Fetch entire bigBed blocks

lib/underscore.js

@@ -13,5 +13,6 @@ declare module "underscore" {
   declare function flatten<S>(a: S[][]): S[];
 
   declare function chain<S>(obj: S): any;
+  declare function any<T>(list: Array<T>, pred: (el: T)=>boolean): boolean;
 }
 

src/BigBed.js

@@ -173,7 +173,7 @@ type BedRow = {
 
 // All features found in range.
 type BedBlock = {
-  range: ContigRange<string>;
+  range: ContigInterval<string>;
   rows: BedRow[];
 }
 
@@ -235,7 +235,7 @@ class BigBed {
    * Because these features must all be fetched, decompressed and parsed
    * anyway, this can be helpful for upstream caching.
    */
-  getFeatureBlocksOverlapping(range: ContigRange): Q.Promise<Array<BedBlock>> {
+  getFeatureBlocksOverlapping(range: ContigInterval<string>): Q.Promise<Array<BedBlock>> {
     return Q.spread([this.header, this.cirTree, this.contigMap],
                     (header, cirTree, contigMap) => {
       var contigIx = getContigId(contigMap, range.contig);

src/BigBedDataSource.js

@@ -30,9 +30,14 @@ type BedRow = {
   // Remaining fields in the BED row (typically tab-delimited)
   rest: string;
 }
+type BedBlock = {
+  range: ContigInterval<string>;
+  rows: BedRow[];
+}
 
 declare class BigBed {
   getFeaturesInRange: (contig: string, start: number, stop: number) => Q.Promise<Array<BedRow>>;
+  getFeatureBlocksOverlapping(range: ContigInterval): Q.Promise<Array<BedBlock>>;
 }
 
 
@@ -73,6 +78,9 @@ function createBigBedDataSource(remoteSource: BigBed): BigBedSource {
   var genes: Array<Gene> = [];
   window.genes = genes;
 
+  // Ranges for which we have complete information -- no need to hit network.
+  var coveredRanges: Array<ContigInterval<string>> = []
+
   function addGene(newGene) {
     if (!_.findWhere(genes, {id: newGene.id})) {
       genes.push(newGene);
@@ -85,12 +93,20 @@ function createBigBedDataSource(remoteSource: BigBed): BigBedSource {
   }
 
   function fetch(range: GenomeRange) {
-    // TODO: add an API for requesting the entire block of genes.
-    return remoteSource.getFeaturesInRange(range.contig, range.start, range.stop)
-        .then(features => {
-          var genes = features.map(parseBedFeature);
-          genes.forEach(gene => addGene(gene));
-        });
+    var interval = new ContigInterval(range.contig, range.start, range.stop);
+
+    // Check if this interval is already in the cache.
+    if (_.any(coveredRanges, r => r.intersects(interval))) {
+      return Q.when();
+    }
+
+    return remoteSource.getFeatureBlocksOverlapping(interval).then(featureBlocks => {
+      featureBlocks.forEach(fb => {
+        coveredRanges.push(fb.range);
+        var genes = fb.rows.map(parseBedFeature);
+        genes.forEach(gene => addGene(gene));
+      });
+    });
   }
 
   var o = {

src/RemoteFile.js

@@ -41,7 +41,6 @@ class RemoteFile {
     // TODO: handle partial overlap of request w/ cache.
 
     // Need to fetch from the network.
-    console.log('fetching from network: ', start, '+', length); 
     return this.getFromNetwork(start, stop);
   }
 

src/Root.js

@@ -38,8 +38,8 @@ var Root = React.createClass({
       // this is here to facilitate faster iteration
       this.handleRangeChange({
         contig: 'chr17',
-        start: 100,
-        stop: 150
+        start: 7512444,
+        stop: 7512484
       });
     });
 

src/TwoBitDataSource.js

@@ -82,7 +82,6 @@ var createTwoBitDataSource = function(remoteSource: TwoBit): TwoBitSource {
       return Q.when();  // empty promise
     }
     if (isEntirelyKnown(range)) {
-      console.log('skipping TwoBit.js');
       return Q.when();
     }
 

test/TwoBitDataSource-test.js

@@ -52,7 +52,7 @@ describe('TwoBitDataSource', function() {
         source = createTwoBitDataSource(tb);
 
     source.on('newdata', () => {
-      expect(source.getRange({contig: 'chr22', start: 1, stop: 18}))
+      expect(source.getRange({contig: 'chr22', start: 1, stop: 15}))
           .to.deep.equal({
             'chr22:1':  'N',
             'chr22:2':  'T',
@@ -68,10 +68,7 @@ describe('TwoBitDataSource', function() {
             'chr22:12': 'C',
             'chr22:13': 'C',
             'chr22:14': 'A',
-            'chr22:15': 'T',  // 5 past end of request
-            'chr22:16': null,
-            'chr22:17': null,
-            'chr22:18': null
+            'chr22:15': 'T',
           });
       done();
     });