scout-browser 4.98.0__py3-none-any.whl → 4.100.0__py3-none-any.whl

scout/server/blueprints/login/controllers.py

@@ -1,22 +1,20 @@
 import logging
+from datetime import datetime
+from typing import Optional
 
-from flask import current_app, flash
+import requests
+from flask import Response, current_app, flash, redirect, session, url_for
+from flask_login import login_user
 
-from scout.server.extensions import ldap_manager
-
-LOG = logging.getLogger(__name__)
+from scout.server.extensions import ldap_manager, oauth_client, store
 
+from .models import LoginUser
 
-def ldap_authorized(userid, password):
-    """Log in a LDAP user
+LOG = logging.getLogger(__name__)
 
-    Args:
-        userid(str): user id provided in ldap login form (usually and email)
-        password(str): user passord provided in ldap loding form
 
-    Returns:
-        authorized(bool): True or False
-    """
+def ldap_authorized(userid: str, password: str) -> bool:
+    """Log in an LDAP user."""
     authorized = False
     try:
         authorized = ldap_manager.authenticate(
@@ -63,3 +61,105 @@ def users(store):
     return dict(
         users=sorted(user_objs, key=lambda user: -user["events"]),
     )
+
+
+def user_has_consented(user_consent: Optional[str]) -> bool:
+    """Check if user has given consent for activity logging."""
+    if not current_app.config.get("USERS_ACTIVITY_LOG_PATH"):
+        return True
+
+    if user_consent 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 False
+    return True
+
+
+def ldap_login(ldap_user: Optional[str], ldap_password: Optional[str]) -> Optional[str]:
+    """Authenticate user via LDAP and return user ID if authorized."""
+
+    if not ldap_user or not ldap_password:
+        return None
+
+    authorized: bool = ldap_authorized(ldap_user, ldap_password)
+
+    if authorized:
+        return ldap_user
+
+    flash("User not authorized by LDAP server", "warning")
+
+
+def google_login() -> Optional[Response]:
+    """Authenticate user via Google OIDC and redirect to the redirect URI. The name of this endpoint should be present on the Google login settings."""
+    if "email" in session:
+        return redirect(url_for("public.login"))  # Redirect to the login route with session info
+
+    redirect_uri: str = url_for("login.authorized", _external=True)
+    try:
+        return oauth_client.google.authorize_redirect(redirect_uri)
+    except Exception:
+        flash("An error has occurred while logging in user using Google OAuth", "warning")
+        return None
+
+
+def keycloak_login() -> Optional[Response]:
+    """Authenticate user via Keycloak OIDC and redirect to the redirect URI. The name of this endpoint should be present on the Keycloak login settings."""
+
+    redirect_uri: str = url_for("login.authorized", _external=True)
+    try:
+        return oauth_client.keycloak.authorize_redirect(redirect_uri)
+    except Exception:
+        flash("An error has occurred while logging in user using Keycloak", "warning")
+        return None
+
+
+def database_login(user_mail: Optional[str]) -> Optional[str]:
+    """Authenticate user against the Scout database and return email if successful."""
+    return user_mail
+
+
+def validate_and_login_user(user_mail: Optional[str], user_id: Optional[str]) -> Response:
+    """Validate user in Scout database and log them in."""
+    user_obj: Optional[dict] = store.user(email=user_mail, user_id=user_id)
+
+    if user_obj is None:
+        flash("User not found in Scout database", "warning")
+        session.pop("email", None)
+        return redirect(url_for("public.index"))
+
+    user_obj["accessed_at"] = datetime.now()
+
+    if session.get("name"):  # Set name & locale if available (Google Auth)
+        user_obj["name"] = session.get("name")
+        user_obj["locale"] = session.get("locale")
+
+    store.update_user(user_obj)
+    return perform_flask_login(LoginUser(user_obj))
+
+
+def perform_flask_login(user_dict: "LoginUser") -> Response:
+    """Login user using Flask-Login."""
+    if login_user(user_dict, remember=True):
+        flash(f"Welcome {user_dict.name}", "success")
+        return redirect(url_for("cases.index"))
+
+    flash("Sorry, you could not log in", "warning")
+    return redirect(url_for("public.index"))
+
+
+def logout_oidc_user(session, provider: str):
+    """Log out a user from an OIDC login provider-"""
+    logout_url = current_app.config[provider].get("logout_url")
+    if not logout_url or not session.get("token_response"):
+        return
+    refresh_token = session["token_response"]["refresh_token"]
+    requests.post(
+        logout_url,
+        data={
+            "client_id": current_app.config[provider]["client_id"],
+            "client_secret": current_app.config[provider]["client_secret"],
+            "refresh_token": refresh_token,
+        },
+    )

scout/server/blueprints/login/views.py

@@ -1,9 +1,10 @@
 # -*- coding: utf-8 -*-
 import logging
-from datetime import datetime
+from typing import Optional
 
 from flask import (
     Blueprint,
+    Response,
     current_app,
     flash,
     redirect,
@@ -45,82 +46,67 @@ def load_user(user_id):
 
 @login_bp.route("/login", methods=["GET", "POST"])
 @public_endpoint
-def login():
+def login() -> Response:
     """Login a user if they have access."""
 
