scout-browser 4.101.0__py3-none-any.whl → 4.102.0__py3-none-any.whl

scout/server/blueprints/cases/views.py

@@ -36,6 +36,7 @@ from scout.server.utils import (
     html_to_pdf_file,
     institute_and_case,
     jsonconverter,
+    safe_redirect_back,
     templated,
     user_cases,
     user_institutes,
@@ -148,7 +149,7 @@ def beacon_add_variants(institute_id, case_name):
         store, institute_id, case_name
     )  # This function checks if user has permissions to access the case
     beacon.add_variants(store, case_obj, request.form)
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/beacon_remove_variants/<institute_id>/<case_name>", methods=["GET"])
@@ -158,7 +159,7 @@ def beacon_remove_variants(institute_id, case_name):
         store, institute_id, case_name
     )  # This function checks if user has permissions to access the case
     beacon.remove_variants(store, institute_id, case_obj)
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/mme_matches", methods=["GET", "POST"])
@@ -175,7 +176,7 @@ def matchmaker_match(institute_id, case_name, target):
     """Starts an internal match or a match against one or all MME external nodes"""
     institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
     match_results = controllers.matchmaker_match(request, target, institute_id, case_name)
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/mme_add", methods=["POST"])
@@ -183,7 +184,7 @@ def matchmaker_add(institute_id, case_name):
     """Add or update a case in MatchMaker"""
     # Call matchmaker_delete controller to add a patient to MatchMaker
     controllers.matchmaker_add(request, institute_id, case_name)
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/mme_delete", methods=["POST"])
@@ -191,7 +192,7 @@ def matchmaker_delete(institute_id, case_name):
     """Remove a case from MatchMaker"""
     # Call matchmaker_delete controller to delete a patient from MatchMaker
     controllers.matchmaker_delete(request, institute_id, case_name)
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/individuals", methods=["POST"])
@@ -212,7 +213,7 @@ def update_individual(institute_id, case_name):
         age=age,
         tissue=tissue,
     )
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/samples", methods=["POST"])
@@ -237,7 +238,7 @@ def update_cancer_sample(institute_id, case_name):
         tumor_type=tumor_type,
         tumor_purity=tumor_purity,
     )
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/synopsis", methods=["POST"])
@@ -247,7 +248,7 @@ def case_synopsis(institute_id, case_name):
     user_obj = store.user(current_user.email)
     new_synopsis = request.form.get("synopsis")
     controllers.update_synopsis(store, institute_obj, case_obj, user_obj, new_synopsis)
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/api/v1/<institute_id>/<case_name>/case_report", methods=["GET"])
@@ -344,7 +345,7 @@ def mt_report(institute_id, case_name):
     shutil.rmtree(temp_excel_dir)
 
     flash("No MT report excel file could be exported for this sample", "warning")
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/diagnose", methods=["POST"])
@@ -366,7 +367,7 @@ def case_diagnosis(institute_id, case_name):
         affected_inds=affected_inds,
         remove=True if request.args.get("remove") == "yes" else False,
     )
-    return redirect("#".join([link, "disease_assign"]))
+    return safe_redirect_back(request, "#".join([link, "disease_assign"]))
 
 
 @cases_bp.route("/<institute_id>/<case_name>/phenotypes", methods=["POST"])
@@ -414,7 +415,7 @@ def phenotypes(institute_id, case_name, phenotype_id=None):
             )
             return redirect(case_url)
 
-    return redirect("#".join([case_url, "phenotypes_panel"]))
+    return safe_redirect_back(request, "#".join([case_url, "phenotypes_panel"]))
 
 
 @cases_bp.route("/<institute_id>/<case_name>/phenotype_export", methods=["POST"])
@@ -526,7 +527,7 @@ def phenotypes_actions(institute_id, case_name):
         hgnc_ids = [result[0] for result in results if result[1] >= hpo_count]
         store.update_dynamic_gene_list(case_obj, hgnc_ids=hgnc_ids, phenotype_ids=hpo_ids)
 
-    return redirect("#".join([case_url, "phenotypes_panel"]))
+    return safe_redirect_back(request, "#".join([case_url, "phenotypes_panel"]))
 
 
 @cases_bp.route("/<institute_id>/<case_name>/events", methods=["POST"])
@@ -567,7 +568,7 @@ def events(institute_id, case_name, event_id=None):
             # create a case comment
             store.comment(institute_obj, case_obj, user_obj, link, content=content)
 
