external link

Author: root

config.json.template

@@ -8,7 +8,13 @@
     "expression_unit": "My unit",
     "externalSearch": false,
     "redirectSearch": "",
-    "redirectSearchAttribute": ""
+    "redirectSearchAttribute": "",
+    "gene_dbxref": [
+       {"url": "https://test_url_gene/#GENEID", "label": "my gene label"}
+    ],
+    "protein_dbxref": [
+       {"url": "https://test_url_protein/#PROTEINID", "label": "my protein label"}
+    ]
   },
   "externalSearchOptions": {
     "url": "http://0.0.0.0:80",

imports/ui/genetable/columns/AttributeValue.jsx

@@ -13,17 +13,29 @@ function isArray(x) {
 }
 
 function notDbxref({ value }) {
+  if (typeof value === "object" && !Array.isArray(value)){
+    return true
+  }
+
+  let val = String(value)
   return !(
-    DBXREF_REGEX.go.test(value)
-    || DBXREF_REGEX.interpro.test(value)
+    DBXREF_REGEX.go.test(val)
+    || DBXREF_REGEX.interpro.test(val)
   );
 }
 
 function SimpleAttribute({ value }) {
-  return value;
+  // Manage custom dbxref
+  if (typeof value === "object" && !Array.isArray(value)){
+    return(
+    <><a href={value.url}>{value.label}</a></>
+    )
+  }
+  return String(value);
 }
 
 function dbxrefTracker({ value: dbxrefId }) {
+  dbxrefId = String(dbxrefId)
   const sub = Meteor.subscribe('dbxref', { dbxrefId });
   const loading = !sub.ready();
   const dbxref = dbxrefCollection.findOne({ dbxrefId });
@@ -67,7 +79,7 @@ function AttributeValueArray({
         values.map((value) => (
           <li key={value} className="list-group-item py-0 px-0">
             <DetailedSingleAttribute
-              value={String(value)}
+              value={value}
             />
           </li>
         ))
@@ -97,16 +109,6 @@ function AttributeValueArray({
 }
 
 
-function AttributeValueObject({attrObject}) {
-  return (
-    <ul>
-      <li key={attrObject.label} className="list-group-item py-0 px-0">
-          <a href={attrObject.url}>{attrObject.label}</a>
-      </li>
-    </ul>
-  );
-}
-
 export default function AttributeValue({ attributeValue }) {
   const [showAll, setShowAll] = useState(false);
   function toggleShowAll() {
@@ -117,14 +119,6 @@ export default function AttributeValue({ attributeValue }) {
     return <p />;
   }
 
-  if (typeof attributeValue === 'object') {
-    return (
-      <AttributeValueObject
-        attrObject={attributeValue}
-      />
-    );
-  }
-
   const attrArray = isArray(attributeValue)
     ? attributeValue
     : [attributeValue];

imports/ui/singleGenePage/GeneralInfo.jsx

@@ -230,30 +230,37 @@ function GeneInfo({
   } = gene;
   const currentVersion = editHistory[0];
 
-  if( Meteor.settings.public.protein_dbxref && typeof Meteor.settings.public.protein_dbxref == "array" && Meteor.settings.public.protein_dbxref.length > 0){
+  if( Meteor.settings.public.protein_dbxref && Array.isArray(Meteor.settings.public.protein_dbxref) && Meteor.settings.public.protein_dbxref.length > 0){
+    if (! gene.attributes['Dbxref']){
+      gene.attributes['Dbxref'] = []
+    }
+
     const protein_ids = gene.subfeatures
       .filter((sub) => sub.type === 'mRNA')
       .map((transcript) => transcript.protein_id)
       .sort();
 
-    for (dbxref in Meteor.settings.public.protein_dbxref ){
-      if (! dbxref.url){continue}
-      for (prot_id in protein_ids){
+    Meteor.settings.public.protein_dbxref.forEach((dbxref) => {
+      if (! dbxref.url){return}
+      protein_ids.forEach((prot_id) => { 
         let prot_url = dbxref.url.replace("#PROTEINID", prot_id)
         let prot_label = dbxref.label ? dbxref.label.replace("#PROTEINID", prot_id) : ""
         gene.attributes['Dbxref'].unshift({url: prot_url, label: prot_label})
-      }
-    }
+      })
+    })
   }
 
-  if( Meteor.settings.public.gene_dbxref && typeof Meteor.settings.public.gene_dbxref == "array" && Meteor.settings.public.gene_dbxref.length > 0){
-    for (dbxref in Meteor.settings.public.gene_dbxref ){
-      if (! dbxref.url){continue}
+  if( Meteor.settings.public.gene_dbxref && Array.isArray(Meteor.settings.public.gene_dbxref) && Meteor.settings.public.gene_dbxref.length > 0){
+    if (! gene.attributes['Dbxref']){
+      gene.attributes['Dbxref'] = []
+    }
 
+    Meteor.settings.public.gene_dbxref.forEach((dbxref) => {
+      if (! dbxref.url){return}
       let gene_url = dbxref.url.replace("#GENEID", gene.ID)
       let gene_label = dbxref.label ? dbxref.label.replace("#GENEID", gene.ID) : ""
       gene.attributes['Dbxref'].unshift({url: gene_url, label: gene_label})
-    }
+    })
   }
 
   const [reversions, setReversions] = useState(0);