scout-browser 4.101.0__py3-none-any.whl → 4.103.0__py3-none-any.whl

scout/server/blueprints/clinvar/views.py

@@ -1,10 +1,11 @@
 import logging
 from json import dumps
 from tempfile import NamedTemporaryFile
-from typing import List, Tuple
+from typing import List, Optional, Tuple
 
 from flask import (
     Blueprint,
+    Response,
     flash,
     redirect,
     render_template,
@@ -18,9 +19,10 @@ from scout.constants.clinvar import (
     CASEDATA_HEADER,
     CLINVAR_HEADER,
     GERMLINE_CLASSIF_TERMS,
+    ONCOGENIC_CLASSIF_TERMS,
 )
 from scout.server.extensions import clinvar_api, store
-from scout.server.utils import institute_and_case
+from scout.server.utils import institute_and_case, safe_redirect_back
 
 from . import controllers
 
@@ -40,8 +42,13 @@ def clinvar_submission_status(submission_id):
     """Sends a request to ClinVar to retrieve and display the status of a submission."""
 
     # flash a message with current submission status for a ClinVar submission
+    clinvar_resp_status = dict(
+        clinvar_api.json_submission_status(
+            submission_id=submission_id, api_key=request.form.get("apiKey")
+        )
+    )
     flash(
-        f'Response from ClinVar: {clinvar_api.json_submission_status( submission_id=submission_id, api_key=request.form.get("apiKey"))}',
+        f"Response from ClinVar: {clinvar_resp_status}",
         "primary",
     )
     return redirect(request.referrer)
@@ -76,8 +83,8 @@ def clinvar_add_variant(institute_id, case_name):
 
 
 @clinvar_bp.route("/<institute_id>/<case_name>/clinvar/save", methods=["POST"])
-def clinvar_save(institute_id, case_name):
-    """Adds one variant with eventual CaseData observations to an open (or new) ClinVar submission"""
+def clinvar_save(institute_id: str, case_name: str):
+    """Adds one germline variant with eventual CaseData observations to an open (or new) ClinVar submission."""
     institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
     controllers.add_variant_to_submission(
         institute_obj=institute_obj, case_obj=case_obj, form=request.form
@@ -85,14 +92,14 @@ def clinvar_save(institute_id, case_name):
     return redirect(url_for("cases.case", institute_id=institute_id, case_name=case_name))
 
 
-@clinvar_bp.route("/<institute_id>/clinvar_submissions", methods=["GET"])
-def clinvar_submissions(institute_id):
+@clinvar_bp.route("/<institute_id>/clinvar_germline_submissions", methods=["GET"])
+def clinvar_germline_submissions(institute_id):
     """Handle clinVar submission objects and files"""
 
     institute_obj = institute_and_case(store, institute_id)
     institute_clinvar_submitters: List[str] = institute_obj.get("clinvar_submitters", [])
     data = {
-        "submissions": store.clinvar_submissions(institute_id),
+        "submissions": store.get_clinvar_germline_submissions(institute_id),
         "institute": institute_obj,
         "variant_header_fields": CLINVAR_HEADER,
         "casedata_header_fields": CASEDATA_HEADER,
@@ -131,24 +138,94 @@ def clinvar_update_submission(institute_id, submission):
 
 
 @clinvar_bp.route("/<submission>/download/json/<clinvar_id>", methods=["GET"])
-def clinvar_download_json(submission, clinvar_id):
-    """Download a json for a clinVar submission"""
+def clinvar_download_json(submission: str, clinvar_id: Optional[str]) -> Response:
+    """Download a json for a clinVar submission.
+
+    Accepts:
+        submission:. It's the _id of the submission in the database
+        clinvar_id: It's the submission number (i.e. SUB123456). Might be available or not in the submission dictionary
+
+    """
+    filename = clinvar_id if clinvar_id != "None" else submission
 
     code, conversion_res = controllers.json_api_submission(submission_id=submission)
 
     if code in [200, 201]:
         # Write temp CSV file and serve it in response
-        tmp_json = NamedTemporaryFile(mode="a+", prefix=clinvar_id, suffix=".json")
+        tmp_json = NamedTemporaryFile(mode="a+", prefix=filename, suffix=".json")
         tmp_json.write(dumps(conversion_res, indent=4))
 