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/status", methods=["POST"])
@@ -588,7 +589,7 @@ def status(institute_id, case_name):
     if tags or case_obj.get("tags") and tags != case_obj.get("tags"):
         store.tag_case(institute_obj, case_obj, user_obj, tags, link)
 
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/assign", methods=["POST"])
@@ -605,7 +606,7 @@ def assign(institute_id, case_name, user_id=None, inactivate=False):
         store.unassign(institute_obj, case_obj, user_obj, link, inactivate)
     else:
         store.assign(institute_obj, case_obj, user_obj, link)
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/api/v1/cases", defaults={"institute_id": None})
@@ -688,7 +689,7 @@ def pin_variant(institute_id, case_name, variant_id):
         store.pin_variant(institute_obj, case_obj, user_obj, link, variant_obj)
     elif request.form["action"] == "DELETE":
         store.unpin_variant(institute_obj, case_obj, user_obj, link, variant_obj)
-    return redirect(request.referrer or link)
+    return safe_redirect_back(request, request.referrer or link)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/<variant_id>/validate", methods=["POST"])
@@ -705,7 +706,7 @@ def mark_validation(institute_id, case_name, variant_id):
         variant_id=variant_id,
     )
     store.validate(institute_obj, case_obj, user_obj, link, variant_obj, validate_type)
-    return redirect(request.referrer or link)
+    return safe_redirect_back(request, request.referrer or link)
 
 
 @cases_bp.route(
@@ -748,8 +749,7 @@ def mark_causative(institute_id, case_name, variant_id, partial_causative=False)
             store.unmark_causative(institute_obj, case_obj, user_obj, link, variant_obj)
 
     # send the user back to the case that was marked as solved
-    case_url = url_for(".case", institute_id=institute_id, case_name=case_name)
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/check-case", methods=["POST"])
@@ -761,7 +761,7 @@ def check_case(institute_id, case_name):
     store.case_collection.find_one_and_update(
         {"_id": case_obj["_id"]}, {"$set": {"needs_check": False}}
     )
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/report/<report_type>")
@@ -835,7 +835,7 @@ def share(institute_id, case_name):
     except ValueError as ex:
         flash(str(ex), "warning")
 
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/update_rerun_status")
@@ -846,7 +846,7 @@ def update_rerun_status(institute_id, case_name):
     link = url_for("cases.case", institute_id=institute_id, case_name=case_name)
 
     store.update_rerun_status(institute_obj, case_obj, user_obj, link)
-    return redirect(link)
+    return safe_redirect_back(request, link)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/monitor", methods=["POST"])
@@ -860,7 +860,7 @@ def rerun_monitor(institute_id, case_name):
     else:
         store.unmonitor(institute_obj, case_obj, user_obj, link)
 
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/reanalysis", methods=["POST"])
@@ -876,7 +876,7 @@ def reanalysis(institute_id, case_name):
         LOG.error(msg)
         flash(msg, "danger")
 
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/research", methods=["POST"])
@@ -886,7 +886,7 @@ def research(institute_id, case_name):
     user_obj = store.user(current_user.email)
     link = url_for(".case", institute_id=institute_id, case_name=case_name)
     store.open_research(institute_obj, case_obj, user_obj, link)
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/reset_research", methods=["GET"])
@@ -895,7 +895,7 @@ def reset_research(institute_id, case_name):
     user_obj = store.user(current_user.email)
     link = url_for(".case", institute_id=institute_id, case_name=case_name)
     store.reset_research(institute_obj, case_obj, user_obj, link)
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/cohorts", methods=["POST"])
@@ -909,7 +909,7 @@ def cohorts(institute_id, case_name):
         store.remove_cohort(institute_obj, case_obj, user_obj, link, cohort_tag)
     else:
         store.add_cohort(institute_obj, case_obj, user_obj, link, cohort_tag)
-    return redirect("#".join([request.referrer, "cohorts"]))
+    return safe_redirect_back(request, "#".join([request.referrer, "cohorts"]))
 
