Merge 04069cf into c6e8def

HISTORY.rst

@@ -31,6 +31,7 @@ End-User Summary
 - Fixed smallvariant flags filter query (#502).
 - Added flags `segregates`, `doesnt_segregate` and `no_disease_association` to file export (#502).
 - Adjusting path to new varfish-annotator db download (#546).
+- Adding feature to enable and configure link-out to HGMD (#576).
 
 Full Change List
 ================
@@ -61,6 +62,7 @@ Full Change List
 - Added flags `segregates`, `doesnt_segregate` and `no_disease_association` to file export (#502).
 - Adjusting path to new varfish-annotator db download (#546).
 - Fixing issue with sync-from-remote when no remote is defined (#570).
+- Adding feature to enable and configure link-out to HGMD (#576).
 
 ------
 v1.2.0

config/settings/base.py

@@ -567,6 +567,17 @@ def set_logging(level=None):
 # Configure experimental SV filtration feature.
 VARFISH_ENABLE_SVS = env.bool("VARFISH_ENABLE_SVS", default=False)
 
+# Varfish: HGMD Professional
+# ------------------------------------------------------------------------------
+
+# Enable link-out to HGMD Professional
+VARFISH_ENABLE_HGMD_PRO_LINKOUT = env.bool("VARFISH_ENABLE_HGMD_PRO_LINKOUT", default=False)
+# Configure URL prefix for HGMD Professional
+VARFISH_HGMD_PRO_LINKOUT_URL_PREFIX = env.bool(
+    "VARFISH_HGMD_PRO_LINKOUT_URL_PREFIX",
+    default="https://my.qiagendigitalinsights.com/bbp/view/hgmd/pro",
+)
+
 # Varfish: GAGH Beacon
 # ------------------------------------------------------------------------------
 

docs_manual/admin_config.rst

@@ -208,6 +208,17 @@ You can configure sentry support as follows
     A sentry DSN to report to.
     See Sentry documentation for details.
 
+-------------------------------
+HGMD Professional Documentation
+-------------------------------
+
+Users can enable a gene and variant wise link-out to HGMD professional as follows.
+
+``VARFISH_ENABLE_HGMD_PRO_LINKOUT=0``
+    Enable HGMD Professional link-out.
+``VARFISH_HGMD_PRO_LINKOUT_URL_PREFIX=https://my.qiagendigitalinsights.com/bbp/view/hgmd/pro/](https://my.qiagendigitalinsights.com/bbp/view/hgmd/pro``
+    Configure the URL prefix for HGMD Professional link-outs.
+
 ----------------------------------
 System and Docker (Compose) Tweaks
 ----------------------------------

variants/templates/variants/filter_result/row.html

@@ -7,6 +7,8 @@
 
 {% get_app_setting "variants" "umd_predictor_api_token" user=user as umd_predictor_api_token %}
 {% get_django_setting "PROJECTROLES_KIOSK_MODE" as kiosk_mode %}
+{% get_django_setting "VARFISH_ENABLE_HGMD_PRO_LINKOUT" as hgmd_pro_enabled %}
+{% get_django_setting "VARFISH_HGMD_PRO_LINKOUT_URL_PREFIX" as hgmd_pro_prefix %}
 {% get_app_setting "variants" "ga4gh_beacon_network_widget_enabled" user=user as ga4gh_beacon_network_widget_enabled %}
 {% ambiguous_frequency_warning entry exac_enabled thousand_genomes_enabled gnomad_exomes_enabled gnomad_genomes_enabled inhouse_enabled as warning %}
 
@@ -307,6 +309,11 @@
           <a class="dropdown-item" href="https://panelapp.genomicsengland.co.uk/panels/entities/{{ symbol }}" target="_blank">
             Gene @PanelApp
           </a>
+          {% if hgmd_pro_enabled %}
+            <a class="dropdown-item" href="{{ hgmd_pro_prefix }}/gene.php?gene={{ symbol }}" target="_blank">
+              Gene @HGMD Professional
+            </a>
+          {% endif %}
           <a class="dropdown-item" href="https://gnomad.broadinstitute.org/gene/{{ entry.ensembl_gene_id }}" target="_blank">
             Gene @gnomAD
           </a>
@@ -565,6 +572,12 @@
             </span>
           {% endif %}
 
+          {% if hgmd_pro_enabled %}
+            <a class="dropdown-item" href="{{ hgmd_pro_prefix }}/gene.php?gene={{ symbol }}" target="_blank">
+              Gene @HGMD Professional
+            </a>
+          {% endif %}
+
           <div class="dropdown-divider"></div>
 
           <a href="javascript:humanSplicingFinder('{{ symbol }}', '{{ entry.hgvs_c }}');"