-    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
+    if controllers.user_has_consented(user_consent=request.form.get("consent_checkbox")) is False:
+        return redirect(url_for("public.index"))
 
-    user_id = None
-    user_mail = None
+    user_id: Optional[str] = None
+    user_mail: Optional[str] = None
 
     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")
+        user_id = controllers.ldap_login(
+            ldap_user=request.form.get("ldap_user"), ldap_password=request.form.get("ldap_password")
         )
-        if ldap_authorized is True:
-            user_id = request.form.get("ldap_user")
-        else:
-            flash("User not authorized by LDAP server", "warning")
+        if user_id is None:
             return redirect(url_for("public.index"))
 
     elif current_app.config.get("GOOGLE"):
         if session.get("email"):
             user_mail = session["email"]
-            session.pop("email", None)
         else:
-            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")
-
-    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)
-    if user_obj is None:
-        flash("User not found in Scout database", "warning")
-        return redirect(url_for("public.index"))
+            # Redirect to Google OAuth if not completed
+            return controllers.google_login()
+
+    elif current_app.config.get("KEYCLOAK"):
+        if session.get("email"):
+            user_mail = session["email"]
+        else:
+            return controllers.keycloak_login()
 
-    user_obj["accessed_at"] = datetime.now()
-    if session.get("name"):  # These args come from google auth
-        user_obj["name"] = session.get("name")
-        user_obj["locale"] = session.get("locale")
-    store.update_user(user_obj)
+    elif request.form.get("email"):
+        user_mail = controllers.database_login(user_mail=request.form.get("email"))
 
-    user_dict = LoginUser(user_obj)
-    return perform_login(user_dict)
+    return controllers.validate_and_login_user(user_mail=user_mail, user_id=user_id)
 
 
 @login_bp.route("/authorized")
 @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()
-    session["name"] = google_user.get("name")
-    session["locale"] = google_user.get("locale")
+    """OIDC callback function."""
+    if current_app.config.get("GOOGLE"):
+        client = oauth_client.google
+    if current_app.config.get("KEYCLOAK"):
+        client = oauth_client.keycloak
+    token = client.authorize_access_token()
+    user = client.parse_id_token(token, None)
+
+    session["email"] = user.get("email").lower()
+    session["name"] = user.get("name")
+    session["locale"] = user.get("locale")
+    session["token_response"] = token
 
     return redirect(url_for(".login"))
 
 
 @login_bp.route("/logout")
 def logout():
-    logout_user()
-    session.pop("email", None)
-    session.pop("name", None)
-    session.pop("locale", None)
-    session.pop("consent_given", None)
+    logout_user()  # logs out user from scout
+    for provider in ["GOOGLE", "KEYCLOAK"]:
+        if current_app.config.get(provider):
+            controllers.logout_oidc_user(session, provider)
+    session.clear()
     flash("you logged out", "success")
     return redirect(url_for("public.index"))
 
@@ -130,11 +116,3 @@ def users():
     """Show all users in the system."""
     data = controllers.users(store)
     return render_template("login/users.html", **data)
-
-
-def perform_login(user_dict):
-    if login_user(user_dict, remember=True):
-        flash("you logged in as: {}".format(user_dict.name), "success")
-        return redirect(url_for("cases.index"))
-    flash("sorry, you could not log in", "warning")
-    return redirect(url_for("public.index"))

scout/server/blueprints/mme/__init__.py

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

scout/server/blueprints/mme/controllers.py

@@ -0,0 +1,18 @@
+from typing import List
+
+from scout.server.extensions import store
+
+
+def institute_mme_cases(institute_id: str) -> List[dict]:
+    """Retrieves all cases for a given institute with an active MatchMaker Exchange submission."""
+    institute_mme_events = store.institute_events_by_verb(
+        category="case", institute_id=institute_id, verb="mme_add"
+    )
+    unique_case_ids = set([event["case"] for event in institute_mme_events])
+    mme_cases = []
+    for case_id in unique_case_ids:
+        case_obj = store.case(case_id=case_id)
+        if not case_obj or not case_obj.get("mme_submission"):
+            continue
+        mme_cases.append(case_obj)
+    return mme_cases