 
 @cases_bp.route("/<institute_id>/<case_name>/default-panels", methods=["POST"])
@@ -917,7 +917,7 @@ def default_panels(institute_id, case_name):
     """Update default panels for a case."""
     panel_ids = request.form.getlist("panel_ids")
     controllers.update_default_panels(store, current_user, institute_id, case_name, panel_ids)
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/update-clinical-filter-hpo", methods=["POST"])
@@ -928,7 +928,7 @@ def update_clinical_filter_hpo(institute_id, case_name):
     controllers.update_clinical_filter_hpo(
         store, current_user, institute_obj, case_obj, hpo_clinical_filter
     )
-    return redirect(request.referrer)
+    return safe_redirect_back(request)
 
 
 @cases_bp.route("/<institute_id>/<case_name>/add_case_group", methods=["GET", "POST"])
@@ -943,8 +943,7 @@ def add_case_group(institute_id, case_name):
         case_name = request.form.get("other_case_name")
 
     controllers.add_case_group(store, current_user, institute_id, case_name, group_id)
-
-    return redirect(request.referrer + "#case_groups")
+    return safe_redirect_back(request, request.referrer + "#case_groups")
 
 
 @cases_bp.route("/<institute_id>/<case_name>/<case_group>/remove_case_group", methods=["GET"])
@@ -952,7 +951,7 @@ def remove_case_group(institute_id, case_name, case_group):
     """Unbind a case group from a case. Remove the group if it is no longer in use."""
     controllers.remove_case_group(store, current_user, institute_id, case_name, case_group)
 
-    return redirect(request.referrer + "#case_groups")
+    return safe_redirect_back(request, request.referrer + "#case_groups")
 
 
 @cases_bp.route("/<case_group>/case_group_update_label", methods=["POST"])
@@ -962,7 +961,7 @@ def case_group_update_label(case_group):
 
     controllers.case_group_update_label(store, case_group, label)
 
-    return redirect(request.referrer + "#case_groups")
+    return safe_redirect_back(request, request.referrer + "#case_groups")
 
 
 @cases_bp.route("/<institute_id>/<case_name>/download-hpo-genes/<category>", methods=["GET"])

scout/server/blueprints/clinvar/controllers.py

@@ -19,6 +19,7 @@ from scout.constants.variant_tags import MANUAL_RANK_OPTIONS
 from scout.models.clinvar import clinvar_variant
 from scout.server.blueprints.variant.utils import add_gene_info
 from scout.server.extensions import clinvar_api, store
+from scout.server.utils import get_case_genome_build
 from scout.utils.hgvs import validate_hgvs
 from scout.utils.scout_requests import fetch_refseq_version
 
@@ -30,7 +31,7 @@ LOG = logging.getLogger(__name__)
 def _get_var_tx_hgvs(case_obj: dict, variant_obj: dict) -> List[Tuple[str, str]]:
     """Retrieve all transcripts / HGVS for a given variant."""
 
-    build = str(case_obj.get("genome_build", "37"))
+    build = get_case_genome_build(case_obj)
     tx_hgvs_list = [("", "Do not specify")]
     case_has_build_37 = "37" in case_obj.get("genome_build", "37")
 
@@ -399,7 +400,7 @@ def json_api_submission(submission_id):
 
     # Retrieve genome build for the case submitted
     case_obj = store.case(case_id=variant_data[0].get("case_id")) or {"genome_build": 37}
-    extra_params["assembly"] = "GRCh37" if "37" in str(case_obj.get("genome_build")) else "GRCh38"
+    extra_params["assembly"] = "GRCh37" if "37" in get_case_genome_build(case_obj) else "GRCh38"
 
     def _write_file(afile, header, lines):  # Write temp CSV file
         writes = csv.writer(afile, delimiter=",", quoting=csv.QUOTE_ALL)

scout/server/blueprints/diagnoses/controllers.py

@@ -1,16 +1,13 @@
 # -*- coding: utf-8 -*-
 
 from scout.adapter import MongoAdapter
+from scout.constants import HPO_LINK_URL
 from scout.server.links import disease_link
 
 
-def disease_entry(store, disease_id) -> dict:
+def disease_entry(store: MongoAdapter, disease_id: str) -> dict:
     """Retrieve specific info for a disease term
 
-    Args:
-        store(obj): an adapter to the scout database
-        disease_id(str): a disease_id
-
     Returns:
         disease_obj(obj): a disease term containing description and genes
     """
@@ -21,6 +18,7 @@ def disease_entry(store, disease_id) -> dict:
         store.hpo_term(hpo_id) for hpo_id in disease_obj.get("hpo_terms", [])
     ]
     disease_obj["disease_link"] = disease_link(disease_id=disease_obj["disease_id"])
+    disease_obj["hpo_link_url"] = HPO_LINK_URL
     return disease_obj
 
