Initial commit to get working BBI reader into Trackster.

client/galaxy/scripts/libs/bbi/jquery-ajax-native.js

@@ -0,0 +1,157 @@
+//     jQuery Ajax Native Plugin
+
+//     (c) 2015 Tarik Zakaria Benmerar, Acigna Inc.
+//      jQuery Ajax Native Plugin may be freely distributed under the MIT license.
+(function (root, factory) {
+    if (typeof define === 'function' && define.amd) {
+        // AMD. Register as an anonymous module.
+        define(['jquery'], factory);
+    } else if (typeof exports === 'object') {
+        // Node. Does not work with strict CommonJS, but
+        // only CommonJS-like environments that support module.exports,
+        // like Node.
+        module.exports = factory(require('jquery'));
+    } else {
+        // Browser globals (root is window)
+        factory(root.jQuery);
+    }
+}(this, function ( $ ) {
+    var ajaxSettings = $.ajaxSettings;
+    ajaxSettings.responseFields.native = 'responseNative';
+    ajaxSettings.converters[ '* native' ] = true;
+    var support = {},
+        xhrId = 0,
+        xhrSuccessStatus = {
+            // file protocol always yields status code 0, assume 200
+            0: 200,
+            // Support: IE9
+            // #1450: sometimes IE returns 1223 when it should be 204
+            1223: 204
+        },
+        xhrCallbacks = {},
+        xhrSupported = jQuery.ajaxSettings.xhr();
+    // Support: IE9
+    // Open requests must be manually aborted on unload (#5280)
+    if ( window.ActiveXObject ) {
+        $( window ).on( "unload", function() {
+            for ( var key in xhrCallbacks ) {
+                xhrCallbacks[ key ]();
+            }
+        });
+    }
+    support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported );
+    support.ajax = xhrSupported = !!xhrSupported;
+
+    //Native Data Type Ajax Transport
+    $.ajaxTransport('native', function ( options ) {
+        var callback;
+        // Cross domain only allowed if supported through XMLHttpRequest
+        if ( support.cors || xhrSupported && !options.crossDomain ) {
+            return {
+                send: function( headers, complete ) {
+                    var i,
+                        xhr = options.xhr(),
+                        id = ++xhrId,
+                        responses = {};
+
+                    xhr.open( options.type, options.url, options.async, options.username, options.password );
+
+                    // Apply custom fields if provided
+                    if ( options.xhrFields ) {
+                        for ( i in options.xhrFields ) {
+                            xhr[ i ] = options.xhrFields[ i ];
+                        }
+                    }
+
+                    // Override mime type if needed
+                    if ( options.mimeType && xhr.overrideMimeType ) {
+                        xhr.overrideMimeType( options.mimeType );
+                    }
+
+                    // X-Requested-With header
+                    // For cross-domain requests, seeing as conditions for a preflight are
+                    // akin to a jigsaw puzzle, we simply never set it to be sure.
+                    // (it can always be set on a per-request basis or even using ajaxSetup)
+                    // For same-domain requests, won't change header if already provided.
+                    if ( !options.crossDomain && !headers["X-Requested-With"] ) {
+                        headers["X-Requested-With"] = "XMLHttpRequest";
+                    }
+
+                    // Set headers
+                    for ( i in headers ) {
+                        xhr.setRequestHeader( i, headers[ i ] );
+                    }
+
+                    // Callback
+                    callback = function( type ) {
+                        return function() {
+                            if ( callback ) {
+                                delete xhrCallbacks[ id ];
+                                callback = xhr.onload = xhr.onerror = null;
+
+                                if ( type === "abort" ) {
+                                    xhr.abort();
+                                } else if ( type === "error" ) {
+                                    complete(
+                                        // file: protocol always yields status 0; see #8605, #14207
+                                        xhr.status,
+                                        xhr.statusText
+                                    );
+                                } else {
+                                    // The native response associated with the responseType
+                                    // Stored in the xhr.response attribute (XHR2 Spec)
+                                    if ( xhr.response ) {
+                                        responses.native = xhr.response;
+                                    }
+
+                                    complete(
+                                        xhrSuccessStatus[ xhr.status ] || xhr.status,
+                                        xhr.statusText,
+                                        responses,
+                                        xhr.getAllResponseHeaders()
+                                    );
+                                }
+                            }
+                        };
+                    };
+
+                    // Listen to events
+                    xhr.onload = callback();
+                    xhr.onerror = callback("error");
+
+                    // Create the abort callback
+                    callback = xhrCallbacks[ id ] = callback("abort");
+
+                    try {
+                        // Do send the request (this may raise an exception)
+                        xhr.send( options.hasContent && options.data || null );
+                    } catch ( e ) {
+                        // #14683: Only rethrow if this hasn't been notified as an error yet
+                        if ( callback ) {
+                            throw e;
+                        }
+                    }
+                },
+
+                abort: function() {
+                    if ( callback ) {
+                        callback();
+                    }
+                }
+            };
+        }
+    });
+
+
+    //$.getNative wrapper
+    $.getNative = function ( url, callback ) {
+        return $.ajax({
+            dataType: 'native',
+            url: url,
+            xhrFields: {
+                responseType: 'arraybuffer'
+            },
+            success: callback
+        });
+    }
+}));

