Added locus link-out for genoox Franklin. (#828)

Closes: #748
Related-Issue: #748
Projected-Results-Impact: none

HISTORY.rst

@@ -27,6 +27,7 @@ End-User Summary
 - Allow to upload per-case gene annotation (#575).
 - Adding varannos app (#747).
 - Adding ACMG v3.0 + v3.1 incidental findings to gene allowlist preset (#829).
+- Adding locus link-out to genoox Franklin (#748).
 
 Full Change List
 ================
@@ -55,6 +56,7 @@ Full Change List
 - Add missing directory in Dockerfile.
 - Adding varannos app (#747).
 - Adding ACMG v3.0 + v3.1 incidental findings to gene allowlist preset (#829).
+- Adding locus link-out to genoox Franklin (#748).
 
 
 -----------------
@@ -68,6 +70,7 @@ End-User Summary
 - Extra annotations in export completed and tested (#495).
 - Fixed bug where Exac and thousand genomes settings were not shown in frequency tab for GRCh37 (#597).
 - Form template reports error if genomebuild variable is not set (#607).
+- Added locus link-out for genoox Franklin (#748).
 
 Full Change List
 ================
@@ -76,6 +79,7 @@ Full Change List
 - Fixing issue with sync-from-remote when no remote is defined (#570).
 - Fixed bug where Exac and thousand genomes settings were not shown in frequency tab for GRCh37 (#597).
 - Form template reports error if genomebuild variable is not set (#607).
+- Added locus link-out for genoox Franklin (#748).
 
 -----------------
 v1.2.1 (anthenea)

svs/templates/svs/filter_result/row_sv.html

@@ -182,6 +182,15 @@
         <a class="dropdown-item" href="http://gnomad.broadinstitute.org/region/{{ first_entry.chromosome }}-{{ first_entry.start }}-{{ first_entry.end }}" target="_blank">
           Locus @gnomAD
         </a>
+        {% if first_entry.sv_type == "DEL" or first_entry.sv_type == "DUP" %}
+          <a class="dropdown-item" href="{% linkout_base_url "franklin_sv" first_entry.release %}{{ first_entry.chromosome }}-{{ first_entry.start }}-{{ first_entry.end }}-{{ first_entry.sv_type }}{% if first_entry.release == "GRCh38" %}-hg38{% endif %}" target="_blank">
+            Locus @Franklin
+          </a>
+        {% else %}
+          <a class="dropdown-item disabled">
+            Locus @Franklin
+          </a>
+        {% endif %}
       </div>
     </div>
   </td>

variants/templates/variants/filter_result/row.html

@@ -578,6 +578,17 @@
             </span>
           {% endif %}
 
+          {% linkout_available_for "franklin" entry.release as franklin_available %}
+          {% if franklin_available %}
+            <a class="dropdown-item" href="{% linkout_base_url "franklin" entry.release %}{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}{% if entry.release == "GRCh38" %}-hg38{% endif %}" target="_blank">
+            Locus @Franklin
+            </a>
+          {% else %}
+            <span class="dropdown-item disabled">
+              Locus @Franklin
+            </span>
+          {% endif %}
+
           {% if hgmd_pro_enabled %}
             <a class="dropdown-item" href="{{ hgmd_pro_prefix }}/gene.php?gene={{ symbol }}" target="_blank">
               Gene @HGMD Professional

variants/templatetags/variants_tags.py

@@ -554,6 +554,10 @@ def get_term_description(term):
     ("umd", "GRCh37"): "http://umd-predictor.eu/webservice.php?",
     ("varsome", "GRCh37"): "https://varsome.com/variant/hg19/chr",
     ("varsome", "GRCh38"): "https://varsome.com/variant/hg38/",
+    ("franklin", "GRCh37"): "https://franklin.genoox.com/clinical-db/variant/snp/chr",
+    ("franklin", "GRCh38"): "https://franklin.genoox.com/clinical-db/variant/snp/chr",
+    ("franklin_sv", "GRCh37"): "https://franklin.genoox.com/clinical-db/variant/sv/chr",
+    ("franklin_sv", "GRCh38"): "https://franklin.genoox.com/clinical-db/variant/sv/chr",
     ("variant_validator", "GRCh37"): True,  # no URL, via javascript
     ("variant_validator", "GRCh38"): True,  # no URL, via javascript
 }