 
@@ -43,6 +41,4 @@ def disease_terms(store: MongoAdapter, query: str, source: str) -> dict:
             )
         disease.update({"genes": gene_ids_symbols})
 
-    data = {"terms": list(disease_data)}
-
-    return data
+    return {"terms": list(disease_data)}

scout/server/blueprints/diagnoses/templates/diagnoses/diagnoses.html

@@ -95,7 +95,7 @@
     </td>
     <td id="hpo-container">
       <span class="text-body">
-        <a id="hpo-link" class="badge bg-secondary text-white m-1" href="https://hpo.jax.org/app/browse/term/{{term}}" target="_blank" rel="noopener" ></a>
+        <a id="hpo-link" class="badge bg-secondary text-white m-1" href="{{hpo_link_url}}{{term}}" target="_blank" rel="noopener" ></a>
       </span>
     </td>
   </tr>

scout/server/blueprints/diagnoses/templates/diagnoses/disease_term.html

@@ -47,7 +47,7 @@
           <ul class="list-group list-group-flush">
             {% for pheno in hpo_complete %}
               <li class="list-group-item">
-                <a href="http://hpo.jax.org/app/browse/term/{{pheno.hpo_id}}" target="_blank">{{ pheno.hpo_id }}</a>
+                <a href="{{hpo_link_url}}{{pheno.hpo_id}}" target="_blank">{{ pheno.hpo_id }}</a>
                 {{pheno.description}}
               </li>
             {% else %}

scout/server/blueprints/diagnoses/views.py

@@ -2,6 +2,7 @@ from typing import Union
 
 from flask import Blueprint, jsonify, request
 
+from scout.constants import HPO_LINK_URL
 from scout.server.extensions import store
 from scout.server.utils import public_endpoint, templated
 
@@ -30,8 +31,7 @@ def diagnosis(disease_id):
 def count_diagnoses():
     """Display the diagnosis counts for each coding system available in database"""
 
-    data = {"counts": store.disease_terminology_count()}
-    return data
+    return {"counts": store.disease_terminology_count(), "hpo_link_url": HPO_LINK_URL}
 
 
 @omim_bp.route("/api/v1/diagnoses")

scout/server/blueprints/institutes/controllers.py

@@ -25,7 +25,11 @@ from scout.server.blueprints.variant.utils import (
     update_representative_gene,
 )
 from scout.server.extensions import beacon, store
-from scout.server.utils import institute_and_case, user_institutes
+from scout.server.utils import (
+    get_case_genome_build,
+    institute_and_case,
+    user_institutes,
+)
 
 from .forms import BeaconDatasetForm, CaseFilterForm
 
@@ -47,6 +51,28 @@ VAR_SPECIFIC_EVENTS = [
     "cancel_sanger",
 ]
 
+# Projection for fetching cases
+ALL_CASES_PROJECTION = {
+    "analysis_date": 1,
+    "assignees": 1,
+    "beacon": 1,
+    "case_id": 1,
+    "display_name": 1,
+    "genome_build": 1,
+    "individuals": 1,
+    "is_rerun": 1,
+    "is_research": 1,
+    "mme_submission": 1,
+    "owner": 1,
+    "panels": 1,
+    "phenotype_terms": 1,
+    "rank_model_version": 1,
+    "status": 1,
+    "sv_rank_model_version": 1,
+    "track": 1,
+    "vcf_files": 1,
+}
+
 
 def get_timeline_data(limit):
     """Retrieve chronologially ordered events from the database to display them in the timeline page
@@ -519,92 +545,106 @@ def export_case_samples(institute_id, filtered_cases) -> Response:
     )
 
 
-def cases(store: MongoAdapter, request: request, institute_id: str) -> dict:
-    """Preprocess case objects for the 'cases' view."""
-    data = {}
+def get_cases_by_query(
+    store: MongoAdapter,
+    request: request,
+    institute_id: str,
+) -> list:
+    """Fetch additional cases based on filters given in request query form.
 
