Fix some issues with the bgzip file dialog driver and add tests

GMOD · Sep 13, 2018 · 07d5dde · 07d5dde
1 parent 6b76611
commit 07d5dde
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Showing 3 changed files with 25 additions and 5 deletions.
diff --git a/src/JBrowse/Browser.js b/src/JBrowse/Browser.js
@@ -1370,7 +1370,6 @@ openFasta: function() {
                       alert('Unindexed file too large. You must have an index file (.fai) for sequence files larger than 100 MB.')
                       return reject('sequence file too large')
                   }
-                    console.log(storeConf)
 
                   const store = new storeClass(
                       Object.assign({ browser: this }, storeConf)

diff --git a/src/JBrowse/View/FileDialog/TrackList/BgzipIndexedFASTADriver.js b/src/JBrowse/View/FileDialog/TrackList/BgzipIndexedFASTADriver.js
@@ -40,7 +40,7 @@ return declare( null, {
             for( var n in configs ) {
                 var c = configs[n];
                 if( Util.basename( c[this.indexConfKey] ? c[this.indexConfKey ].url || c[this.indexConfKey].blob.name : c[this.indexUrlConfKey], this.indexExtensionMap ) == basename ||
-                    Util.basename( c[this.doubleIndexConfKey] ? c[this.doubleIndexConfKey ].url || c[this.doubleIndexConfKey].blob.name : c[this.doubleIndexUrlConfKey], this.doubleExtensionMap ) == basename ) {
+                    Util.basename( c[this.doubleIndexConfKey] ? c[this.doubleIndexConfKey ].url || c[this.doubleIndexConfKey].blob.name : c[this.doubleIndexUrlConfKey], this.doubleIndexExtensionMap ) == basename ) {
 
                     // it's a match, put it in
                     c[this.fileConfKey] = this._makeBlob( resource );
@@ -70,7 +70,7 @@ return declare( null, {
             for( var n in configs ) {
                 var c = configs[n];
                 if( Util.basename( c[this.fileConfKey] ? c[this.fileConfKey ].url || c[this.fileConfKey].blob.name : c[this.fileConfKey], this.fileExtensionMap ) == basename ||
-                    Util.basename( c[this.doubleIndexConfKey] ? c[this.doubleIndexConfKey ].url || c[this.doubleIndexConfKey].blob.name : c[this.doubleIndexUrlConfKey], this.doubleExtensionMap ) == basename ) {
+                    Util.basename( c[this.doubleIndexConfKey] ? c[this.doubleIndexConfKey ].url || c[this.doubleIndexConfKey].blob.name : c[this.doubleIndexUrlConfKey], this.doubleIndexExtensionMap ) == basename ) {
 
                     // it's a match, put it in
                     c[this.indexConfKey] = this._makeBlob( resource );
@@ -133,7 +133,6 @@ return declare( null, {
                 var v2 = (conf[this.fileConfKey] || conf[this.fileUrlConfKey])
                 var v3 = (conf[this.doubleIndexConfKey] || conf[this.doubleIndexUrlConfKey])
                 if(!(v1 && v2 && v3)) {
-                    console.log(configs[n], configs, n)
                     delete configs[n]
                 }
             }

diff --git a/tests/js_tests/spec/AddFiles.spec.js b/tests/js_tests/spec/AddFiles.spec.js
@@ -121,7 +121,7 @@ describe( 'FileDialog drivers', function() {
         expect( confs.foo.fasta.blob.name ).toEqual( 'zee.fa' );
     });
 
-    it( 'BGZIP FASTA file', function( ) {
+    it( 'BGZIP FASTA file variant 1', function( ) {
         var confs = { foo: { bgzfa: { blob: { name :'zee.fa.gz'} } } };
         var driver = new BgzipIndexedFastaDriver();
         expect( driver.tryResource( confs, { type: 'fasta.gz.fai', file: { name: 'zee.fa.gz.fai'} } ) ).toBeTruthy();
@@ -131,6 +131,28 @@ describe( 'FileDialog drivers', function() {
         expect( confs.foo.gzi.blob.name ).toEqual( 'zee.fa.gz.gzi' );
         expect( confs.foo.bgzfa.blob.name ).toEqual( 'zee.fa.gz' );
     });
+
+    it( 'BGZIP FASTA file variant 2', function( ) {
+        var confs = { foo: { fai: { blob: { name :'zee.fa.gz.fai'} } } };
+        var driver = new BgzipIndexedFastaDriver();
+        expect( driver.tryResource( confs, { type: 'fasta.gz', file: { name: 'zee.fa.gz'} } ) ).toBeTruthy();
+        expect( driver.tryResource( confs, { type: 'gzi', file: { name: 'zee.fa.gz.gzi'} } ) ).toBeTruthy();
+        driver.finalizeConfiguration(confs);
+        expect( confs.foo.fai.blob.name ).toEqual( 'zee.fa.gz.fai' );
+        expect( confs.foo.gzi.blob.name ).toEqual( 'zee.fa.gz.gzi' );
+        expect( confs.foo.bgzfa.blob.name ).toEqual( 'zee.fa.gz' );
+    });
+
+    it( 'BGZIP FASTA file variant 3', function( ) {
+        var confs = { foo: { bgzfa: { blob: { name :'zee.fa.gz'} } } };
+        var driver = new BgzipIndexedFastaDriver();
+        expect( driver.tryResource( confs, { type: 'gzi', file: { name: 'zee.fa.gz.gzi'} } ) ).toBeTruthy();
+        expect( driver.tryResource( confs, { type: 'fasta.gz.fai', file: { name: 'zee.fa.gz.fai'} } ) ).toBeTruthy();
+        driver.finalizeConfiguration(confs);
+        expect( confs.foo.fai.blob.name ).toEqual( 'zee.fa.gz.fai' );
+        expect( confs.foo.gzi.blob.name ).toEqual( 'zee.fa.gz.gzi' );
+        expect( confs.foo.bgzfa.blob.name ).toEqual( 'zee.fa.gz' );
+    });
 });
 });