scout/server/blueprints/mme/templates/mme/mme_submissions.html

@@ -0,0 +1,153 @@
+{% extends "layout.html" %}
+{% from "overview/institute_sidebar.html" import institute_actionbar %}
+{% from "utils.html" import db_table_external_scripts, db_table_external_stylesheets %}
+
+{% block title %}
+{{ super() }} - Institutes
+{% endblock %}
+
+{% block css %}
+{{ super() }}
+ {{ db_table_external_stylesheets() }}
+{% endblock %}
+
+{% block top_nav %}
+  {{ super() }}
+  <li class="nav-item">
+    <a class="nav-link" href="{{ url_for('cases.index') }}">Institutes</a>
+  </li>
+  <li class="nav-item">
+    <a class="nav-link" href="{{ url_for('overview.cases', institute_id=institute._id) }}">{{ institute.display_name }}</a>
+  </li>
+  <li class="nav-item active d-flex align-items-center">
+    <span class="navbar-text">Cases in MatchMaker Exchange</span>
+  </li>
+{% endblock %}
+
+{% block content_main %}
+<div class="container-float">
+  <div class="row mt-3" id="body-row"> <!--sidebar and main container are on the same row-->
+    <div class="col">
+      {{ mme_submitted() }}
+    </div>
+  </div>
+</div>
+{% endblock %}
+
+{% macro mme_submitted() %}
+<table class="table table-bordered table-striped" id="mmeTable">
+  <thead>
+    <tr>
+      <th>Case Name</th>
+      <th>Synopsis</th>
+      <th>Status</th>
+      <th>Case Assignees</th>
+      <th>MME Submission Updated</th>
+      <th>MME Patient(s)</th>
+      <th>MME Phenotype Features</th>
+      <th>MME Genomic Features</th>
+    </tr>
+  </thead>
+  <tbody>
+    {% for case in mme_cases %}
+      <tr>
+        <td>
+          <a class="me-2" href="{{ url_for('cases.case', institute_id=case.owner, case_name=case.display_name) }}" target="_blank" rel="noopener">
+          {{ case.display_name }}
+          </a>
+        </td>
+        <td class="synopsis-cell" style="max-width: 300px;">
+          {% set collapse_id = 'collapse-' + case._id %}
+          {% set max_chars = 300 %}
+
+          {% if case.synopsis|length > max_chars %}
+            <div>
+              {{ case.synopsis[:max_chars] }}…
+            </div>
+
+            <a
+              class="btn btn-link p-0"
+              data-bs-toggle="collapse"
+              href="#{{ collapse_id }}"
+              role="button"
+              aria-expanded="false"
+              aria-controls="{{ collapse_id }}"
+            >More…</a>
+
+            <div class="collapse mt-1" id="{{ collapse_id }}">
+              <div class="card card-body p-2">
+                {{ case.synopsis }}
+              </div>
+            </div>
+          {% else %}
+            {{ case.synopsis }}
+          {% endif %}
+        </td>
+        <td>{{ case.status }}</td>
+        <td>
+          {% for assignee in case.assignees %}
+            <div>{{ assignee }}</div>
+          {% endfor %}
+        </td>
+        <td>
+          {{ case.mme_submission.updated_at.strftime('%Y-%m-%d %H:%M') }}
+        </td>
+        <td>
+          {% for patient in case.mme_submission.patients %}
+            <div>
+              <strong>{{ patient.label }}</strong> ({{ patient.sex }})<br>
+              <small>Contact: {{ patient.contact.name }} - <a href="{{ patient.contact.href }}">{{ patient.contact.href }}</a></small>
+            </div>
+          {% endfor %}
+        </td>
+        <td>
+          {% for disorder in case.mme_submission.disorders %}
+            <div>{{ disorder.label }} ({{ disorder.id }})</div>
+          {% endfor %}
+        </td>
+        <td>
+          {% for patient in case.mme_submission.patients %}
+            {% for gf in patient.genomicFeatures %}
+              <div>
+                <strong>{{ gf.gene.id }}</strong><br>
+                {% if gf.variant %}
+                  Chr{{ gf.variant.referenceName }}:
+                  {{ gf.variant.start|human_longint|safe }}-{{ gf.variant.end|human_longint|safe }}<br>
+                  {{ gf.variant.referenceBases }} → {{ gf.variant.alternateBases }}<br>
+                  Assembly: {{ gf.variant.assembly }}<br>
+                  Zygosity: {{ gf.zygosity }}
+                {% endif %}
+              </div>
+              <hr>
+            {% endfor %}
+          {% endfor %}
+        </td>
+      </tr>
+    {% endfor %}
+  </tbody>
+</table>
+{% endmacro %}
+
+
+{% block scripts %}
+  {{ super() }}
+    {{ db_table_external_scripts() }}
+  <script>
+    $(document).ready(function () {
+    $('#mmeTable').DataTable({
+      paging: true,
+      searching: true,
+      ordering: true,
+      responsive: true,
+      language: {
+        search: "Search all fields:",
+        lengthMenu: "Show _MENU_ entries",
+        info: "Showing _START_ to _END_ of _TOTAL_ cases",
+      },
+      columnDefs: [
+        { orderable: false, targets: [3, 5, 6, 7] }  // Disable sorting for multi-line complex columns
+      ]
+    });
+  });
+  </script>
+{% endblock %}

