Merge 448ce48 into 2e34f88

HISTORY.rst

@@ -30,6 +30,7 @@ End-User Summary
 - Rebuild of variant summary database table happens every Sunday at 2:22am.
 - Added celery queues ``maintenance`` and ``export``.
 - Adding support for connecting two sites via the GAGH Beacon protocol.
+- Adding link-out to "GenCC"
 
 Full Change List
 ================
@@ -58,6 +59,7 @@ Full Change List
 - Added celery queues ``maintenance`` and ``export``.
 - Adding support for connecting two sites via the GAGH Beacon protocol.
 - Making CADD version behind CADD REST API configurable.
+- Adding link-out to "GenCC"
 
 -------
 v0.22.1

Makefile

@@ -5,6 +5,10 @@ MANAGE = time python manage.py
 black:
 	black -l 100 --exclude '/(\.eggs|\.git|\.hg|\.mypy_cache|\.nox|\.tox|\.?v?env|_build|buck-out|build|dist|src)/' $(arg) .
 
+.PHONY: npm-install
+npm-install:
+	cd varfish/vueapp && npm ci
+
 .PHONY: serve
 serve:
 	$(MANAGE) runserver

variants/queries.py

@@ -223,6 +223,8 @@ def __init__(self, *args, **kwargs):
                     func.max(Hgnc.sa.gene_family).label("gene_family"),
                     func.max(Hgnc.sa.pubmed_id).label("pubmed_id"),
                     func.max(Hgnc.sa.ucsc_id_novers).label("ucsc_id_novers"),
+                    func.max(Hgnc.sa.hgnc_id).label("hgnc_id"),
+                    func.max(Hgnc.sa.uniprot_ids).label("uniprot_ids"),
                 ]
             )
             .select_from(Hgnc.sa)
@@ -242,6 +244,8 @@ def extend_fields(self, _query_parts):
             func.coalesce(self.subquery_hgnc.c.name, "").label("gene_name"),
             func.coalesce(self.subquery_hgnc.c.gene_family, "").label("gene_family"),
             func.coalesce(self.subquery_hgnc.c.pubmed_id, "").label("pubmed_id"),
+            func.coalesce(self.subquery_hgnc.c.hgnc_id, "").label("hgnc_id"),
+            func.coalesce(self.subquery_hgnc.c.uniprot_ids, "").label("uniprot_ids"),
         ]
 
 

variants/templates/variants/filter_result/row.html

@@ -322,6 +322,24 @@
             Gene @MGI
           </span>
           {% endif %}
+          {% if entry.hgnc_id %}
+          <a class="dropdown-item" href="https://search.thegencc.org/genes/{{ entry.hgnc_id }}" target="_blank">
+            Gene @GenCC
+          </a>
+          {% else %}
+          <span class="dropdown-item disabled">
+            Gene @GenCC
+          </span>
+          {% endif %}
+          {% if entry.uniprot_ids %}
+          <a class="dropdown-item" href="http://missense3d.bc.ic.ac.uk:8080/search_direct?uniprot={{ entry.uniprot_ids }}" target="_blank">
+            Gene @Missense3D-DB
+          </a>
+          {% else %}
+          <span class="dropdown-item disabled">
+            Gene @Missense3D-DB
+          </span>
+          {% endif %}
           {% if hpoterms %}
             <a class="dropdown-item" href="https://www.ncbi.nlm.nih.gov/pubmed/?term={{ entry|get_pubmed_linkout:hpoterms }}" target="_blank">
               Gene+Phenotypes @PubMed