diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py index bda10d45bee..0b102269c4f 100644 --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -738,7 +738,7 @@ class SummaryTreeDataProvider( GenomeDataProvider ): st = summary_tree_from_file( self.converted_dataset.file_name ) return st.chrom_blocks.keys() - def get_data( self, chrom, start, end, level=None, resolution=None, detail_cutoff=None, draw_cutoff=None ): + def get_data( self, chrom, start, end, level=None, resolution=None, detail_cutoff=None, draw_cutoff=None, **kwargs ): """ Returns summary tree data for a given genomic region. """ @@ -779,7 +779,8 @@ class SummaryTreeDataProvider( GenomeDataProvider ): 'data': results, 'max': stats[ level ][ "max" ], 'avg': stats[ level ][ "avg" ], - 'delta': stats[ level ][ "delta" ] + 'delta': stats[ level ][ "delta" ], + 'level': level } def has_data( self, chrom ): @@ -1015,6 +1016,9 @@ class BBIDataProvider( GenomeDataProvider ): return all_dat is not None def get_data( self, chrom, start, end, start_val=0, max_vals=None, num_samples=1000, **kwargs ): + start = int( start ) + end = int( end ) + # Bigwig can be a standalone bigwig file, in which case we use # original_dataset, or coming from wig->bigwig conversion in # which we use converted_dataset @@ -1111,7 +1115,10 @@ class BBIDataProvider( GenomeDataProvider ): # Cleanup and return. f.close() - return { 'data': result } + return { + 'data': result, + 'dataset_type': self.dataset_type + } class BigBedDataProvider( BBIDataProvider ): def _get_dataset( self ): diff --git a/lib/galaxy/web/api/datasets.py b/lib/galaxy/web/api/datasets.py index 14f2d106c2e..155873381e4 100644 --- a/lib/galaxy/web/api/datasets.py +++ b/lib/galaxy/web/api/datasets.py @@ -139,15 +139,11 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ): if mode == "Coverage": # Get summary using minimal cutoffs. indexer = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' ) - summary = indexer.get_data( chrom, low, high, - resolution=kwargs[ 'resolution' ], - level=kwargs.get( 'level', None ), - detail_cutoff=0, draw_cutoff=0 ) + summary = indexer.get_data( chrom, low, high, detail_cutoff=0, draw_cutoff=0, **kwargs ) if summary == "detail": # Use maximum level of detail--2--to get summary data no matter the resolution. summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], level=2, detail_cutoff=0, draw_cutoff=0 ) - frequencies, max_v, avg_v, delta = summary - return { 'dataset_type': indexer.dataset_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } + return summary if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and mode == "Auto": # Only check for summary_tree if it's Auto mode (which is the default) diff --git a/static/scripts/libs/underscore.js b/static/scripts/libs/underscore.js index 208d4cd890c..a3d378aa3b0 100644 --- a/static/scripts/libs/underscore.js +++ b/static/scripts/libs/underscore.js @@ -1,10 +1,7 @@ -// Underscore.js 1.3.1 +// Underscore.js 1.4.0 +// http://underscorejs.org // (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc. -// Underscore is freely distributable under the MIT license. -// Portions of Underscore are inspired or borrowed from Prototype, -// Oliver Steele's Functional, and John Resig's Micro-Templating. -// For all details and documentation: -// http://documentcloud.github.com/underscore +// Underscore may be freely distributed under the MIT license. (function() { @@ -24,7 +21,9 @@ var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype; // Create quick reference variables for speed access to core prototypes. - var slice = ArrayProto.slice, + var push = ArrayProto.push, + slice = ArrayProto.slice, + concat = ArrayProto.concat, unshift = ArrayProto.unshift, toString = ObjProto.toString, hasOwnProperty = ObjProto.hasOwnProperty; @@ -46,7 +45,11 @@ nativeBind = FuncProto.bind; // Create a safe reference to the Underscore object for use below. - var _ = function(obj) { return new wrapper(obj); }; + var _ = function(obj) { + if (obj instanceof _) return obj; + if (!(this instanceof _)) return new _(obj); + this._wrapped = obj; + }; // Export the Underscore object for **Node.js**, with // backwards-compatibility for the old `require()` API. If we're in @@ -62,7 +65,7 @@ } // Current version. - _.VERSION = '1.3.1'; + _.VERSION = '1.4.0'; // Collection Functions // -------------------- @@ -71,12 +74,11 @@ // Handles objects with the built-in `forEach`, arrays, and raw objects. // Delegates to **ECMAScript 5**'s native `forEach` if available. var each = _.each = _.forEach = function(obj, iterator, context) { - if (obj == null) return; if (nativeForEach && obj.forEach === nativeForEach) { obj.forEach(iterator, context); } else if (obj.length === +obj.length) { for (var i = 0, l = obj.length; i < l; i++) { - if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return; + if (iterator.call(context, obj[i], i, obj) === breaker) return; } } else { for (var key in obj) { @@ -91,12 +93,10 @@ // Delegates to **ECMAScript 5**'s native `map` if available. _.map = _.collect = function(obj, iterator, context) { var results = []; - if (obj == null) return results; if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context); each(obj, function(value, index, list) { results[results.length] = iterator.call(context, value, index, list); }); - if (obj.length === +obj.length) results.length = obj.length; return results; }; @@ -104,7 +104,6 @@ // or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available. _.