client/galaxy/scripts/libs/bbi/spans.js

@@ -0,0 +1,257 @@
+/* -*- mode: javascript; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+//
+// Dalliance Genome Explorer
+// (c) Thomas Down 2006-2010
+//
+// spans.js: JavaScript Intset/Location port.
+//
+
+define([], function() {
+
+"use strict";
+
+
+function Range(min, max)
+{
+    if (typeof(min) != 'number' || typeof(max) != 'number')
+        throw 'Bad range ' + min + ',' + max;
+    this._min = min;
+    this._max = max;
+}
+
+Range.prototype.min = function() {
+    return this._min;
+}
+
+Range.prototype.max = function() {
+    return this._max;
+}
+
+Range.prototype.contains = function(pos) {
+    return pos >= this._min && pos <= this._max;
+}
+
+Range.prototype.isContiguous = function() {
+    return true;
+}
+
+Range.prototype.ranges = function() {
+    return [this];
+}
+
+Range.prototype._pushRanges = function(ranges) {
+    ranges.push(this);
+}
+
+Range.prototype.toString = function() {
+    return '[' + this._min + '-' + this._max + ']';
+}
+
+function _Compound(ranges) {
+    // given: a set of unsorted possibly overlapping ranges
+    // sort the input ranges
+    var sorted = ranges.sort(_rangeOrder);
+    // merge overlaps between adjacent ranges
+    var merged = [];
+    var current = sorted.shift();
+    sorted.forEach(function(range) {
+        if (range._min <= current._max) {
+            if (range._max > current._max) {
+                current._max = range._max;
+            }
+        }
+        else {
+            merged.push(current);
+            current = range;
+        }
+    });
+    merged.push(current);
+    this._ranges = merged;
+}
+
+_Compound.prototype.min = function() {
+    return this._ranges[0].min();
+}
+
+_Compound.prototype.max = function() {
+    return this._ranges[this._ranges.length - 1].max();
+}
+
+// returns the index of the first range that is not less than pos
+_Compound.prototype.lower_bound = function(pos) {
+    // first check if pos is out of range
+    var r = this.ranges();
+    if (pos > this.max()) return r.length;
+    if (pos < this.min()) return 0;
+    // do a binary search
+    var a=0, b=r.length - 1;
+    while (a <= b) {
+        var m = Math.floor((a+b)/2);
+        if (pos > r[m]._max) {
+            a = m+1;
+        }
+        else if (pos < r[m]._min) {
+            b = m-1;
+        }
+        else {
+            return m;
+        }
+    }
+    return a;
+}
+
+_Compound.prototype.contains = function(pos) {
+    var lb = this.lower_bound(pos);
+    if (lb < this._ranges.length && this._ranges[lb].contains(pos)) {
+        return true;
+    }
+    return false;
+}
+
+_Compound.prototype.insertRange = function(range) {
+    var lb = this.lower_bound(range._min);
+    if (lb === this._ranges.length) { // range follows this
+        this._ranges.push(range);
+        return;
+    }
+
+    var r = this.ranges();
+    if (range._max < r[lb]._min) { // range preceeds lb
+        this._ranges.splice(lb,0,range);
+        return;
+    }
+
+    // range overlaps lb (at least)
+    if (r[lb]._min < range._min) range._min = r[lb]._min;
+    var ub = lb+1;
+    while (ub < r.length && r[ub]._min <= range._max) {
+        ub++;
+    }
+    ub--;
+    // ub is the upper bound of the new range
+    if (r[ub]._max > range._max) range._max = r[ub]._max;
+
+    // splice range into this._ranges
+    this._ranges.splice(lb,ub-lb+1,range);
+    return;
+}
+
+_Compound.prototype.isContiguous = function() {
+    return this._ranges.length > 1;
+}
+
+_Compound.prototype.ranges = function() {
+    return this._ranges;
+}
+
+_Compound.prototype._pushRanges = function(ranges) {
+    for (var ri = 0; ri < this._ranges.length; ++ri)
+        ranges.push(this._ranges[ri]);
+}
+
+_Compound.prototype.toString = function() {
+    var s = '';
+    for (var r = 0; r < this._ranges.length; ++r) {
+        if (r>0) {
+            s = s + ',';
+        }
+        s = s + this._ranges[r].toString();
+    }
+    return s;
+}
+
+function union(s0, s1) {
+    if (! (s0 instanceof _Compound)) {
+        if (! (s0 instanceof Array))
+            s0 = [s0];
+        s0 = new _Compound(s0);
+    }
+
+    if (s1)
+        s0.insertRange(s1);
+
+    return s0;
+}
+
+function intersection(s0, s1) {
+    var r0 = s0.ranges();
+    var r1 = s1.ranges();
+    var l0 = r0.length, l1 = r1.length;
+    var i0 = 0, i1 = 0;
+    var or = [];
+
+    while (i0 < l0 && i1 < l1) {
+        var s0 = r0[i0], s1 = r1[i1];
+        var lapMin = Math.max(s0.min(), s1.min());
+        var lapMax = Math.min(s0.max(), s1.max());
+        if (lapMax >= lapMin) {
+            or.push(new Range(lapMin, lapMax));
+        }
+        if (s0.max() > s1.max()) {
+            ++i1;
+        } else {
+            ++i0;
+        }
+    }
+
+    if (or.length == 0) {
+        return null; // FIXME
+    } else if (or.length == 1) {
+        return or[0];
+    } else {
+        return new _Compound(or);
+    }
+}
+
+function coverage(s) {
+    var tot = 0;
+    var rl = s.ranges();
+    for (var ri = 0; ri < rl.length; ++ri) {
+        var r = rl[ri];
+        tot += (r.max() - r.min() + 1);
+    }
+    return tot;
+}
+
+
+
+function rangeOrder(a, b)
+{
+    if (a.min() < b.min()) {
+        return -1;
+    } else if (a.min() > b.min()) {
+        return 1;
+    } else if (a.max() < b.max()) {
+        return -1;
+    } else if (b.max() > a.max()) {
+        return 1;
+    } else {
+        return 0;
+    }
+}
+
+function _rangeOrder(a, b)
+{
+    if (a._min < b._min) {
+        return -1;
+    } else if (a._min > b._min) {
+        return 1;
+    } else if (a._max < b._max) {
+        return -1;
+    } else if (b._max > a._max) {
+        return 1;
+    } else {
+        return 0;
+    }
+}
+
+return {
+        Range: Range,
+        union: union,
+        intersection: intersection,
+        coverage: coverage,
+        rangeOver: rangeOrder,
+        _rangeOrder: _rangeOrder
+};
+});