scout/server/blueprints/mme/views.py

@@ -0,0 +1,34 @@
+import logging
+
+from flask import (
+    Blueprint,
+    render_template,
+    url_for,
+)
+
+from scout.server.extensions import store
+from scout.server.utils import institute_and_case
+
+from . import controllers
+
+LOG = logging.getLogger(__name__)
+
+mme_bp = Blueprint(
+    "mme",
+    __name__,
+    template_folder="templates",
+    static_folder="static",
+    static_url_path="/mme/static",
+)
+
+
+@mme_bp.route("/<institute_id>/mme_submissions", methods=["GET"])
+def mme_submissions(institute_id: str):
+    """Retrieve all cases for an institute with associated a MME submission."""
+
+    institute_obj = institute_and_case(store, institute_id)
+    data = {
+        "institute": institute_obj,
+        "mme_cases": controllers.institute_mme_cases(institute_id=institute_id),
+    }
+    return render_template("mme/mme_submissions.html", **data)

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

@@ -10,12 +10,25 @@
   <li class="nav-item">
     <a class="nav-link" href="{{ url_for('cases.index') }}">Institutes</a>
   </li>
-  <li class="nav-item">
-    <a class="nav-link" href="{{ url_for('panels.panels') }}">Gene Panels</a>
-  </li>
-  <li class="nav-item active d-flex align-items-center">
-    <span class="navbar-text">{{ panel.display_name }} {{ panel.version }}</span>
-  </li>
+  {% if case %}
+    <li class="nav-item">
+      <a class="nav-link" href="{{ url_for('overview.cases', institute_id=institute._id) }}">
+        {{ institute.display_name }}
+      </a>
+    </li>
+    <li class="nav-item d-flex align-items-center">
+      <a class="nav-link" href="{{ url_for('cases.case', institute_id=institute._id, case_name=case.display_name) }}">
+        {{ case.display_name }}
+      </a>
+    </li>
+  {% else %}
+    <li class="nav-item">
+      <a class="nav-link" href="{{ url_for('panels.panels') }}">Gene Panels</a>
+    </li>
+  {% endif %}
+    <li class="nav-item active d-flex align-items-center">
+      <span class="navbar-text">{{ panel.display_name }} {{ panel.version }}</span>
+    </li>
 {% endblock %}
 
 {% block content_main %}

scout/server/blueprints/phenotypes/templates/phenotypes/hpo_terms.html

@@ -56,7 +56,14 @@
       $('#phenotypes_table').DataTable( {
           paging: true,
           pageLength: 50,
-          dom: 'fBrtip',
+          layout: {
+            topStart: 'buttons',
+            topEnd: {
+                search: {
+                    placeholder: 'Filter...'
+                }
+            }
+          },
           buttons: [
             {
               extend: 'excelHtml5',

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

@@ -21,7 +21,11 @@
       </p>
     {% else %}
       <form class="row" method="POST" action="{{ url_for('login.login') }}">
-        {% if config.GOOGLE %}
+        {% if config.KEYCLOAK %}
+          <button name="googleLogin" class="btn btn-primary btn-lg text-white" href="{{ url_for('login.login') }}" type="submit">
+            Login with Keycloak
+          </button>
+        {% elif config.GOOGLE %}
           <button name="googleLogin" class="btn btn-primary btn-lg text-white" href="{{ url_for('login.login') }}" type="submit">
             Login with Google
           </button>

scout/server/blueprints/variant/controllers.py

@@ -367,11 +367,13 @@ def variant(
     if variant_id in case_clinvars:
         variant_obj["clinvar_clinsig"] = case_clinvars.get(variant_id)["clinsig"]
 