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) { var initial = arguments.length > 2; - if (obj == null) obj = []; if (nativeReduce && obj.reduce === nativeReduce) { if (context) iterator = _.bind(iterator, context); return initial ? obj.reduce(iterator, memo) : obj.reduce(iterator); @@ -125,14 +124,26 @@ // Delegates to **ECMAScript 5**'s native `reduceRight` if available. _.reduceRight = _.foldr = function(obj, iterator, memo, context) { var initial = arguments.length > 2; - if (obj == null) obj = []; if (nativeReduceRight && obj.reduceRight === nativeReduceRight) { if (context) iterator = _.bind(iterator, context); - return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator); + return arguments.length > 2 ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator); } - var reversed = _.toArray(obj).reverse(); - if (context && !initial) iterator = _.bind(iterator, context); - return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator); + var length = obj.length; + if (length !== +length) { + var keys = _.keys(obj); + length = keys.length; + } + each(obj, function(value, index, list) { + index = keys ? keys[--length] : --length; + if (!initial) { + memo = obj[index]; + initial = true; + } else { + memo = iterator.call(context, memo, obj[index], index, list); + } + }); + if (!initial) throw new TypeError('Reduce of empty array with no initial value'); + return memo; }; // Return the first value which passes a truth test. Aliased as `detect`. @@ -152,7 +163,6 @@ // Aliased as `select`. _.filter = _.select = function(obj, iterator, context) { var results = []; - if (obj == null) return results; if (nativeFilter && obj.filter === nativeFilter) return obj.filter(iterator, context); each(obj, function(value, index, list) { if (iterator.call(context, value, index, list)) results[results.length] = value; @@ -163,7 +173,6 @@ // Return all the elements for which a truth test fails. _.reject = function(obj, iterator, context) { var results = []; - if (obj == null) return results; each(obj, function(value, index, list) { if (!iterator.call(context, value, index, list)) results[results.length] = value; }); @@ -174,13 +183,13 @@ // Delegates to **ECMAScript 5**'s native `every` if available. // Aliased as `all`. _.every = _.all = function(obj, iterator, context) { + iterator || (iterator = _.identity); var result = true; - if (obj == null) return result; if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context); each(obj, function(value, index, list) { if (!(result = result && iterator.call(context, value, index, list))) return breaker; }); - return result; + return !!result; }; // Determine if at least one element in the object matches a truth test. @@ -189,7 +198,6 @@ var any = _.some = _.any = function(obj, iterator, context) { iterator || (iterator = _.identity); var result = false; - if (obj == null) return result; if (nativeSome && obj.some === nativeSome) return obj.some(iterator, context); each(obj, function(value, index, list) { if (result || (result = iterator.call(context, value, index, list))) return breaker; @@ -197,11 +205,10 @@ return !!result; }; - // Determine if a given value is included in the array or object using `===`. - // Aliased as `contains`. - _.include = _.contains = function(obj, target) { + // Determine if the array or object contains a given value (using `===`). + // Aliased as `include`. + _.contains = _.include = function(obj, target) { var found = false; - if (obj == null) return found; if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1; found = any(obj, function(value) { return value === target; @@ -213,7 +220,7 @@ _.invoke = function(obj, method) { var args = slice.call(arguments, 2); return _.map(obj, function(value) { - return (_.isFunction(method) ? method || value : value[method]).apply(value, args); + return (_.isFunction(method) ? method : value[method]).apply(value, args); }); }; @@ -222,9 +229,25 @@ return _.map(obj, function(value){ return value[key]; }); }; + // Convenience version of a common use case of `filter`: selecting only objects + // with specific `key:value` pairs. + _.where = function(obj, attrs) { + if (_.isEmpty(attrs)) return []; + return _.filter(obj, function(value) { + for (var key in attrs) { + if (attrs[key] !