client/galaxy/scripts/viz/bbi-data-manager.js

@@ -0,0 +1,60 @@
+define( ["viz/visualization", "libs/bbi/bigwig"],
+        function(visualization, bigwig) {
+
+    /**
+     * Data manager for BBI datasets/files, including BigWig and BigBed.
+     */
+    var BBIDataManager = visualization.GenomeDataManager.extend({
+
+        /**
+         * Load data from server and manages data entries. Adds a Deferred to manager
+         * for region; when data becomes available, replaces Deferred with data.
+         * Returns the Deferred that resolves when data is available.
+         */
+        load_data: function(region, mode, resolution, extra_params) {
+            var deferred = $.Deferred();
+            this.set_data(region, deferred);
+
+            var url = galaxy_config.root + 'datasets/' + this.get('dataset').id + '/display',
+                self = this;
+                var promise = new $.Deferred();
+                $.when(bigwig.makeBwg(url)).then(function(bb, err) {
+                    $.when(bb.readWigData(region.get("chrom"), region.get("start"), region.get("end"))).then(function(data) {
+                    // Transform data into "bigwig" format. "bigwig" format is an array of 2-element arrays
+                    // where each array is [position, score].
+                    var result = [];
+                    data.forEach(function(d) {
+                        // Each data element includes a min and max. If min and max are the same,
+                        // then entry is single base-pair resolution and only a single data point
+                        // is added. Otherwise entry is multiple base pairs and two data points are
+                        // added, one for the start and one for the end.
+
+                        // Add data point for entry start.
+                        result.push([d.min, d.score]);
+
+                        if (d.min !== d.max) {
+                            // Multi base-pair entry, so two data points are generated.
+                            result.push([d.max, d.score]);
+                        }
+                    });
+
+                    var entry = {
+                            data: result,
+                            region: region,
+                            dataset_type: 'bigwig'
+                        };
+
+                    self.set_data(region, entry);
+                    deferred.resolve(entry);
+                });
+            });
+
+            return deferred;
+        },
+    });
+
+    return {
+        BBIDataManager: BBIDataManager
+    };
+
+});