-    overlapping_vars = []
+    overlapping_variants, overlapping_outliers = [], []
     if get_overlapping:
-        for var in store.overlapping(variant_obj):
+        overlapping_variants, overlapping_outliers = map(list, store.hgnc_overlapping(variant_obj))
+
+        for var in overlapping_variants:
             var.update(predictions(var.get("genes", [])))
-            overlapping_vars.append(var)
+
     variant_obj["end_chrom"] = variant_obj.get("end_chrom", variant_obj["chromosome"])
 
     dismiss_options = DISMISS_VARIANT_OPTIONS
@@ -395,7 +397,8 @@ def variant(
         "causatives": other_causatives,
         "managed_variant": managed_variant,
         "events": events,
-        "overlapping_vars": overlapping_vars,
+        "overlapping_vars": overlapping_variants,
+        "overlapping_outliers": overlapping_outliers,
         "manual_rank_options": MANUAL_RANK_OPTIONS,
         "cancer_tier_options": CANCER_TIER_OPTIONS,
         "dismiss_variant_options": dismiss_options,
@@ -406,9 +409,6 @@ def variant(
         "inherit_palette": INHERITANCE_PALETTE,
         "igv_tracks": get_igv_tracks("38" if variant_obj["is_mitochondrial"] else genome_build),
         "has_rna_tracks": case_has_rna_tracks(case_obj),
-        "gene_has_full_coverage": get_gene_has_full_coverage(
-            institute_obj, case_obj, variant_obj, genome_build
-        ),
         "gens_info": gens.connection_settings(genome_build),
         "evaluations": evaluations,
         "ccv_evaluations": ccv_evaluations,
@@ -416,16 +416,19 @@ def variant(
     }
 
 
-def get_gene_has_full_coverage(
-    institute_obj, case_obj, variant_obj, genome_build
-) -> Dict[int, bool]:
+def get_gene_has_full_coverage(institute_obj, case_obj, variant_obj) -> Dict[int, bool]:
     """
     Query chanjo2, if configured and d4 files are available for this case,
     for coverage completeness on the genes touching this variant.
     """
+    case_has_chanjo2_coverage(case_obj)
     if not case_obj.get("chanjo2_coverage"):
         return {}
 
+    genome_build = str(case_obj.get("genome_build", "37"))
+    if genome_build not in ["37", "38"]:
+        genome_build = "37"
+
     gene_has_full_coverage: dict = {
         hgnc_id: chanjo2.get_gene_complete_coverage(
             hgnc_id=hgnc_id,
@@ -653,6 +656,12 @@ def variant_acmg(store: MongoAdapter, institute_id: str, case_name: str, variant
         store, variant_obj, institute_id, case_name
     )
 
+    genome_build = str(case_obj.get("genome_build", "37"))
+    if genome_build not in ["37", "38"]:
+        genome_build = "37"
+
+    add_gene_info(store, variant_obj, genome_build=genome_build)
+
     return dict(
         institute=institute_obj,
         case=case_obj,

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

@@ -79,7 +79,11 @@
                       <div class="row">
                         <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" %}
+                          {% set sa_level = "Stand-alone" %}
+                          {% if category == "pathogenicity" %}
+                            {% set sa_level = "Very Strong" %}
+                          {% endif %}
+                          {% for level in sa_level, "Strong", "Moderate", "Supporting" %}
                             {% if(level != evidence) %}
                               <option id="{{ criterion_code }}-{{ level }}" value="{{ level }}" {% if modifier == level %}selected{% endif %}>{{ level }}</option>
                             {% endif %}
@@ -101,6 +105,15 @@
           </div>
         {% endfor %}
       </div>
+    <!-- external links -->
+    <div class="card panel-default mt-3">
+      <div class="card-body">
+        Search ClinGen Criteria Specifications (CSPEC):
+        {% for gene in variant.genes %}
+          <a href="{{ gene.cspec_link }}" class="btn btn-secondary text-white" rel="noopener" referrerpolicy="no-referrer" target="_blank">{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}</a>
+        {% endfor %}
+      </div>
+    </div>
     <!-- classification preview in the footer-->
       <div class="mt-3 fixed-bottom bg-light border">
         <div class="row">
@@ -148,7 +161,7 @@
 
     function update_classification() {
       var criteria = $(':checked').map(function(idx, elem) {
-        const modifiers = ["Strong", "Moderate", "Supporting"];
+        const modifiers = ["Stand-alone", "Very Strong", "Strong", "Moderate", "Supporting"];
         for (possible_modifier of modifiers) {
           var modifier_option;
           if(elem.value !== null && elem.value !== '') {