== value[key]) return false; + } + return true; + }); + }; + // Return the maximum element or (element-based computation). + // Can't optimize arrays of integers longer than 65,535 elements. + // See: https://bugs.webkit.org/show_bug.cgi?id=80797 _.max = function(obj, iterator, context) { - if (!iterator && _.isArray(obj)) return Math.max.apply(Math, obj); + if (!iterator && _.isArray(obj) && obj[0] === +obj[0] && obj.length < 65535) { + return Math.max.apply(Math, obj); + } if (!iterator && _.isEmpty(obj)) return -Infinity; var result = {computed : -Infinity}; each(obj, function(value, index, list) { @@ -236,7 +259,9 @@ // Return the minimum element (or element-based computation). _.min = function(obj, iterator, context) { - if (!iterator && _.isArray(obj)) return Math.min.apply(Math, obj); + if (!iterator && _.isArray(obj) && obj[0] === +obj[0] && obj.length < 65535) { + return Math.min.apply(Math, obj); + } if (!iterator && _.isEmpty(obj)) return Infinity; var result = {computed : Infinity}; each(obj, function(value, index, list) { @@ -248,81 +273,107 @@ // Shuffle an array. _.shuffle = function(obj) { - var shuffled = [], rand; - each(obj, function(value, index, list) { - if (index == 0) { - shuffled[0] = value; - } else { - rand = Math.floor(Math.random() * (index + 1)); - shuffled[index] = shuffled[rand]; - shuffled[rand] = value; - } + var rand; + var index = 0; + var shuffled = []; + each(obj, function(value) { + rand = _.random(index++); + shuffled[index - 1] = shuffled[rand]; + shuffled[rand] = value; }); return shuffled; }; + // An internal function to generate lookup iterators. + var lookupIterator = function(value) { + return _.isFunction(value) ? value : function(obj){ return obj[value]; }; + }; + // Sort the object's values by a criterion produced by an iterator. - _.sortBy = function(obj, iterator, context) { + _.sortBy = function(obj, value, context) { + var iterator = lookupIterator(value); return _.pluck(_.map(obj, function(value, index, list) { return { value : value, + index : index, criteria : iterator.call(context, value, index, list) }; }).sort(function(left, right) { - var a = left.criteria, b = right.criteria; - return a < b ? -1 : a > b ? 1 : 0; + var a = left.criteria; + var b = right.criteria; + if (a !== b) { + if (a > b || a === void 0) return 1; + if (a < b || b === void 0) return -1; + } + return left.index < right.index ? -1 : 1; }), 'value'); }; - // Groups the object's values by a criterion. Pass either a string attribute - // to group by, or a function that returns the criterion. - _.groupBy = function(obj, val) { + // An internal function used for aggregate "group by" operations. + var group = function(obj, value, context, behavior) { var result = {}; - var iterator = _.isFunction(val) ? val : function(obj) { return obj[val]; }; + var iterator = lookupIterator(value); each(obj, function(value, index) { - var key = iterator(value, index); - (result[key] || (result[key] = [])).push(value); + var key = iterator.call(context, value, index, obj); + behavior(result, key, value); }); return result; }; - // Use a comparator function to figure out at what index an object should - // be inserted so as to maintain order. Uses binary search. - _.sortedIndex = function(array, obj, iterator) { - iterator || (iterator = _.identity); + // Groups the object's values by a criterion. Pass either a string attribute + // to group by, or a function that returns the criterion. + _.groupBy = function(obj, value, context) { + return group(obj, value, context, function(result, key, value) { + (_.has(result, key) ? result[key] : (result[key] = [])).push(value); + }); + }; + + // Counts instances of an object that group by a certain criterion. Pass + // either a string attribute to count by, or a function that returns the + // criterion. + _.countBy = function(obj, value, context) { + return group(obj, value, context, function(result, key, value) { + if (!