Restore GenBank accession support, restore some tests, simplify

zhuying412 · Aug 29, 2019 · a5dee70 · a5dee70
1 parent 083547f
commit a5dee70
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Showing 2 changed files with 40 additions and 50 deletions.
diff --git a/src/js/services/services.js b/src/js/services/services.js
@@ -1,4 +1,4 @@
-import {d3, hasGenBankAssembly} from '../lib';
+import {d3} from '../lib';
 import {
   esearch, esummary, elink, getAssemblySearchUrl
 } from './eutils-config.js';
@@ -11,41 +11,31 @@ function getNuccoreLink(asmUid, ideo) {
 
   // Get a list of IDs for the chromosomes in this genome.
   //
-  // If assembly is GenBank-only or if a GenBank assembly was explicitly
-  // requested (GCA_), then query chromosomes sequences in Nucleotide DB via
-  // INSDC link.  (GenBank is the American INSDC repository.)
-  // Otherwise, query RefSeq chromosomes in Nucleotide DB.
-  if (hasGenBankAssembly(ideo)) {
-    // TODO: account for GenBank-only
-    qs = '&db=nuccore&linkname=assembly_nuccore_insdc&from_uid=' + asmUid;
-    return ideo.elink + qs;
-  } else {
-    qs = ('&db=nuccore&dbfrom=assembly&linkname=assembly_nuccore_refseq&' +
-      'cmd=neighbor_history&from_uid=' + asmUid);
-    return d3.json(ideo.elink + qs)
-      .then(function(data) {
-        var webenv = data.linksets[0].webenv;
-        qs =
-          '&db=nuccore' +
-          '&term=%231+AND+%28' +
-            'sequence_from_chromosome[Properties]+OR+' +
-            'sequence_from_plastid[Properties]+OR+' +
-            'sequence_from_mitochondrion[Properties]%29' +
-          '&WebEnv=' + webenv + '&usehistory=y&retmax=1000';
-        return ideo.esearch + qs;
-      });
-  }
+  // Query chromosomes sequences in Nucleotide DB (nuccore) via
+  // Assembly DB E-Utils link.
+  qs = ('&db=nuccore&dbfrom=assembly&linkname=assembly_nuccore&' +
+    'cmd=neighbor_history&from_uid=' + asmUid);
+
+  return d3.json(ideo.elink + qs)
+    .then(function(data) {
+      var webenv = data.linksets[0].webenv;
+      qs =
+        '&db=nuccore' +
+        '&term=%231+AND+%28' +
+          'sequence_from_chromosome[Properties]+OR+' +
+          'sequence_from_plastid[Properties]+OR+' +
+          'sequence_from_mitochondrion[Properties]%29' +
+        '&WebEnv=' + webenv + '&usehistory=y&retmax=1000';
+      return ideo.esearch + qs;
+    });
 }
 
 function fetchNucleotideSummary(data, ideo) {
-  var links, ntSummary;
+  var ids, ntSummary;
 
-  if ('esearchresult' in data) {
-    links = data.esearchresult.idlist.join(',');
-  } else {
-    links = data.linksets[0].linksetdbs[0].links.join(',');
-  }
-  ntSummary = ideo.esummary + '&db=nucleotide&id=' + links;
+  ids = data.esearchresult.idlist.join(',');
+
+  ntSummary = ideo.esummary + '&db=nucleotide&id=' + ids;
 
   return d3.json(ntSummary);
 }

diff --git a/test/web-test.js b/test/web-test.js
@@ -1,3 +1,4 @@
+/* eslint-disable no-new */
 /* eslint-disable spaced-comment */
 /* eslint-disable no-use-before-define */
 /* eslint-disable no-unused-vars */
@@ -1570,23 +1571,23 @@ describe('Ideogram', function() {
   // These tests fail due to an upstream breaking change in NCBI E-Utils.
   // Specifically, the Entrez GenColl database was retired without notice.
   //
-  // it('should support GenBank accessions in "assembly" parameter', function(done) {
-  //   // Tests use case for non-default assemblies.
-  //   // GCA_000002125.2 is commonly called HuRef
-  //   // https://www.ncbi.nlm.nih.gov/assembly/GCA_000002125.2
+  it('should support GenBank accessions in "assembly" parameter', function(done) {
+    // Tests use case for non-default assemblies.
+    // GCA_000002125.2 is commonly called HuRef
+    // https://www.ncbi.nlm.nih.gov/assembly/GCA_000002125.2
 
-  //   function callback() {
-  //     var chr1Length = ideogram.chromosomes['9606']['1'].length;
-  //     // For reference, see length section of LOCUS field in GenBank record at
-  //     // https://www.ncbi.nlm.nih.gov/nuccore/CM001609.2
-  //     assert.equal(chr1Length, 219475005);
-  //     done();
-  //   }
+    function callback() {
+      var chr1Length = ideogram.chromosomes['9606']['1'].length;
+      // For reference, see length section of LOCUS field in GenBank record at
+      // https://www.ncbi.nlm.nih.gov/nuccore/CM001609.2
+      assert.equal(chr1Length, 219475005);
+      done();
+    }
 
-  //   config.assembly = 'GCA_000002125.2';
-  //   config.onLoad = callback;
-  //   var ideogram = new Ideogram(config);
-  // });
+    config.assembly = 'GCA_000002125.2';
+    config.onLoad = callback;
+    var ideogram = new Ideogram(config);
+  });
 
   // it('should recover chromosomes when given scaffolds', function(done) {
   //   // Tests use case from ../examples/vanilla/human.html
@@ -1627,10 +1628,9 @@ describe('Ideogram', function() {
   //     var numHumanChromosomes = 24; // (22,X,Y)
   //     var numChromosomes = ideo.chromosomesArray.length;
 
-  //     if(numTimesOnLoadHasBeenCalled === 1) {
+  //     if (numTimesOnLoadHasBeenCalled === 1) {
   //       assert.equal(numChromosomes, numChimpChromosomes);
-  //     }
-  //     else if(numTimesOnLoadHasBeenCalled === 2) {
+  //     } else if (numTimesOnLoadHasBeenCalled === 2) {
   //       assert.equal(numChromosomes, numHumanChromosomes);
   //       done();
   //     }