-    # Initialize data (institute info, filters, and case counts)
-    institute_obj = institute_and_case(store, institute_id)
-    data["institute"] = institute_obj
-    data["form"] = CaseFilterForm(request.form)
-    data["status_ncases"] = store.nr_cases_by_status(institute_id=institute_id)
-    data["nr_cases"] = sum(data["status_ncases"].values())
+    Sets metadata in data, e.g. sort order.
+    """
 
-    # Fetch Sanger unevaluated and validated cases
-    sanger_ordered_not_validated = get_sanger_unevaluated(store, institute_id, current_user.email)
-    data["sanger_unevaluated"], data["sanger_validated_by_others"] = sanger_ordered_not_validated
+    name_query = request.form
+    all_cases = store.cases(
+        collaborator=institute_id,
+        name_query=name_query,
+        skip_assigned=request.form.get("skip_assigned"),
+        is_research=request.form.get("is_research"),
+        has_rna_data=request.form.get("has_rna"),
+        verification_pending=request.form.get("validation_ordered"),
+        has_clinvar_submission=request.form.get("clinvar_submitted"),
+        projection=ALL_CASES_PROJECTION,
+    )
+    return all_cases
 
-    # Projection for fetching cases
-    ALL_CASES_PROJECTION = {
-        "analysis_date": 1,
-        "assignees": 1,
-        "beacon": 1,
-        "case_id": 1,
-        "display_name": 1,
-        "genome_build": 1,
-        "individuals": 1,
-        "is_rerun": 1,
-        "is_research": 1,
-        "mme_submission": 1,
-        "owner": 1,
-        "panels": 1,
-        "phenotype_terms": 1,
-        "rank_model_version": 1,
-        "status": 1,
-        "sv_rank_model_version": 1,
-        "track": 1,
-        "vcf_files": 1,
-    }
+
+def get_and_set_cases_by_status(
+    store: MongoAdapter,
+    request: request,
+    institute_obj: dict,
+    previous_query_result_cases: list,
+    data: dict,
+) -> dict:
+    """Process cases for statuses that require all cases to be shown.
+    Group cases by status, process additional cases for the remaining statuses
+    and ensure that we don't dim cases that already appeared in query search results.
+    """
+
+    status_show_all_cases = institute_obj.get("show_all_cases_status", ["prioritized"])
+    nr_cases_showall_statuses = 0
 
     # Group cases by status
     case_groups = {status: [] for status in CASE_STATUSES}
-    nr_cases_showall_statuses = 0
-    status_show_all_cases = institute_obj.get("show_all_cases_status") or ["prioritized"]
 
-    # Process cases for statuses that require all cases to be shown
     for status in status_show_all_cases:
         cases_in_status = store.cases_by_status(
-            institute_id=institute_id, status=status, projection=ALL_CASES_PROJECTION
+            institute_id=institute_obj["_id"], status=status, projection=ALL_CASES_PROJECTION
         )
         cases_in_status = _sort_cases(data, request, cases_in_status)
         for case_obj in cases_in_status:
             populate_case_obj(case_obj, store)
+            case_obj["dimmed_in_search"] = True
             case_groups[status].append(case_obj)
             nr_cases_showall_statuses += 1
 
-    # Fetch additional cases based on filters
-    name_query = request.form
-    limit = int(request.form.get("search_limit")) if request.form.get("search_limit") else 100
-    all_cases = store.cases(
-        collaborator=institute_id,
-        name_query=name_query,
-        skip_assigned=request.form.get("skip_assigned"),
-        is_research=request.form.get("is_research"),
-        has_rna_data=request.form.get("has_rna"),
-        verification_pending=request.form.get("validation_ordered"),
-        has_clinvar_submission=request.form.get("clinvar_submitted"),
-        projection=ALL_CASES_PROJECTION,
-    )
+    nr_name_query_matching_displayed_cases = 0
+    limit = int(request.form.get("search_limit", 100))
+    for case_obj in previous_query_result_cases:
+        if case_obj["status"] in status_show_all_cases:
+            for group_case in case_groups[status]:
+                if group_case["_id"] == case_obj["_id"]:
+                    group_case["dimmed_in_search"] = False
+        elif nr_name_query_matching_displayed_cases == limit:
+            break
+        else:
+            populate_case_obj(case_obj, store)
+            case_groups[case_obj["status"]].append(case_obj)
+            nr_name_query_matching_displayed_cases += 1
+
+    data["found_cases"] = nr_name_query_matching_displayed_cases + nr_cases_showall_statuses
+    data["limit"] = limit
+    return case_groups
+
+
+def cases(store: MongoAdapter, request: request, institute_id: str):
+    """Preprocess case objects for the 'cases' view.
+
+    Returns data dict for view display, or response in case of file export.
+    """
+    data = {}
+
+    # Initialize data (institute info, filters, and case counts)
+    institute_obj = institute_and_case(store, institute_id)
+    data["institute"] = institute_obj
+    data["form"] = CaseFilterForm(request.form)
+    data["status_ncases"] = store.nr_cases_by_status(institute_id=institute_id)
+    data["nr_cases"] = sum(data["status_ncases"].values())
+
+    # Fetch Sanger unevaluated and validated cases
+    sanger_ordered_not_validated = get_sanger_unevaluated(store, institute_id, current_user.email)
+    data["sanger_unevaluated"], data["sanger_validated_by_others"] = sanger_ordered_not_validated
+
+    all_cases = get_cases_by_query(store, request, institute_id)
     all_cases = _sort_cases(data, request, all_cases)
 