         tmp_json.flush()
         tmp_json.seek(0)
         return send_file(
             tmp_json.name,
-            download_name=f"{clinvar_id}.json",
+            download_name=f"{filename}.json",
             mimetype="application/json",
             as_attachment=True,
         )
     else:
-        flash(f"JSON file could not be crated for ClinVar submission: {clinvar_id} ", "warning")
+        flash(
+            f"JSON file could not be crated for ClinVar submission: {filename}: {conversion_res}",
+            "warning",
+        )
         return redirect(request.referrer)
+
+
+### ClinVar oncogenicity variants submissions views
+
+
+@clinvar_bp.route("/<institute_id>/clinvar_onc_submissions", methods=["GET"])
+def clinvar_onc_submissions(institute_id):
+    """Handle clinVar submission objects and files"""
+
+    institute_obj = institute_and_case(store, institute_id)
+    institute_clinvar_submitters: List[str] = institute_obj.get("clinvar_submitters", [])
+    data = {
+        "submissions": list(store.get_clinvar_onc_submissions(institute_id)),
+        "institute": institute_obj,
+        "show_submit": current_user.email in institute_clinvar_submitters
+        or not institute_clinvar_submitters,
+    }
+    return render_template("clinvar/clinvar_onc_submissions.html", **data)
+
+
+@clinvar_bp.route("/<institute_id>/<case_name>/clinvar/clinvar_add_onc_variant", methods=["POST"])
+def clinvar_add_onc_variant(institute_id: str, case_name: str):
+    """Create a ClinVar submission document in database for one or more variants from a case."""
+    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
+    data = {
+        "institute": institute_obj,
+        "case": case_obj,
+        "onc_classif_terms": ONCOGENIC_CLASSIF_TERMS,
+    }
+    controllers.set_onc_clinvar_form(request.form.get("var_id"), data)
+    return render_template("clinvar/multistep_add_onc_variant.html", **data)
+
+
+@clinvar_bp.route(
+    "/<institute_id>/<case_name>/clinvar_onc/clinvar_save_onc_variant", methods=["POST"]
+)
+def clinvar_onc_save(institute_id: str, case_name: str):
+    """Adds one somatic variant with eventual CaseData observations to an open (or new) ClinVar congenicity submission"""
+    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
+    controllers.add_onc_variant_to_submission(
+        institute_obj=institute_obj, case_obj=case_obj, form=request.form
+    )
+    return redirect(url_for("cases.case", institute_id=institute_id, case_name=case_name))
+
+
+@clinvar_bp.route("/<submission>/clinvar_onc/delete_variant", methods=["POST"])
+def clinvar_delete_onc_variant(submission: str):
+    """Delete a single variant (oncogenicitySubmission) from the ClinVar submissions collection."""
+    store.delete_clinvar_onc_var(
+        submission=submission,
+        variant_id=request.form.get("delete_object"),
+    )
+    return safe_redirect_back(request)
+
+
+@clinvar_bp.route("/<submission>/download", methods=["GET"])
+def clinvar_download(submission):
+    """Download a json file for a clinVar submission. This function is only used for oncogenocity submissions for the time being"""
+
+    return store.get_onc_submission_json(submission)

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 +51,33 @@ VAR_SPECIFIC_EVENTS = [
     "cancel_sanger",
 ]
 
+# Query terms in default, non-specific queries for cases
+NONSPECIFIC_QUERY_TERMS = [
+    "collaborators",
+]
+
+# 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 +550,136 @@ 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,
+    )
 
-    # 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,
-    }
+    return all_cases
+
+
+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,
-    )
+    def get_specific_query(request: request) -> bool:
+        """Check if only non-specific query terms were used in query,
+        by yielding the query without actually executing it.
+
+        If so we assume this is a default query, and dim all cases
+        that match the "show_all_cases_status", highlighting the
+        (max limit number) other cases that were returned.
+
+        If this is a specific query, cases returned by this query part will be explicitly
+        highlighted even if they have a status that matches "show_all_cases_status".
+        """
+        cases_query: dict = store.cases(
+            collaborator=institute_obj["_id"],
+            name_query=request.form,
+            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"),
+            yield_query=True,
+        )
+        for key, value in cases_query.items():
+            if key not in NONSPECIFIC_QUERY_TERMS and value not in [None, ""]:
+                return True
+        return False
+
+    specific_query_asked = get_specific_query(request)
+
+    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:
+            if specific_query_asked:
+                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 +690,9 @@ 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 = {
@@ -626,7 +703,7 @@ def populate_case_obj(case_obj: dict, store: MongoAdapter):
         all_analyses_dates
     )
 
-    case_obj["clinvar_variants"] = store.case_to_clinVars(case_obj["_id"])
+    case_obj["clinvar_variants"] = store.case_to_clinvars(case_obj["_id"])
     case_obj["display_track"] = TRACKS.get(case_obj.get("track", "rare"))
 
 
@@ -788,7 +865,9 @@ def export_gene_variants(
         )  # CADD score
         variant_line.append(" | ".join(variant.get("region_annotations", [])))  # Region
         variant_line.append(" | ".join(variant.get("functional_annotations", [])))  # Function
-        variant_line.append(variant.get("hgvs", "-"))  # HGVS
+        variant_line.append(
+            " | ".join(current_app.custom_filters.format_variant_canonical_transcripts(variant))
+        )
 
         export_lines.append(",".join(variant_line))
 
@@ -818,10 +897,12 @@ def gene_variants(store, pymongo_cursor, variant_count, page=1, per_page=50):
     for variant_obj in variant_res:
         # Populate variant case_display_name
         variant_case_obj = store.case(case_id=variant_obj["case_id"])
+        if variant_case_obj is None:
+            continue
         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 +966,6 @@ 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/forms.py

