diff --git a/HISTORY.rst b/HISTORY.rst index dec337a55..d9fab69f9 100644 --- a/HISTORY.rst +++ b/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 diff --git a/Makefile b/Makefile index 933ceb27a..59166b548 100644 --- a/Makefile +++ b/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 diff --git a/variants/queries.py b/variants/queries.py index 1192c5125..dbde32ed6 100644 --- a/variants/queries.py +++ b/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"), ] diff --git a/variants/templates/variants/filter_result/row.html b/variants/templates/variants/filter_result/row.html index 854c53173..fdeba9f96 100644 --- a/variants/templates/variants/filter_result/row.html +++ b/variants/templates/variants/filter_result/row.html @@ -322,6 +322,24 @@ Gene @MGI {% endif %} + {% if entry.hgnc_id %} + + Gene @GenCC + + {% else %} + + Gene @GenCC + + {% endif %} + {% if entry.uniprot_ids %} + + Gene @Missense3D-DB + + {% else %} + + Gene @Missense3D-DB + + {% endif %} {% if hpoterms %} Gene+Phenotypes @PubMed