client/galaxy/scripts/viz/trackster/tracks.js

@@ -9,8 +9,9 @@ define([
     "mvc/dataset/data",
     "mvc/tool/tools",
     "utils/config",
+    "viz/bbi-data-manager",
     "ui/editable-text",
-], function(_, visualization, viz_views, util, slotting, painters, filters_mod, data, tools_mod, config_mod) {
+], function(_, visualization, viz_views, util, slotting, painters, filters_mod, data, tools_mod, config_mod, bbi) {
 
 
 var extend = _.extend;
@@ -187,6 +188,18 @@ function round(num, places) {
     return Math.round(num * val) / val;
 }
 
+/**
+ * Check if a server can do byte range requests.
+ */
+function supportsByteRanges(url) {
+    var promise = $.Deferred();
+    $.get(url).success(function (result, status, xhr) {
+        promise.resolve(xhr.getResponseHeader("Accept-Ranges") === "bytes");
+    });
+
+    return promise;
+}
+
 /**
  * Drawables hierarchy:
  *
@@ -3078,7 +3091,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {
         if ( [undefined, null, 0].indexOf(this.config.get_value("max_value")) !== -1 ) {
             this.config.set_value("max_value", _.max( _.map(result.data, function(d) { return d[1]; }) ) || 0);
         }
-        
+
         var canvas = ctx.canvas,
             painter = new painters.LinePainter(result.data, region.get('start'), region.get('end'), this.config.to_key_value_dict(), mode);
         painter.draw(ctx, canvas.width, canvas.height, w_scale);
@@ -3601,7 +3614,22 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
 var LineTrack = function (view, container, obj_dict) {
     this.mode = "Histogram";
     TiledTrack.call(this, view, container, obj_dict);
+
+    // var self = this;
+    // $.when(supportsByteRanges(galaxy_config.root + 'datasets/' + this.dataset.id + '/display'))
+    //  .then(function(supportsByteRanges) {
+    //      if (supportsByteRanges) {
+    //          self.data_manager = new bbi.BBIDataManager({
+    //              dataset: this.dataset
+    //          });
+    //      }
+    //
+    // });
+    this.data_manager = new bbi.BBIDataManager({
+        dataset: this.dataset
+    });
 };
+
 extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     display_modes: CONTINUOUS_DATA_MODES,
 

static/maps/libs/bbi/jquery-ajax-native.js.map

@@ -0,0 +1 @@
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static/maps/libs/bbi/spans.js.map

@@ -0,0 +1 @@
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static/maps/viz/bbi-data-manager.js.map

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static/scripts/libs/bbi/jquery-ajax-native.js

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+!function(a,b){"function"==typeof define&&define.amd?define(["jquery"],b):"object"==typeof exports?module.exports=b(require("jquery")):b(a.jQuery)}(this,function(a){var b=a.ajaxSettings;b.responseFields.native="responseNative",b.converters["* native"]=!0;var c={},d=0,e={0:200,1223:204},f={},g=jQuery.ajaxSettings.xhr();window.ActiveXObject&&a(window).on("unload",function(){for(var a in f)f[a]()}),c.cors=!!g&&"withCredentials"in g,c.ajax=g=!!g,a.ajaxTransport("native",function(a){var b;return c.cors||g&&!a.crossDomain?{send:function(c,g){var h,i=a.xhr(),j=++d,k={};if(i.open(a.type,a.url,a.async,a.username,a.password),a.xhrFields)for(h in a.xhrFields)i[h]=a.xhrFields[h];a.mimeType&&i.overrideMimeType&&i.overrideMimeType(a.mimeType),a.crossDomain||c["X-Requested-With"]||(c["X-Requested-With"]="XMLHttpRequest");for(h in c)i.setRequestHeader(h,c[h]);b=function(a){return function(){b&&(delete f[j],b=i.onload=i.onerror=null,"abort"===a?i.abort():"error"===a?g(i.status,i.statusText):(i.response&&(k.native=i.response),g(e[i.status]||i.status,i.statusText,k,i.getAllResponseHeaders())))}},i.onload=b(),i.onerror=b("error"),b=f[j]=b("abort");try{i.send(a.hasContent&&a.data||null)}catch(l){if(b)throw l}},abort:function(){b&&b()}}:void 0}),a.getNative=function(b,c){return a.ajax({dataType:"native",url:b,xhrFields:{responseType:"arraybuffer"},success:c})}});
+//# sourceMappingURL=../../../maps/libs/bbi/jquery-ajax-native.js.map

