Franklin variant link (#5041)

* Add button with variant Franklin link. * Fix code style issues with Black * Make specific link for cancer track * Fix code style issues with Black * Apply suggestions from code review to simplify track check Co-authored-by: Daniel Nilsson <[email protected]> * one more case_obj for the road * fix sonarcloud complaint * one more button to link * it could have said that before - probably did really --------- Co-authored-by: molu <[email protected]> Co-authored-by: Lint Action <[email protected]> Co-authored-by: Chiara Rasi <[email protected]>
Clinical-Genomics · Nov 19, 2024 · f3a9778 · f3a9778
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
 ## [unreleased]
 ### Added
+- Variant link to Franklin in database buttons (different depending on rare or cancer track)
 - MANE badges on list of variant's Genes/Transcripts/Proteins table, this way also SVs will display MANE annotations
 - Export variant type and callers-related info fields when exporting variants from variants pages
 - Cases advanced search on the dashboard page

diff --git a/scout/server/blueprints/variant/templates/variant/buttons.html b/scout/server/blueprints/variant/templates/variant/buttons.html
@@ -1,33 +1,34 @@
 {% macro database_buttons(variant) %}
 <div class="mt-3">
-  <a class="btn btn-sm btn-info text-white me-1 mb-1" role="button" href="{{ variant.swegen_link }}" target="_blank">SweGen</a>
-  <a class="btn btn-sm btn-info text-white me-1 mb-1" role="button" href="{{ variant.beacon_link }}" target="_blank">Beacon</a>
+  <a class="btn btn-sm btn-info text-white me-1 mb-1"  href="{{ variant.swegen_link }}" rel="noreferrer noopener" target="_blank">SweGen</a>
+  <a class="btn btn-sm btn-info text-white me-1 mb-1"  href="{{ variant.beacon_link }}" rel="noreferrer noopener" target="_blank">Beacon</a>
+    <a class="btn btn-sm btn-info text-white me-1 mb-1"  href="{{ variant.franklin_link }}" rel="noreferrer noopener" target="_blank">Franklin</a>
   {% if variant.cosmic_links %} <!-- This is a list of tuples : [(id1, link1), (id2, link2), ..] -->
     {% for cosmic_link in variant.cosmic_links %}
-      <a data-bs-toggle="tooltip" title="COSMIC" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" href="{{cosmic_link[1]}}" target="_blank">{{cosmic_link[0]}}</a>
+      <a data-bs-toggle="tooltip" title="COSMIC" class="btn btn-sm btn-info text-white me-1 mb-1"  rel="noreferrer noopener" href="{{cosmic_link[1]}}" target="_blank">{{cosmic_link[0]}}</a>
     {% endfor %}
   {% endif %}
   {% if variant.dbsnp_id %}
     {% for snp in variant.dbsnp_id.split(';') %}
-      <a class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank" href="{{variant.snp_links[snp]}}">dbSNP ({{ snp }})</a>
+      <a class="btn btn-sm btn-info text-white me-1 mb-1"  target="_blank" rel="noreferrer noopener" href="{{variant.snp_links[snp]}}">dbSNP ({{ snp }})</a>
     {% endfor %}
   {% endif %}
 </div>
 <div class="btn-group">
   {% if primary_transcript and primary_transcript.varsome_link %}
-  <a href="{{ primary_transcript.varsome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank"
+  <a href="{{ primary_transcript.varsome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1"  rel="noreferrer noopener" target="_blank"
     data-bs-toggle="tooltip" title="Varsome">V</a>
   {% endif %}
   {% if primary_transcript and primary_transcript.tp53_link %}
-    <a href="{{ primary_transcript.tp53_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank"
+    <a href="{{ primary_transcript.tp53_link }}" class="btn btn-sm btn-info text-white me-1 mb-1"  rel="noreferrer noopener" target="_blank"
       data-bs-toggle="tooltip" title="MutanTP53">TP53</a>
   {% endif %}
   {% if primary_transcript and primary_transcript.cbioportal_link %}
-    <a href="{{ primary_transcript.cbioportal_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank"
+    <a href="{{ primary_transcript.cbioportal_link }}" class="btn btn-sm btn-info text-white me-1 mb-1"  rel="noreferrer noopener" target="_blank"
       data-bs-toggle="tooltip" title="cBioPortal">CBP</a>
   {% endif %}
   {% if primary_transcript and primary_transcript.mycancergenome_link %}
-    <a href="{{ primary_transcript.mycancergenome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1" role="button" target="_blank"
+    <a href="{{ primary_transcript.mycancergenome_link }}" class="btn btn-sm btn-info text-white me-1 mb-1"  rel="noreferrer noopener" target="_blank"
       data-bs-toggle="tooltip" title="MyCancerGenome">MCG</a>
   {% endif %}
 </div>

diff --git a/scout/server/links.py b/scout/server/links.py
@@ -355,7 +355,7 @@ def add_tx_links(tx_obj, build=37, hgnc_symbol=None):
     return tx_obj
 
 
-##  Transcript links
+# Transcript links
 def refseq(refseq_id):
     link = "http://www.ncbi.nlm.nih.gov/nuccore/{}"
     if not refseq_id:
@@ -480,6 +480,7 @@ def get_variant_links(institute_obj: dict, variant_obj: dict, build: int = None)
         swegen_link=swegen_link(variant_obj),
         cosmic_links=cosmic_links(variant_obj),
         beacon_link=beacon_link(variant_obj, build),
+        franklin_link=franklin_link(variant_obj, build),
         ucsc_link=ucsc_link(variant_obj, build),
         decipher_link=decipher_link(variant_obj, build),
         ensembl_link=ensembl_link(variant_obj, build),
@@ -633,6 +634,23 @@ def swegen_link(variant_obj):
     return url_template.format(this=variant_obj)
 
 
+def franklin_link(variant_obj: dict, build: int = 37):
+    """Compose link to Franklin Variant Frequency Database."""
+    if variant_obj["category"] in ["cancer", "cancer_sv"]:
+        url_template = (
+            "https://franklin.genoox.com/clinical-db/variant/snpTumor/chr{this[chromosome]}-"
+            "{this[position]}-{this[reference]}-{this[alternative]}"
+        )
+    else:
+        url_template = (
+            "https://franklin.genoox.com/clinical-db/variant/snp/chr{this[chromosome]}-"
+            "{this[position]}-{this[reference]}-{this[alternative]}"
+        )
+    if build == 38:
+        url_template += "-hg38"
+    return url_template.format(this=variant_obj)
+
+
 def cosmic_links(variant_obj):
     """Compose link to COSMIC Database.