Fixing ensembl gene link-out to wrong genome build (#156).

varfish-org · Dec 7, 2021 · b3de674 · b3de674
1 parent 392b842
commit b3de674
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Showing 4 changed files with 8 additions and 6 deletions.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -20,6 +20,7 @@ End-User Summary
 - Allowing project owners and delegates to import cases via API (#207).
 - Fix for broken link-out into MutationTaster (#240).
 - Fixing SODAR Core template inconsistency (#150).
+- Fixing ensembl gene link-out to wrong genome build (#156).
 
 Full Change List
 ================
@@ -39,6 +40,7 @@ Full Change List
 - Allowing project owners and delegates to import cases via API (#207).
 - Fix for broken link-out into MutationTaster (#240).
 - Fixing SODAR Core template inconsistency (#150).
+- Fixing ensembl gene link-out to wrong genome build (#156).
 
 -------
 v0.23.9

diff --git a/geneinfo/templates/gene_info/gene_info.html b/geneinfo/templates/gene_info/gene_info.html
@@ -217,11 +217,11 @@
             <i>No EnsEMBL gene id.</i>
           </div>
         {% elif gene.ensembl_gene_id %}
-          <a href="https://www.ensembl.org/Homo_sapiens/Gene/Summary?g={{ gene.ensembl_gene_id }}" target="_blank">
+          <a href="https://{% if small_var.release == "GRCh37" %}grch37{% else %}www{% endif %}.ensembl.org/Homo_sapiens/Gene/Summary?g={{ gene.ensembl_gene_id }}" target="_blank">
             {{ gene.ensembl_gene_id }}
           </a>
         {% else %} {# small_var.ensembl_gene_id #}
-          <a href="https://www.ensembl.org/Homo_sapiens/Gene/Summary?g={{ small_var.ensembl_gene_id }}" target="_blank">
+          <a href="https://{% if small_var.release == "GRCh37" %}grch37{% else %}www{% endif %}.ensembl.org/Homo_sapiens/Gene/Summary?g={{ small_var.ensembl_gene_id }}" target="_blank">
             {{ small_var.ensembl_gene_id }}
           </a>
         {% endif %}

diff --git a/svs/templates/svs/filter_result/row_sv.html b/svs/templates/svs/filter_result/row_sv.html
@@ -167,8 +167,8 @@
         <a class="dropdown-item" href="https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg19&position={{ first_entry.chromosome }}:{{ first_entry.start }}-{{ first_entry.end }}" target="_blank">
           Locus @UCSC
         </a>
-        <a class="dropdown-item" href="https://grch37.ensembl.org/Homo_sapiens/Location/View?r={{ first_entry.chromosome }}:{{ first_entry.start }}-{{ first_entry.end }}" target="_blank">
-          Locus @ENSEMBL
+        <a class="dropdown-item" href="https://{% if first_entry.release == "GRCh37" %}grch37{% else %}www{% endif %}.ensembl.org/Homo_sapiens/Location/View?r={{ first_entry.chromosome }}:{{ first_entry.start }}-{{ first_entry.end }}" target="_blank">
+          Locus @EnsEMBL
         </a>
         <a class="dropdown-item" href="http://dgv.tcag.ca/gb2/gbrowse/dgv2_hg19/?name={{ first_entry.chromosome }}:{{ first_entry.start }}-{{ first_entry.end }};search=Search" target="_blank">
           Locus @DGV

diff --git a/variants/templates/variants/filter_result/row.html b/variants/templates/variants/filter_result/row.html
@@ -301,7 +301,7 @@
           <a class="dropdown-item" href="https://www.ncbi.nlm.nih.gov/clinvar/?term={{ symbol }}" target="_blank">
             Gene @ClinVar
           </a>
-          <a class="dropdown-item" href="https://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g={{ entry.ensembl_gene_id }}" target="_blank">
+          <a class="dropdown-item" href="https://{% if entry.release == "GRCh37" %}grch37{% else %}www{% endif %}.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g={{ entry.ensembl_gene_id }}" target="_blank">
             Gene @EnsEMBL
           </a>
           <a class="dropdown-item" href="https://stuart.radboudumc.nl/metadome/dashboard/transcript/{{ entry.ensembl_transcript_id }}/" target="_blank">
@@ -491,7 +491,7 @@
         <a class="dropdown-item" href="https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg19&position={{ entry.chromosome }}:{{ entry.start }}-{{ entry.end }}" target="_blank">
           Locus @UCSC
         </a>
-        <a class="dropdown-item" href="https://grch37.ensembl.org/Homo_sapiens/Location/View?r={{ entry.chromosome }}:{{ entry.start }}-{{ entry.end }}">
+        <a class="dropdown-item" href="https://{% if entry.release == "GRCh37" %}grch37{% else %}www{% endif %}.ensembl.org/Homo_sapiens/Location/View?r={{ entry.chromosome }}:{{ entry.start }}-{{ entry.end }}" target="_blank">
           Locus @EnsEMBL
         </a>
         <a class="dropdown-item" href="http://dgv.tcag.ca/gb2/gbrowse/dgv2_hg19/?name={{ entry.chromosome }}:{{ entry.start }}-{{ entry.end }};search=Search" target="_blank">