@@ -152,6 +152,7 @@ class GeneVariantFiltersForm(FlaskForm):
         "HGNC Symbols (comma-separated, case sensitive)",
         validators=[validators.InputRequired()],
     )
+    institute = SelectMultipleField(choices=[])
     rank_score = IntegerField(default=15)
     phenotype_terms = TagListField("HPO terms (comma-separated)")
     phenotype_groups = TagListField("Phenotype groups")

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/institutes/templates/overview/gene_variants.html

@@ -2,7 +2,7 @@
 {% from "variants/components.html" import frequency_cell_general, variant_funct_anno_cell, variant_gene_symbols_cell %}
 {% from "utils.html" import comments_table %}
 {% from "overview/institute_sidebar.html" import institute_actionbar %}
-{% from "variants/utils.html" import pagination_footer, pagination_hidden_div %}
+{% from "variants/utils.html" import pagination_footer, pagination_hidden_div, variant_rank_score %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - All SNVs and INDELs
@@ -96,17 +96,22 @@
         {{ variant.sub_category|upper }}({{ variant.chromosome }}{{ variant.cytoband_start }}-{{ variant.end_chrom }}{{ variant.cytoband_end }})
        {% endif %}
   {% else %}
-    <a href="{{ url_for('variant.variant', institute_id=variant.institute,
+      <a href="{{ url_for('variant.variant', institute_id=variant.institute,
             case_name=variant.case_display_name, variant_id=variant._id) }}" target="_blank">
-    {{ (variant.hgvs or '')|url_decode }}
-  {% endif %}
-  </a>
+      {% set lines = variant | format_variant_canonical_transcripts %}
+      {% if lines | length > 1 %}
+        {{ lines | join('<br>') | safe }}
+      {% elif lines %}
+        {{ lines[0] }}
+      {% endif %}
+   {% endif %}
+   </a>
 {% endmacro %}
 
 {% macro cell_rank(variant) %}
    {{ variant.case_display_name }}
     :
-    <span class="badge bg-info">{{ variant.rank_score|int }}</span>
+    <span class="badge bg-info">{{ variant_rank_score(variant) }}</span>
 {% endmacro %}
 
 {% macro cell_cadd(variant) %}
@@ -130,6 +135,10 @@
           {{ form.hgnc_symbols.label(class="control-label") }}
           {{ form.hgnc_symbols(class="form-control") }}
         </div>
+        <div class="col col-md-2">
+          {{ form.institute.label(class="control-label") }}
+          {{ form.institute(class="form-control", class="selectpicker", data_style="btn-secondary") }}
+        </div>
         <div class="col col-md-1">
           <label class="control-label" for="rank_score">Rank Score</label>
           <input type="number" class="form-control" id="rank_score" name="rank_score" min="5" value={{form.rank_score.data}}>

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

@@ -44,12 +44,38 @@
       </a>
 
       <!-- ClinVar data menu item -->
-      <a href="{{ url_for('clinvar.clinvar_submissions', institute_id=institute._id) }}" class="bg-dark list-group-item list-group-item-action flex-column align-items-start">
+      <a href="#submenu1" aria-controls="submenu1" data-bs-toggle="collapse" aria-expanded="false" class="bg-dark list-group-item list-group-item-action flex-column align-items-start">
           <div class="d-flex w-100 justify-content-start align-items-center">
               <span class="fas fa-file-medical me-3"></span>
-              <span class="menu-collapsed">ClinVar submissions</span>
+              <span class="menu-collapsed text-nowrap flex-grow-1">ClinVar submissions</span>
+              <span class="submenu-icon ms-auto"></span>
           </div>
       </a>
+      <div id='submenu1' class="collapse sidebar-submenu">
+        <div href="#" class="bg-dark list-group-item text-white">
+
+          <div class="d-flex flex-row flex-fill bd-highlight">
+            <div>
+              <span class="menu-collapsed">Germline</span>
+            </div>
+            <div>
+              <a href="{{ url_for('clinvar.clinvar_germline_submissions', institute_id=institute._id) }}" target="_blank" rel="noopener">
+                    <span class="fa fa-link"></span></a>
+            </div>
+          </div>
+
+          <div class="d-flex flex-row flex-fill bd-highlight">
+            <div>
+              <span class="menu-collapsed">Oncogenic</span>
+            </div>
+            <div>
+              <a href="{{ url_for('clinvar.clinvar_onc_submissions', institute_id=institute._id) }}" target="_blank" rel="noopener">
+                    <span class="fa fa-link"></span></a>
+            </div>
+          </div>
+
+         </div>
+      </div>
 
      <!-- MME data menu item -->
       <a href="{{ url_for('mme.mme_submissions', institute_id=institute._id) }}" class="bg-dark list-group-item list-group-item-action flex-column align-items-start">

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

@@ -25,7 +25,7 @@
         </div>
         <div class="col-md-1 mb-3">
             {{ form.search_limit.label(class="form-label") }}
-            {{ form.search_limit(class="form-control") }}
+            {{ form.search_limit(class="form-control", type="number", min="1", step="1", required=True) }}
         </div>
         <div class="btn-sm mb-2 col-md-3 mx-auto">
           {{ form.search(class="btn btn-primary mt-4") }}