start of logic that assembles messes of files into store definitions

src/JBrowse/View/FileDialog.js

@@ -8,9 +8,10 @@ define( [ 'dojo/_base/declare',
           'dijit/form/RadioButton',
           'dojox/form/Uploader',
           'dojox/form/uploader/plugins/IFrame',
-          './FileDialog/SuperFileList'
+          './FileDialog/SuperFileList',
+          './FileDialog/TrackList'
         ],
-        function( declare, aspect, on, Dialog, TextBox, Select, Button, RadioButton, Uploader, ignore, FileList ) {
+        function( declare, aspect, on, Dialog, TextBox, Select, Button, RadioButton, Uploader, ignore, FileList, TrackList ) {
 
 return declare(null,{
     constructor: function( args ) {
@@ -47,6 +48,7 @@ return declare(null,{
                          }
 
                         updateInputs();
+                        that.trackList.update();
                     },
                     onMouseOut: updateInputs
                 });
@@ -106,10 +108,9 @@ return declare(null,{
         var id = 'localInput'+(inputCounter++);
 
         var cont = dojo.create('div', {
-            innerHTML: '<h2>Local files</h2>'
-                       +'<h3>'
-                         + (dndSupported ? 'Drag or select files to open.' : 'Select files to open.')
-                         + '</h3>'
+            innerHTML: '<h3>'
+                       + (dndSupported ? 'Drag or select files to open.' : 'Select files to open.')
+                       + '</h3>'
         });
 
         var fileBox = new dojox.form.Uploader({
@@ -152,34 +153,50 @@ return declare(null,{
         return actionBar;
     },
 
+    // files and URLS
+    // -> stores
+    // -> tracks
+    // -> tracks with user modifications
+    _makeTrackList: function( container ) {
+        this.trackList = new TrackList({ dialog: this });
+        dojo.connect( this.localFileList, 'onChange', this.trackList, 'update' );
+        return this.trackList.domNode;
+    },
+
     show: function( args ) {
         var dialog = this.dialog = new Dialog(
             { title: "Open files", className: 'fileDialog' }
             );
 
-        dialog.set(
-            'content',
-            [
+        var content = [
+                dojo.create('hr'),
+                dojo.create('h2',{ innerHTML: 'Local files' }),
                 this._localControls( dialog.domNode ),
                 dojo.create('hr'),
+                dojo.create('h2',{ innerHTML: 'Remote files' }),
                 this._remoteControls(),
                 this._actionBar( args.openCallback, args.cancelCallback )
-            ]);
+            ];
+        content.unshift( this._makeTrackList() );
+        content.unshift( dojo.create('h2',{ innerHTML: 'Tracks' }) );
+
+
+        dialog.set( 'content', content );
         dialog.show();
 
         aspect.after( dialog, 'hide', function() {
                           dialog.destroyRecursive();
                       });
     },
 
-    _filesToOpen: function() {
+    filesToOpen: function() {
         if( ! this.localFileList )
             return [];
 
         return this.localFileList.getFiles();
     },
 
-    _urlsToOpen: function() {
+    urlsToOpen: function() {
         var urls = [];
         for( var id in this.inputs ) {
             var input = this.inputs[id];

src/JBrowse/View/FileDialog/SuperFileList.js

@@ -9,7 +9,11 @@ return declare( FileList,
 {
     _onUploaderChange: function(fileArray){
         var seenFile = {};
-        this._files = array.filter( ( this._files || [] ).concat( fileArray ).reverse(), function( file ) {
+        var allFiles = [].concat( this._files||[] );
+        array.forEach( this.uploader._files, function(f) {
+            allFiles.unshift( f );
+        });
+        this._files = array.filter( allFiles, function( file ) {
             var key = file.name;
             if( seenFile[key] ) {
                 return false;
@@ -22,10 +26,20 @@ return declare( FileList,
 	array.forEach( this._files, function(f, i){
 			  this._addRow(i+1, this.getFileType(f.name), f.name, f.size);
 		      }, this);
+
+        this.onChange();
     },
 