static/scripts/libs/bbi/spans.js

@@ -0,0 +1,2 @@
+define([],function(){"use strict";function a(a,b){if("number"!=typeof a||"number"!=typeof b)throw"Bad range "+a+","+b;this._min=a,this._max=b}function b(a){var b=a.sort(g),c=[],d=b.shift();b.forEach(function(a){a._min<=d._max?a._max>d._max&&(d._max=a._max):(c.push(d),d=a)}),c.push(d),this._ranges=c}function c(a,c){return a instanceof b||(a instanceof Array||(a=[a]),a=new b(a)),c&&a.insertRange(c),a}function d(c,d){for(var e=c.ranges(),f=d.ranges(),g=e.length,h=f.length,i=0,j=0,k=[];g>i&&h>j;){var c=e[i],d=f[j],l=Math.max(c.min(),d.min()),m=Math.min(c.max(),d.max());m>=l&&k.push(new a(l,m)),c.max()>d.max()?++j:++i}return 0==k.length?null:1==k.length?k[0]:new b(k)}function e(a){for(var b=0,c=a.ranges(),d=0;d<c.length;++d){var e=c[d];b+=e.max()-e.min()+1}return b}function f(a,b){return a.min()<b.min()?-1:a.min()>b.min()?1:a.max()<b.max()?-1:b.max()>a.max()?1:0}function g(a,b){return a._min<b._min?-1:a._min>b._min?1:a._max<b._max?-1:b._max>a._max?1:0}return a.prototype.min=function(){return this._min},a.prototype.max=function(){return this._max},a.prototype.contains=function(a){return a>=this._min&&a<=this._max},a.prototype.isContiguous=function(){return!0},a.prototype.ranges=function(){return[this]},a.prototype._pushRanges=function(a){a.push(this)},a.prototype.toString=function(){return"["+this._min+"-"+this._max+"]"},b.prototype.min=function(){return this._ranges[0].min()},b.prototype.max=function(){return this._ranges[this._ranges.length-1].max()},b.prototype.lower_bound=function(a){var b=this.ranges();if(a>this.max())return b.length;if(a<this.min())return 0;for(var c=0,d=b.length-1;d>=c;){var e=Math.floor((c+d)/2);if(a>b[e]._max)c=e+1;else{if(!(a<b[e]._min))return e;d=e-1}}return c},b.prototype.contains=function(a){var b=this.lower_bound(a);return b<this._ranges.length&&this._ranges[b].contains(a)?!0:!1},b.prototype.insertRange=function(a){var b=this.lower_bound(a._min);if(b===this._ranges.length)return void this._ranges.push(a);var c=this.ranges();if(a._max<c[b]._min)return void this._ranges.splice(b,0,a);c[b]._min<a._min&&(a._min=c[b]._min);for(var d=b+1;d<c.length&&c[d]._min<=a._max;)d++;d--,c[d]._max>a._max&&(a._max=c[d]._max),this._ranges.splice(b,d-b+1,a)},b.prototype.isContiguous=function(){return this._ranges.length>1},b.prototype.ranges=function(){return this._ranges},b.prototype._pushRanges=function(a){for(var b=0;b<this._ranges.length;++b)a.push(this._ranges[b])},b.prototype.toString=function(){for(var a="",b=0;b<this._ranges.length;++b)b>0&&(a+=","),a+=this._ranges[b].toString();return a},{Range:a,union:c,intersection:d,coverage:e,rangeOver:f,_rangeOrder:g}});
+//# sourceMappingURL=../../../maps/libs/bbi/spans.js.map

static/scripts/viz/bbi-data-manager.js

@@ -0,0 +1,2 @@
+define(["viz/visualization","libs/bbi/bigwig"],function(a,b){var c=a.GenomeDataManager.extend({load_data:function(a){var c=$.Deferred();this.set_data(a,c);{var d=galaxy_config.root+"datasets/"+this.get("dataset").id+"/display",e=this;new $.Deferred}return $.when(b.makeBwg(d)).then(function(b){$.when(b.readWigData(a.get("chrom"),a.get("start"),a.get("end"))).then(function(b){var d=[];b.forEach(function(a){d.push([a.min,a.score]),a.min!==a.max&&d.push([a.max,a.score])});var f={data:d,region:a,dataset_type:"bigwig"};e.set_data(a,f),c.resolve(f)})}),c}});return{BBIDataManager:c}});
+//# sourceMappingURL=../../maps/viz/bbi-data-manager.js.map