_.has(result, key)) result[key] = 0; + result[key]++; + }); + }; + + // Use a comparator function to figure out the smallest index at which + // an object should be inserted so as to maintain order. Uses binary search. + _.sortedIndex = function(array, obj, iterator, context) { + iterator = iterator == null ? _.identity : lookupIterator(iterator); + var value = iterator.call(context, obj); var low = 0, high = array.length; while (low < high) { - var mid = (low + high) >> 1; - iterator(array[mid]) < iterator(obj) ? low = mid + 1 : high = mid; + var mid = (low + high) >>> 1; + iterator.call(context, array[mid]) < value ? low = mid + 1 : high = mid; } return low; }; // Safely convert anything iterable into a real, live array. - _.toArray = function(iterable) { - if (!iterable) return []; - if (iterable.toArray) return iterable.toArray(); - if (_.isArray(iterable)) return slice.call(iterable); - if (_.isArguments(iterable)) return slice.call(iterable); - return _.values(iterable); + _.toArray = function(obj) { + if (!obj) return []; + if (obj.length === +obj.length) return slice.call(obj); + return _.values(obj); }; // Return the number of elements in an object. _.size = function(obj) { - return _.toArray(obj).length; + return (obj.length === +obj.length) ? obj.length : _.keys(obj).length; }; // Array Functions // --------------- // Get the first element of an array. Passing **n** will return the first N - // values in the array. Aliased as `head`. The **guard** check allows it to work - // with `_.map`. - _.first = _.head = function(array, n, guard) { + // values in the array. Aliased as `head` and `take`. The **guard** check + // allows it to work with `_.map`. + _.first = _.head = _.take = function(array, n, guard) { return (n != null) && !guard ? slice.call(array, 0, n) : array[0]; }; - // Returns everything but the last entry of the array. Especcialy useful on + // Returns everything but the last entry of the array. Especially useful on // the arguments object. Passing **n** will return all the values in // the array, excluding the last N. The **guard** check allows it to work with // `_.map`. @@ -340,12 +391,12 @@ } }; - // Returns everything but the first entry of the array. Aliased as `tail`. - // Especially useful on the arguments object. Passing an **index** will return - // the rest of the values in the array from that index onward. The **guard** + // Returns everything but the first entry of the array. Aliased as `tail` and `drop`. + // Especially useful on the arguments object. Passing an **n** will return + // the rest N values in the array. The **guard** // check allows it to work with `_.map`. - _.rest = _.tail = function(array, index, guard) { - return slice.call(array, (index == null) || guard ? 1 : index); + _.rest = _.tail = _.drop = function(array, n, guard) { + return slice.call(array, (n == null) || guard ? 1 : n); }; // Trim out all falsy values from an array. @@ -353,13 +404,21 @@ return _.filter(array, function(value){ return !!value; }); }; + // Internal implementation of a recursive `flatten` function. + var flatten = function(input, shallow, output) { + each(input, function(value) { + if (_.isArray(value)) { + shallow ? push.apply(output, value) : flatten(value, shallow, output); + } else { + output.push(value); + } + }); + return output; + }; + // Return a completely flattened version of an array. _.flatten = function(array, shallow) { - return _.reduce(array, function(memo, value) { - if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value)); - memo[memo.length] = value; - return memo; - }, []); + return flatten(array, shallow, []); }; // Return a version of the array that does not contain the specified value(s). @@ -370,28 +429,28 @@ // Produce a duplicate-free version of the array. If the array has already // been sorted, you have the option of using a faster algorithm. // Aliased as `unique`. - _.uniq = _.unique = function(array, isSorted, iterator) { - var initial = iterator ? _.map(array, iterator) : array; - var result = []; - _.reduce(initial, function(memo, el, i) { - if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) { - memo[memo.length] = el; - result[result.length] = array[i]; + _.uniq = _.unique = function(array, isSorted, iterator, context) { + var initial = iterator ? _.map(array, iterator, context) : array; + var results = []; + var seen = []; + each(initial, function(value, index) { + if (isSorted ? (!index || seen[seen.length - 1] !== value) : !_.contains(seen, value)) { + seen.push(value); + results.push(array[index]); } - return memo; - }, []); - return result; + }); + return results; }; // Produce an array that contains the union: each distinct element from all of // the passed-in arrays. _.union = function() { - return _.uniq(_.flatten(arguments, true)); + return _.uniq(concat.apply(ArrayProto, arguments)); }; // Produce an array that contains every item shared between all the - // passed-in arrays. (Aliased as "intersect" for back-compat.) - _.intersection = _.intersect = function(array) { + // passed-in arrays. + _.intersection = function(array) { var rest = slice.call(arguments, 1); return _.filter(_.uniq(array), function(item) { return _.every(rest, function(other) { @@ -403,8 +462,8 @@ // Take the difference between one array and a number of other arrays. // Only the elements present in just the first array will remain. _.difference = function(array) { - var rest = _.flatten(slice.call(arguments, 1)); - return _.filter(array, function(value){ return !