheritance modes will not be shown on the general case report.">
                       <td>
                           <a href="http://omim.org/entry/{{ gene.common.omim_id }}" rel="noopener" target="_blank">
                             {{ gene.common.hgnc_symbol }}

scout/server/config.py

@@ -151,3 +151,6 @@ SV_RANK_MODEL_LINK_POSTFIX = "-.ini"
 # BIONANO_ACCESS = "https://bionano-access.scilifelab.se"
 # BIONANO_USERNAME = "USERNAME"
 # BIONANO_PASSWORD = "PASSWORD"
+
+# Uncomment and customise to log users' activity to file
+# USERS_ACTIVITY_LOG_PATH = "users_activity.log"

scout/server/extensions/__init__.py

@@ -10,6 +10,7 @@ from scout.utils.track_resources import AlignTrackHandler
 
 from .beacon_extension import Beacon
 from .bionano_extension import BioNanoAccessAPI
+from .chanjo2_extension import Chanjo2Client
 from .chanjo_extension import ChanjoReport
 from .clinvar_extension import ClinVarApi
 from .gens_extension import GensViewer
@@ -37,3 +38,4 @@ beacon = Beacon()
 config_igv_tracks = AlignTrackHandler()
 bionano_access = BioNanoAccessAPI()
 chanjo_report = ChanjoReport()
+chanjo2 = Chanjo2Client()

scout/server/extensions/chanjo2_extension.py

@@ -0,0 +1,46 @@
+import logging
+from typing import Dict
+
+import requests
+from flask import current_app
+
+REF_CHROM = "14"
+MT_CHROM = "MT"
+LOG = logging.getLogger(__name__)
+
+
+class Chanjo2Client:
+    """Runs requests to chanjo2 and returns results in the expected format."""
+
+    def mt_coverage_stats(self, individuals: dict) -> Dict[str, dict]:
+        """Sends a POST requests to the chanjo2 coverage/d4/interval to collect stats for the MT case report."""
+
+        chanjo2_chrom_cov_url: str = "/".join(
+            [current_app.config.get("CHANJO2_URL"), "coverage/d4/interval/"]
+        )
+        coverage_stats = {}
+        for ind in individuals:
+
+            if not ind.get("d4_file"):
+                continue
+            chrom_cov_query = {"coverage_file_path": ind["d4_file"]}
+
+            # Get mean coverage over chr14
+            chrom_cov_query["chromosome"] = REF_CHROM
+            resp = requests.post(chanjo2_chrom_cov_url, json=chrom_cov_query)
+            autosome_cov = resp.json().get("mean_coverage")
+
+            # Get mean coverage over chrMT
+            chrom_cov_query["chromosome"] = MT_CHROM
+            resp = requests.post(chanjo2_chrom_cov_url, json=chrom_cov_query)
+
+            mt_cov = resp.json().get("mean_coverage")
+
+            coverage_info = dict(
+                mt_coverage=mt_cov,
+                autosome_cov=autosome_cov,
+                mt_copy_number=round((mt_cov / autosome_cov) * 2, 2),
+            )
+            coverage_stats[ind["individual_id"]] = coverage_info
+
+        return coverage_stats

scout/server/extensions/chanjo_extension.py

@@ -2,13 +2,16 @@
     Generate coverage reports using chanjo and chanjo-report. Documentation under -> `docs/admin-guide/chanjo_coverage_integration.md`
 """
 
+import json
 import logging
 
-from flask import current_app, request
+import requests
+from flask import current_app, request, url_for
 from flask_babel import Babel
 from markupsafe import Markup
 
 LOG = logging.getLogger(__name__)
+REF_CHROM_MT_STATS = "14"
 