     if request.form.get("export"):
         return export_case_samples(institute_id, all_cases)
 
-    # Process additional cases for the remaining statuses
-    nr_cases = 0
-    for case_obj in all_cases:
-        if case_obj["status"] not in status_show_all_cases:
-            if nr_cases == limit:
-                break
-            populate_case_obj(case_obj, store)
-            case_groups[case_obj["status"]].append(case_obj)
-            nr_cases += 1
+    case_groups = get_and_set_cases_by_status(store, request, institute_obj, all_cases, data)
 
     # Compile the final data
     data["cases"] = [(status, case_groups[status]) for status in CASE_STATUSES]
-    data["found_cases"] = nr_cases + nr_cases_showall_statuses
-    data["limit"] = limit
-
     return data
 
 
@@ -615,7 +655,9 @@ def populate_case_obj(case_obj: dict, store: MongoAdapter):
         analysis_types = set(["mixed"])
     case_obj["analysis_types"] = list(analysis_types)
 
-    case_obj["assignees"] = [store.user(user_email) for user_email in case_obj.get("assignees", [])]
+    case_obj["assignees"] = [
+        store.user(user_id=user_id) for user_id in case_obj.get("assignees", [])
+    ]
 
     last_analysis_date = case_obj.get("analysis_date", datetime.datetime.now())
     all_analyses_dates = {
@@ -821,7 +863,7 @@ def gene_variants(store, pymongo_cursor, variant_count, page=1, per_page=50):
         case_display_name = variant_case_obj.get("display_name")
         variant_obj["case_display_name"] = case_display_name
 
-        genome_build = get_genome_build(variant_case_obj)
+        genome_build = get_case_genome_build(variant_case_obj)
         update_variant_genes(store, variant_obj, genome_build)
         variants.append(variant_obj)
 
@@ -885,14 +927,6 @@ def update_variant_genes(store, variant_obj, genome_build):
     variant_obj["functional_annotations"] = get_annotations(gene_symbols, functional_annotations)
 
 
-def get_genome_build(variant_case_obj):
-    """Find genom build in `variant_case_obj`. If not found use build #37"""
-    build = str(variant_case_obj.get("genome_build"))
-    if build in ["37", "38"]:
-        return build
-    return "37"
-
-
 def get_hgvs(gene_obj: Dict) -> Tuple[str, str, str]:
     """Analyse gene object for hgvs info
     Return:

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

@@ -63,7 +63,7 @@
 
 
 {% macro case_row(case) %}
-  <tr class="{% if case.status == 'solved' %}causative{% endif %}">
+  <tr class="{% if case.status == 'solved' %}causative{% elif case.dimmed_in_search %}dismiss{% endif %}">
     <td>
       <a class="me-2"
          {% if case.individuals|length == 1 %} data-bs-toggle="tooltip" title="{{case.individuals[0].display_name}}" {% endif %}

scout/server/blueprints/login/controllers.py

@@ -98,7 +98,7 @@ def google_login() -> Optional[Response]:
 
     redirect_uri: str = url_for("login.authorized", _external=True)
     try:
-        return oauth_client.google.authorize_redirect(redirect_uri)
+        return oauth_client.google.authorize_redirect(redirect_uri, prompt="select_account")
     except Exception:
         flash("An error has occurred while logging in user using Google OAuth", "warning")
         return None
@@ -151,6 +151,7 @@ def perform_flask_login(user_dict: "LoginUser") -> Response:
 
 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