     getFiles: function() {
-        return this._files || [];
-    }
+        return array.map( this._files || [], function(f) {
+          return { file: f,
+                   type: (this.getFileType(f.name)||'').toLowerCase()
+                 };
+        },this);
+    },
+
+    // change event stub
+    onChange: function() {}
+
 });
 });

src/JBrowse/View/FileDialog/TrackList.js

@@ -0,0 +1,47 @@
+define(['dojo/_base/declare',
+        'dojo/_base/array',
+       './TrackList/BAMDriver'],
+       function(declare, array, BAMDriver ) {
+
+return declare( null, {
+
+constructor: function( args ) {
+    this.fileDialog = args.dialog;
+    this.domNode = dojo.create('div', { className: 'trackList', innerHTML: 'track list!' });
+    this.types = [ BAMDriver ];
+},
+
+// offer a given resource record (either a file or a URL) to the
+// driver for a given store type.  returns true if that driver will
+// make use of that resource
+_offerResource: function( resource, typeDriver ) {
+    return typeDriver.tryResource( this.storeConfs, resource );
+},
+
+update: function() {
+    // when called, rebuild the store and track configurations that we are going to add
+    this.storeConfs = this.storeConfs || {};
+
+    // anneal the given resources into a set of data store
+    // configurations by offering each file to each type driver in
+    // turn until no more are being accepted
+    var resources = this.fileDialog.filesToOpen().concat( this.fileDialog.urlsToOpen() );
+    var lastLength = 0;
+    while( resources.length && resources.length != lastLength ) {
+        resources = array.filter( resources, function( rec ) {
+            return ! array.some( this.types, function( typeDriver ) {
+               return this._offerResource( rec, typeDriver );
+            },this);
+        },this);
+
+        lastLength = resources.length;
+    }
+    if( resources.length )
+        console.warn("warning: not all resources could be used", resources );
+
+    console.log( this.storeConfs );
+}
+
+});
+});
+

src/JBrowse/View/FileDialog/TrackList/BAMDriver.js

@@ -0,0 +1,106 @@
+define([
+           'JBrowse/Util',
+           'JBrowse/Model/FileBlob',
+           'JBrowse/Model/XHRBlob'
+       ],
+       function( Util, FileBlob, XHRBlob ) {
+var uniqCounter = 0;
+return {
+
+    storeType: 'JBrowse/Store/SeqFeature/BAM',
+
+    tryResource: function( configs, resource ) {
+        if( resource.type == 'bam' ) {
+            var basename = Util.basename(
+                resource.file ? resource.file.name :
+                resource.url  ? resource.url       :
+                                ''
+            );
+            if( !basename )
+                return false;
+
+            // go through the configs and see if there is one with a BAI that seems to match
+            for( var n in configs ) {
+                var c = configs[n];
+                if( Util.basename( c.bai ? c.bai.blob.name : c.baiUrlTemplate, '.bai' ) == basename ) {
+                    // it's a match, put it in
+                    c.bam = this._makeBlob( resource );
+                    return true;
+                }
+            }
+            // go through again and look for BAIs that don't have .bam on them
+            basename = Util.basename( basename, '.bam' );
+            for( var n in configs ) {
+                var c = configs[n];
+                if( Util.basename( c.bai ? c.bai.blob.name : c.baiUrlTemplate, '.bai' ) == basename ) {
+                    // it's a match, put it in
+                    c.bam = this._makeBlob( resource );
+                    return true;
+                }
+            }
+
+            // otherwise make a new store config for it
+            var newName = 'bam_'+uniqCounter++;
+            configs[newName] = {
+                type: this.storeType,
+                bam: this._makeBlob( resource ),
+                name: newName
+            };
+            return true;
+        } else if( resource.type == 'bai' ) {
+            var basename = Util.basename(
+                resource.file ? resource.file.name :
+                resource.url  ? resource.url       :
+                                ''
+                , '.bai'
+            );
+            if( !basename )
+                return false;
+
+            // go through the configs and look for BAMs that match like zee.bam -> zee.bam.bai
+            for( var n in configs ) {
+                var c = configs[n];
+                if( Util.basename( c.bam ? c.bam.blob.name : c.urlTemplate ) == basename ) {
+                    // it's a match, put it in
+                    c.bai = this._makeBlob( resource );
+                    return true;
+                }
+            }
+            // go through again and look for BAMs that match like zee.bam -> zee.bai
+            for( var n in configs ) {
+                var c = configs[n];
+                if( Util.basename( c.bam ? c.bam.blob.name : c.urlTemplate, '.bam' ) == basename ) {
+                    // it's a match, put it in
+                    c.bai = this._makeBlob( resource );
+                    return true;
+                }
+            }
+
+            // otherwise make a new store
+            var newName = 'bam_'+uniqCounter++;
+            configs[newName] = {
+                bai: this._makeBlob( resource ),
+                name: newName,
+                type: this.storeType
+            };
+            return true;
+        }
+        else
+            return false;
+    },
+
+    _makeBlob: function( resource ) {
+        var r = resource.file ? new FileBlob( resource.file ) :
+                resource.url  ? new XHRBlob( resource.url )   :
+                                null;
+        if( ! r )
+            throw 'unknown resource type';
+        return r;
+
+    },
+
+    confIsValid: function( conf ) {
+        return (conf.bam || conf.urlTemplate) && ( conf.bai || conf.baiUrlTemplate || conf.urlTemplate );
+    }
+};
+});