 
 class ChanjoReport:
@@ -57,3 +60,43 @@ class ChanjoReport:
         app.register_blueprint(report_bp, url_prefix="/reports")
         app.config["chanjo_report"] = True
         app.config["SQLALCHEMY_TRACK_MODIFICATIONS"] = True if app.debug else False
+
+    def mt_coverage_stats(self, individuals: dict) -> dict:
+        """Send a request to chanjo endpoint to retrieve MT vs autosome coverage stats
+
+        Args:
+            individuals(dict): case_obj["individuals"] object
+
+        Returns:
+            coverage_stats(dict): a dictionary with mean MT and autosome transcript coverage stats
+        """
+        coverage_stats = {}
+        ind_ids = []
+        for ind in individuals:
+            ind_ids.append(ind["individual_id"])
+
+        # Prepare complete url to Chanjo report chromosome mean coverage calculation endpoint
+        cov_calc_url = url_for("report.json_chrom_coverage", _external=True)
+        # Prepare request data to calculate mean MT coverage
+        data = dict(sample_ids=",".join(ind_ids), chrom="MT")
+        # Send POST request with data to chanjo endpoint
+        resp = requests.post(cov_calc_url, json=data)
+        mt_cov_data = json.loads(resp.text)
+
+        # Change request data to calculate mean autosomal coverage
+        data["chrom"] = REF_CHROM_MT_STATS
+        # Send POST request with data to chanjo endpoint
+        resp = requests.post(cov_calc_url, json=data)
+        ref_cov_data = json.loads(resp.text)  # mean coverage over the transcripts of ref chrom
+
+        for ind in ind_ids:
+            if not (mt_cov_data.get(ind) and ref_cov_data.get(ind)):
+                continue
+            coverage_info = dict(
+                mt_coverage=round(mt_cov_data[ind], 2),
+                autosome_cov=round(ref_cov_data[ind], 2),
+                mt_copy_number=round((mt_cov_data[ind] / ref_cov_data[ind]) * 2, 2),
+            )
+            coverage_stats[ind] = coverage_info
+
+        return coverage_stats

scout/server/extensions/matchmaker_extension.py

@@ -3,7 +3,6 @@
 """
 
 import datetime
-import json
 import logging
 
 from werkzeug.datastructures import Headers

scout/server/links.py

@@ -819,6 +819,15 @@ def alamut_gene_link(
         url_template(str): link to Alamut browser
     """
 
+    def get_gene_canonical_tx(gene: dict) -> str:
+        """Returns the canonical transcript of a gene."""
+        if gene.get("canonical_transcript"):
+            return gene["canonical_transcript"]
+
+        for tx in gene.get("transcripts"):
+            if tx.get("is_canonical"):
+                return tx["transcript_id"]
+
     if current_app.config.get("HIDE_ALAMUT_LINK"):
         return False
 
@@ -828,7 +837,7 @@ def alamut_gene_link(
     (search_verb, alamut_key_arg, alamut_inst_arg) = _get_alamut_config(institute_obj)
 
     url_template = (
-        "http://localhost:10000/{search_verb}?{alamut_key_arg}{alamut_inst_arg}request={this[canonical_transcript]}{build_str}:"
+        "http://localhost:10000/{search_verb}?{alamut_key_arg}{alamut_inst_arg}request={canonical_transcript}{build_str}:"
         "{hgvs_identifier}"
     )
 
@@ -845,7 +854,7 @@ def alamut_gene_link(
         search_verb=search_verb,
         alamut_key_arg=alamut_key_arg,
         alamut_inst_arg=alamut_inst_arg,
-        this=gene_obj,
+        canonical_transcript=get_gene_canonical_tx(gene=gene_obj),
         build_str=build_str,
         hgvs_identifier=quote(hgvs_raw),
     )

scout/server/templates/report_base.html

@@ -6,6 +6,7 @@
 	{% block css %}
   <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-1BmE4kWBq78iYhFldvKuhfTAU6auU8tT94WrHftjDbrCEXSU1oBoqyl2QvZ6jIW3" crossorigin="anonymous">
   <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/all.min.css" integrity="sha512-1ycn6IcaQQ40/MKBW2W4Rhis/DbILU74C1vSrLJxCq57o941Ym01SwNsOMqvEBFlcgUa6xLiPY/NS5R+E6ztJQ==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+  <link rel="stylesheet" href="{{ url_for('static', filename='bs_styles.css') }}">
     <style>
 		tr.light-grey td{
 			background-color: LightGray;

scout/utils/convert.py

@@ -53,7 +53,7 @@ def amino_acid_residue_change_3_to_1(protein_sequence_name):
     if protein_sequence_name is None:
         return None
 
-    p = re.compile("p.([A-Za-z]+)(\d+)([A-Za-z]+)")
+    p = re.compile(r"p\.([A-Za-z]+)(\d+)([A-Za-z]+)")
     m = p.match(protein_sequence_name)
     if m is None:
         return None

scout/utils/date.py

@@ -11,7 +11,7 @@ def match_date(date):
     Returns:
         bool
     """
-    date_pattern = re.compile("^(19|20)\d\d[- /.](0[1-9]|1[012])[- /.](0[1-9]|[12][0-9]|3[01])")
+    date_pattern = re.compile(r"^(19|20)\d\d[- /.](0[1-9]|1[012])[- /.](0[1-9]|[12][0-9]|3[01])")
     if re.match(date_pattern, date):
         return True
 

{scout_browser-4.88.1.dist-info → scout_browser-4.89.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.88.1
+Version: 4.89
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson