issue #758 - configure quick links via settings

SACGF · May 13, 2024 · f208b94 · f208b94
1 parent e2e6fb5
commit f208b94
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Showing 5 changed files with 50 additions and 16 deletions.
diff --git a/snpdb/variant_links.py b/snpdb/variant_links.py
@@ -13,18 +13,17 @@ def variant_link_info(variant: Variant, genome_build: GenomeBuild) -> dict[str,
     link_data['variant_string'] = str(variant)
     link_data['variant_svlen'] = variant.svlen
     link_data['genome_build'] = genome_build.name
-    link_data['canonical_c_hgvs'] = variant.get_canonical_c_hgvs(genome_build)
+
+    if cta := variant.get_canonical_transcript_annotation(genome_build):
+        link_data['canonical_c_hgvs'] = cta.get_hgvs_c_with_symbol()
+        link_data['gene_symbol'] = cta.symbol
 
     # If we can include these in link_data we'll get more links
     #
-    # SpecialEKeys.C_HGVS,
-    # SpecialEKeys.VARIANT_COORDINATE,
-    # SpecialEKeys.GENE_SYMBOL,
     # SpecialEKeys.REFSEQ_TRANSCRIPT_ID,
     # SpecialEKeys.P_HGVS,
     #
     # SpecialEKeys.CLINGEN_ALLELE_ID,
-    # SpecialEKeys.GENOME_BUILD,
     # SpecialEKeys.UNIPROT_ID,
     # SpecialEKeys.CLINVAR_VARIANTION_ID,
     # SpecialEKeys.HGNC_ID,

diff --git a/variantgrid/settings/components/default_settings.py b/variantgrid/settings/components/default_settings.py
@@ -987,6 +987,11 @@
 VARIANT_DETAILS_SHOW_SAMPLES = True
 VARIANT_DETAILS_NEARBY_RANGE = 50
 VARIANT_DETAILS_NEARBY_SHOW_GENE = False
+
+# Can only use block or allow list. Use "text" value of link (see vc_links.js)
+VARIANT_DETAILS_QUICK_LINKS_ALLOW_LIST = []
+VARIANT_DETAILS_QUICK_LINKS_BLOCK_LIST = []
+
 VARIANT_VCF_DB_PREFIX = "vg"
 VARIANT_MANUAL_CREATE = True
 VARIANT_MANUAL_CREATE_BY_NON_ADMIN = True

diff --git a/variantgrid/static_files/default_static/js/vc_links.js b/variantgrid/static_files/default_static/js/vc_links.js
@@ -6,6 +6,7 @@ let VCLink = (function() {
         this.missing = params.missing;
         this.title = params.title;
         this.build = params.build;
+        this.geneLink = Boolean(params.geneLink);
     };
 
     VCLink.prototype = {
@@ -59,7 +60,8 @@ EMPTY_LINK = new VCLink({
     href: null,
     missing: true,
     title: null,
-    build: null
+    build: null,
+    geneLink: false,
 });
 
 let VCLinks = (function() {
@@ -142,6 +144,24 @@ let VCLinks = (function() {
             return links;
         },
 
+        filterLinks(links, allowMissing, allowList, blockList) {
+            const allowSet = new Set(allowList);
+            const blockSet = new Set(blockList);
+            if (allowSet.size && blockSet.size) {
+                throw new Error("filterLinks: can only pass EITHER allowList OR blockList not both")
+            }
+            if (!allowMissing) {
+                links = links.filter(link => !link.isMissing());
+            }
+            if (allowSet.size) {
+                links = links.filter(link => allowSet.has(link.text));
+            }
+            if (blockSet.size) {
+                links = links.filter(link => !blockSet.has(link.text));
+            }
+            return links;
+        },
+
         buildName() {
             let genome_build = this.data[SpecialEKeys.GENOME_BUILD];
             if (genome_build) {
@@ -164,36 +184,38 @@ let VCLinks = (function() {
         generateMonarchLink() {
             let hgnc_id = this.hgncIdSafe();
             if (hgnc_id) {
-                return new VCLink({text: 'Monarch Phen.', title:"Monarch Phenotype (Gene)", href: `https://monarchinitiative.org/gene/${hgnc_id}`});
+                return new VCLink({text: 'Monarch Phen.', title:"Monarch Phenotype (Gene)", href: `https://monarchinitiative.org/gene/${hgnc_id}`, geneLink: true});
             }
             let gene_symbol = this.data[SpecialEKeys.GENE_SYMBOL];
             if (gene_symbol) {
-                return new VCLink({text: 'Monarch Phen,', title:"Monarch Phenotype (Gene)", href: `https://monarchinitiative.org/search/${gene_symbol}`});
+                return new VCLink({text: 'Monarch Phen,', title:"Monarch Phenotype (Gene)", href: `https://monarchinitiative.org/search/${gene_symbol}`, geneLink: true});
             }
 
             return new VCLink({
                 text: 'Monarch Phen',
                 href: 'https://monarchinitiative.org',
-                missing: this.eKeys.key(SpecialEKeys.HGNC_ID).label
+                missing: this.eKeys.key(SpecialEKeys.HGNC_ID).label,
+                geneLink: true
             });
         },
 
         generateClingenKb() {
             let hgnc_id = this.hgncIdSafe();
             if (hgnc_id) {
                 let link = `https://search.clinicalgenome.org/kb/genes/${hgnc_id}`;
-                return new VCLink({text: 'ClinGen KB', href: link});
+                return new VCLink({text: 'ClinGen KB', href: link, geneLink: true});
             }
             let gene_symbol = this.data[SpecialEKeys.GENE_SYMBOL];
             if (gene_symbol) {
                 let link = `https://search.clinicalgenome.org/kb/genes?search=${gene_symbol}`;
-                return new VCLink({text: 'ClinGen KB', href: link});
+                return new VCLink({text: 'ClinGen KB', href: link, geneLink: true});
             }
 
             return new VCLink({
                 text: 'ClinGen KB',
                 href: 'https://search.clinicalgenome.org/kb/genes',
-                missing: this.eKeys.key(SpecialEKeys.HGNC_ID).label
+                missing: this.eKeys.key(SpecialEKeys.HGNC_ID).label,
+                geneLink: true,
             });
         },
 
@@ -344,12 +366,13 @@ let VCLinks = (function() {
         },
 
         makeLink(text, link, param, key, title) {
+            let geneLink = key == SpecialEKeys.GENE_SYMBOL;
             let val = this.data[key];
             if (val) {
                 link = link + param.replace('@@', encodeURIComponent(val));
-                return new VCLink({text:text, href:link, title: title});
+                return new VCLink({text:text, href:link, title: title, geneLink: geneLink});
             } else {
-                return new VCLink({text:text, href:link, missing:this.eKeys.key(key).label, title: title});
+                return new VCLink({text:text, href:link, missing:this.eKeys.key(key).label, title: title, geneLink: geneLink});
             }
         }
     };

diff --git a/variantopedia/templates/variantopedia/variant_details.html b/variantopedia/templates/variantopedia/variant_details.html
@@ -339,10 +339,15 @@
     }
 
     EKeys.load().then(eKeys => {
+        const allowList = {{ quick_lists_allow_list | jsonify }};
+        const blockList = {{ quick_links_block_list | jsonify }};
         let vcLinks = new VCLinks(eKeys);
         let links = vcLinks.generateLinks(data.link_data);
-        let anchors = links.filter(link => !link.isMissing()).map(link => link.asAnchor("bootstrap"));
-        $('#quick-links').html($("<ul>", {class:"list-group", html:anchors}));
+        links = vcLinks.filterLinks(links, false, allowList, blockList);
+
+        let variantLinks = links.filter(link => !link.geneLink);
+        let variantAnchors = variantLinks.map(link => link.asAnchor("bootstrap"));
+        $('#quick-links').html($("<ul>", {class:"list-group", html:variantAnchors}));
     });
 }
 

diff --git a/variantopedia/views.py b/variantopedia/views.py
@@ -609,6 +609,8 @@ def variant_details_annotation_version(request, variant_id, annotation_version_i
         "variant_allele": variant_allele_data,
         "variant_annotation": variant_annotation,
         "vts": vts,
+        "quick_links_allow_list": settings.VARIANT_DETAILS_QUICK_LINKS_ALLOW_LIST,
+        "quick_links_block_list": settings.VARIANT_DETAILS_QUICK_LINKS_BLOCK_LIST,
     }
     if extra_context:
         context.update(extra_context)