tests/js_tests/index.html

@@ -21,6 +21,7 @@
   <script type="text/javascript" src="spec/BAM.spec.js"></script>
   <script type="text/javascript" src="spec/RemoteBinaryFile.spec.js"></script>
   <script type="text/javascript" src="spec/Util.spec.js"></script>
+  <script type="text/javascript" src="spec/AddFiles.spec.js"></script>
 
   <script type="text/javascript">
     (function() {

tests/js_tests/spec/AddFiles.spec.js

@@ -0,0 +1,39 @@
+require([
+            'JBrowse/View/FileDialog/TrackList/BAMDriver'
+        ], function( BAMDriver ) {
+
+describe( 'BAM driver', function() {
+              it( 'can match a simple BAM URL with its BAI URL', function( ) {
+                      var confs = { foo: { baiUrlTemplate: 'zee.bam.bai' } };
+                      expect( BAMDriver.tryResource( confs, { type: 'bam', url: 'zee.bam' } ) )
+                          .toBeTruthy();
+                      expect( confs.foo.bam.url ).toEqual( 'zee.bam' );
+                  });
+
+              it( 'can match a simple BAM file with its BAI URL', function( ) {
+                      var confs = { foo: { baiUrlTemplate: 'zee.bam.bai' } };
+                      expect( BAMDriver.tryResource( confs, { type: 'bam', file: { name: 'zee.bam'} } ) )
+                          .toBeTruthy();
+                      expect( confs.foo.bam.blob.name ).toEqual( 'zee.bam' );
+                  });
+
+              it( 'matches a BAI file like zee.bai -> zee.bam', function( ) {
+                      var confs = { foo: { urlTemplate: '/zee.bam' } };
+                      expect( BAMDriver.tryResource( confs, { type: 'bai', file: { name: 'zee.bai'} } ) )
+                          .toBeTruthy();
+                      expect( confs.foo.bai.blob.name ).toEqual( 'zee.bai' );
+                  });
+
+              it( 'matches a BAM file like zee.bam -> zee.bai', function( ) {
+                      var confs = { foo: { baiUrlTemplate: '/zee.bai' } };
+                      expect( BAMDriver.tryResource( confs, { type: 'bam', file: { name: 'zee.bam'} } ) )
+                          .toBeTruthy();
+                      expect( confs.foo.bam.blob.name ).toEqual( 'zee.bam' );
+                  });
+
+
+          });
+
+
+});
+