Support custom organisms

eweitz · Apr 14, 2021 · 76513cc · 76513cc
1 parent 05849a3
commit 76513cc
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Showing 3 changed files with 26 additions and 4 deletions.
diff --git a/examples/vanilla/custom-organism.html b/examples/vanilla/custom-organism.html
@@ -34,7 +34,8 @@ <h1>Custom organism | Ideogram</h1>
   <script type="text/javascript">
 
     var ideogram = new Ideogram({
-      organism: 'custom'
+      organism: 'custom',
+      dataDir: 'https://raw.githubusercontent.com/eweitz/ideogram/05849a37242695d0d3dfb52059c4d0230842cda8/data/bands/native/'
     });
   </script>
 </body>

diff --git a/src/js/init/init.js b/src/js/init/init.js
@@ -165,8 +165,9 @@ function getBandFileNames(taxid, bandFileNames, ideo) {
   }
 
   bandFileName = getBandFileName(taxid, accession, ideo);
+  var isCustomOrganism = taxid === '-1';
 
-  if (taxid in ideo.organismsWithBands) {
+  if (taxid in ideo.organismsWithBands || isCustomOrganism) {
     bandFileNames[taxid] = bandFileName;
   }
   return bandFileNames;

diff --git a/src/js/services/organisms.js b/src/js/services/organisms.js
@@ -9,8 +9,18 @@ function getTaxidFromEutils(orgName, ideo) {
   taxonomySearch = ideo.esearch + '&db=taxonomy&term=' + orgName;
 
   return d3.json(taxonomySearch).then(function(data) {
-    taxid = data.esearchresult.idlist[0];
-    return [orgName, taxid];
+    var idlist = data.esearchresult.idlist;
+    if (idlist.length === 0) {
+      throw Error(
+        'Organism "' + orgName + '" is generally unknown; it was not found ' +
+        'in the NCBI Taxonomy database.  If you did not intend to specify a ' +
+        'novel or custom taxon, then try using the organism\'s ' +
+        'scientific name, e.g. Homo sapiens or Arabidopsis thaliana.'
+      );
+    } else {
+      taxid = data.esearchresult.idlist[0];
+      return [orgName, taxid];
+    }
   });
 }
 
@@ -201,6 +211,16 @@ function populateNonNativeOrg(orgs, ideo) {
           };
 
           Object.assign(ideo.organisms, augmentedOrganismMetadata);
+        }, function(errorMessage) {
+          console.info(errorMessage);
+          var customMetadata = {
+            scientificName: org,
+            commonName: org,
+            assemblies: {default: ''}
+          };
+
+          ideo.organisms['-1'] = customMetadata;
+          augmentedOrganismMetadata['-1'] = customMetadata;
         });
     } else {
       promise = new Promise(function(resolve) {