scout-browser 4.100.2__py3-none-any.whl → 4.102.0__py3-none-any.whl

scout/server/blueprints/cases/templates/cases/utils.html

@@ -293,8 +293,18 @@
 
   {% if variant.category %}
     {% if variant.category in "str" %}
-      {{ variant.str_repid }} {{ variant.alternative | replace("<", " ") | replace(">", "")}}
-
+      {% if variant.str_repid %}
+        {{ variant.str_repid }}
+      {% elif variant.str_trid %}
+        {{ variant.str_trid  }}
+      {% else %}
+        {% for gene in variant.genes %} {{ gene.symbol }} {% endfor %}
+      {% endif %}
+      {% if variant.str_mc %}
+        STR{{ variant.str_mc }}
+      {% else %}
+        {{ variant.alternative|truncate(20,True) }}
+      {% endif %}
     {% elif variant.category in ("snv", "cancer") %}
       {% set display_genes = [] %}
       {% for gene in variant.genes %}
@@ -339,18 +349,24 @@
 {% macro pretty_link_variant(variant, case) %}
 {# Returns human readable links to the corresponding variant page #}
 
-  {% if variant.category in ("mei", "str", "snv", "cancer") %}
-    {% if variant.category == "cancer" %}
-    <a href='{{ url_for('variant.cancer_variant',
+  {% if variant.category in ("mei", "snv") %}
+    <a href='{{ url_for('variant.variant',
                    institute_id=variant.institute,
                    case_name=case.display_name,
                    variant_id=variant._id) }}' target='_blank'>
-    {% else %}
+  {% elif variant.category == "str" %}
     <a href='{{ url_for('variant.variant',
+                   institute_id=variant.institute,
+                   case_name=case.display_name,
+                   variant_id=variant._id) }}'
+       data-bs-toggle='tooltip'
+       title='{{ variant.alternative | replace("<", " ") | replace(">", "")}}'
+       target='_blank'>
+  {% elif variant.category == "cancer" %}
+    <a href='{{ url_for('variant.cancer_variant',
                    institute_id=variant.institute,
                    case_name=case.display_name,
                    variant_id=variant._id) }}' target='_blank'>
-    {% endif %}
   {% elif variant.category == "outlier" %}
     <a href='{{ url_for('omics_variants.outliers',
        institute_id=variant.institute, case_name=case.display_name) }}' target='_blank'>
@@ -360,7 +376,7 @@
                               case_name=case.display_name,
                               variant_id=variant._id) }}' target='_blank'>
   {% endif %}
-    {{ pretty_variant(variant) }}
+  {{ pretty_variant(variant) }}
   </a>
 {% endmacro %}
 
@@ -442,21 +458,7 @@
               <div class="row">
                 <div class="col">
                   <i class="far fa-check-circle"></i>
-                  {% if variant.category == "snv" %}
-                    <a href="{{ url_for('variant.variant',
-                                        institute_id=variant.institute,
-                                        case_name=case.display_name,
-                                        variant_id=variant._id) }}">
-                          {{ variant.hgnc_symbols|join(', ') }} (partial causative)
-  		             {% else %}
-          		      <a href="{{ url_for('variant.sv_variant',
-                                              institute_id=variant.institute,
-                                              case_name=case.display_name,
-                                              variant_id=variant._id) }}">
-  		              {{ variant.sub_category|upper }}({{ variant.chromosome }}{{ variant.cytoband_start }}-{{ variant.chromosome }}{{ variant.cytoband_end }})
-                    (partial causative)
-  		             {% endif %}
-                   </a>
+                  {{ pretty_link_variant(variant, case) }} (partial causative)
                 </div>
                 <div class="col-2" style="width:fit-content;">
                   {{ remove_form(url_for('cases.mark_causative',
@@ -495,7 +497,7 @@
                 </div>
                 <div class="col-8">
                   {% for hpo in variant_phenotypes.hpo_terms %}
-                    <a target="_blank" href="http://hpo.jax.org/app/browse/term/{{hpo.phenotype_id}}">
+                    <a target="_blank" href="https://hpo.jax.org/browse/term/{{hpo.phenotype_id}}">
                       <span class="badge badge-sm bg-info">{{hpo.phenotype_id}}</span>
                     </a>
                   {% else %}
@@ -627,7 +629,7 @@
                 (included in ClinVar submission)
             {% elif variant.category in ('cancer', 'cancer_sv') %}
                 <button data-bs-toggle='tooltip' data-bs-placement="bottom" title="Submission of somatic variants from Scout is temporarily suspended. We are working to harmonize submissions with changes introduced by ClinVar for this variant category." disabled >Add to ClinVar submission</button>
-            {% else %}
+            {% elif variant.category in ('snv', 'sv') %}
                 <button type="submit" name="var_id" value="{{variant._id}}" class="btn btn-secondary btn-sm" style="float: right;">Add to ClinVar submission</button>
             {% endif %}
         </form>

