Merge 1e49f06 into 3fd4370

.gitignore

@@ -354,8 +354,10 @@ mailhog
 
 varfish/media/
 
-src/
+/src/
 
 celerybeat-schedule
 
 staticfiles.bak/
+
+varfish/vueapp/webpack-stats.json

HISTORY.rst

@@ -62,6 +62,7 @@ End-User Summary
 - Fixing hemizygous count display in fold-outs (#646).
 - Fixing clinvar submission sex/gender update (#686).
 - Fixing issue with phenotype name in Clinvar (#689).
+- Initial vue.js implementation for small variant filtration (#563).
 
 Full Change List
 ================
@@ -123,6 +124,7 @@ Full Change List
 - Fixing hemizygous count display in fold-outs (#646).
 - Fixing clinvar submission sex/gender update (#686).
 - Fixing issue with phenotype name in Clinvar (#689).
+- Initial vue.js implementation for small variant filtration (#563).
 
 ------
 v1.2.0

config/settings/base.py

@@ -948,3 +948,5 @@ def set_logging(debug):
 # ICONIFY CONFIGURATION
 # ------------------------------------------------------------------------------
 ICONIFY_JSON_ROOT = os.path.join(STATIC_ROOT, "iconify")
+
+VARFISH_ENABLE_VARIANTS_VUEAPP = env.bool("VARFISH_ENABLE_VARIANTS_VUEAPP", default=False)

config/settings/local.py

@@ -87,3 +87,5 @@
 
 # Your local stuff: Below this line define 3rd party library settings
 # ------------------------------------------------------------------------------
+
+VITE_DEV_SERVER = env.str("VITE_DEV_SERVER", "http://localhost:3000")

config/urls.py

@@ -84,15 +84,23 @@ def handler500(request, *args, **argv):
 ] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
 
 
-# Augment url patterns with proxy for genomics england panelapp.
 urlpatterns += [
+    # Augment url patterns with proxy for genomics england panelapp.
     url(
         r"^proxy/panelapp/(?P<url>.*)$",
         HttpProxy.as_view(
             base_url="https://panelapp.genomicsengland.co.uk/api/",
             ignored_request_headers=HttpProxy.ignored_upstream_headers + ["cookie"],
         ),
-    )
+    ),
+    # Augment url patterns with proxy for variantvalidator.org.
+    url(
+        r"^proxy/variantvalidator/(?P<url>.*)$",
+        HttpProxy.as_view(
+            base_url="https://rest.variantvalidator.org/VariantValidator/variantvalidator/",
+            ignored_request_headers=HttpProxy.ignored_upstream_headers + ["cookie"],
+        ),
+    ),
 ]
 
 if settings.DEBUG:

docs_manual/admin_upgrade.rst

@@ -129,10 +129,10 @@ Note that this will also import a patch to the TAD data in
 In case of any issues, contact us in the `Github Discussion <https://github.com/bihealth/varfish-server/discussions>`__ or directly by email.
 
 ------------------
-v0.23.0 to v1.2.1
+v0.23.0 to v1.2.2
 ------------------
 
-This includes all version in between, v0.23.1, ..., v1.2.1.
+This includes all version in between, v0.23.1, ..., v1.2.2.
 
 **Summary**
 

geneinfo/views.py

@@ -54,7 +54,7 @@ def get_gene_infos(database, gene_id, ensembl_transcript_id):
             "symbol": gene_symbol,
         }
     else:
-        gene = model_to_dict(gene)
+        gene = model_to_dict(gene, exclude=["id"])
         if database == "refseq":
             refseq_to_ensembl = RefseqToEnsembl.objects.filter(entrez_id=gene_id).first()
             ensembl_gene_id = getattr(refseq_to_ensembl, "ensembl_gene_id", None)

varfish/static/css/project.css

@@ -47,6 +47,10 @@
     font-size:0.8em;
 }
 
+.img-light {
+  filter: invert(100%) sepia(0%) saturate(0%) hue-rotate(93deg) brightness(103%) contrast(103%);
+}
+
 .img-light-gray {
   filter: invert(100%) sepia(0%) saturate(966%) hue-rotate(245deg) brightness(85%) contrast(83%);
 }