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")
 
@@ -40,33 +41,27 @@ def _get_var_tx_hgvs(case_obj: dict, variant_obj: dict) -> List[Tuple[str, str]]
         transcripts = gene.get("transcripts", [])
 
         for tx in transcripts:
-
             refseq_id = tx.get("refseq_id")
             coding_seq_name = tx.get("coding_sequence_name")
             if not (refseq_id and coding_seq_name):
                 continue  # Skip transcripts missing required fields
 
-            mane_select = tx.get("mane_select_transcript")
-            mane_plus_clinical = tx.get("mane_plus_clinical_transcript")
-
-            for refseq in tx.get("refseq_identifiers", []):
-                refseq_version = fetch_refseq_version(refseq)  # Adds version to a RefSeq ID
-                hgvs_simple = f"{refseq_version}:{coding_seq_name}"
-
-                refseq_is_mane_select = mane_select == refseq_version
-                refseq_is_mane_plus_clinical = mane_plus_clinical == refseq_version
-
-                # Transcript is validate only when conditions are met
-                validated = (
-                    validate_hgvs(build, hgvs_simple)
-                    if (case_has_build_37 or refseq_is_mane_select or refseq_is_mane_plus_clinical)
-                    else ""
-                )
-
-                label = f"{hgvs_simple}{'_validated_' if validated else ''}{'_mane-select_' if refseq_is_mane_select else ''}{'_mane-plus-clinical_' if refseq_is_mane_plus_clinical else ''}"
-
+            if case_has_build_37:
+                for refseq in tx.get("refseq_identifiers", []):
+                    refseq_version = fetch_refseq_version(refseq)
+                    hgvs_simple = f"{refseq_version}:{coding_seq_name}"
+                    validated = validate_hgvs(build, hgvs_simple)
+                    label = f"{hgvs_simple}{'_validated_' if validated else ''}"
+                    tx_hgvs_list.append((hgvs_simple, label))
+
+            else:  # build 38, collect only MANE Select or MANE Plus Clinical
+                mane_select = tx.get("mane_select_transcript")
+                mane_plus_clinical = tx.get("mane_plus_clinical_transcript")
+                if mane_select is None and mane_plus_clinical is None:
+                    continue
+                hgvs_simple = f"{mane_select or mane_plus_clinical}:{coding_seq_name}"
+                label = f"{hgvs_simple}{'_mane-select_' if mane_select else ''}{'_mane-plus-clinical_' if mane_plus_clinical else ''}"
                 tx_hgvs_list.append((hgvs_simple, label))
-
     return tx_hgvs_list
 
 
@@ -405,7 +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/clinvar/templates/clinvar/multistep_add_variant.html

@@ -154,8 +154,6 @@
                     {% endfor %}
                     </table>
 
-                    <span class="text-danger">HGVS validation is performed only for variants in build GRCh37 or MANE Select and MANE Plus Clinical transcripts. For any other available HGVS present in this list, manual validation can be performed using the VariantValidator link above.</span>
-
                     <br><br>
                     <!-- dbSNP identifier -->
                     {{variant_data.var_form.variations_ids.label(class="fw-bold, text-dark")}}

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")