_.include(rest, value); }); + var rest = concat.apply(ArrayProto, slice.call(arguments, 1)); + return _.filter(array, function(value){ return !_.contains(rest, value); }); }; // Zip together multiple lists into a single array -- elements that share @@ -413,10 +472,27 @@ var args = slice.call(arguments); var length = _.max(_.pluck(args, 'length')); var results = new Array(length); - for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i); + for (var i = 0; i < length; i++) { + results[i] = _.pluck(args, "" + i); + } return results; }; + // Converts lists into objects. Pass either a single array of `[key, value]` + // pairs, or two parallel arrays of the same length -- one of keys, and one of + // the corresponding values. + _.object = function(list, values) { + var result = {}; + for (var i = 0, l = list.length; i < l; i++) { + if (values) { + result[list[i]] = values[i]; + } else { + result[list[i][0]] = list[i][1]; + } + } + return result; + }; + // If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**), // we need this function. Return the position of the first occurrence of an // item in an array, or -1 if the item is not included in the array. @@ -424,23 +500,25 @@ // If the array is large and already in sort order, pass `true` // for **isSorted** to use binary search. _.indexOf = function(array, item, isSorted) { - if (array == null) return -1; - var i, l; + var i = 0, l = array.length; if (isSorted) { - i = _.sortedIndex(array, item); - return array[i] === item ? i : -1; + if (typeof isSorted == 'number') { + i = (isSorted < 0 ? Math.max(0, l + isSorted) : isSorted); + } else { + i = _.sortedIndex(array, item); + return array[i] === item ? i : -1; + } } - if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item); - for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i; + if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item, isSorted); + for (; i < l; i++) if (array[i] === item) return i; return -1; }; // Delegates to **ECMAScript 5**'s native `lastIndexOf` if available. - _.lastIndexOf = function(array, item) { - if (array == null) return -1; - if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item); - var i = array.length; - while (i--) if (i in array && array[i] === item) return i; + _.lastIndexOf = function(array, item, fromIndex) { + if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item, fromIndex); + var i = (fromIndex != null ? fromIndex : array.length); + while (i--) if (array[i] === item) return i; return -1; }; @@ -514,7 +592,7 @@ // it with the arguments supplied. _.delay = function(func, wait) { var args = slice.call(arguments, 2); - return setTimeout(function(){ return func.apply(func, args); }, wait); + return setTimeout(function(){ return func.apply(null, args); }, wait); }; // Defers a function, scheduling it to run after the current call stack has @@ -526,39 +604,46 @@ // Returns a function, that, when invoked, will only be triggered at most once // during a given window of time. _.throttle = function(func, wait) { - var context, args, timeout, throttling, more; + var context, args, timeout, throttling, more, result; var whenDone = _.debounce(function(){ more = throttling = false; }, wait); return function() { context = this; args = arguments; var later = function() { timeout = null; - if (more) func.apply(context, args); + if (more) { + result = func.apply(context, args); + } whenDone(); }; if (!timeout) timeout = setTimeout(later, wait); if (throttling) { more = true; } else { - func.apply(context, args); + throttling = true; + result = func.apply(context, args); } whenDone(); - throttling = true; + return result; }; }; // Returns a function, that, as long as it continues to be invoked, will not // be triggered. The function will be called after it stops being called for - // N milliseconds. - _.debounce = function(func, wait) { - var timeout; + // N milliseconds. If `immediate` is passed, trigger the function on the + // leading edge, instead of the trailing. + _.debounce = function(func, wait, immediate) { + var timeout, result; return function() { var context = this, args = arguments; var later = function() { timeout = null; - func.apply(context, args); + if (!immediate) result = func.apply(context, args); }; + var callNow = immediate && !timeout; clearTimeout(timeout); timeout = setTimeout(later, wait); + if (callNow) result = func.apply(context, args); + return result; }; }; @@ -569,7 +654,9 @@ return function() { if (ran) return memo; ran = true; - return memo = func.apply(this, arguments); + memo = func.apply(this, arguments); + func = null; + return memo; }; }; @@ -578,7 +665,8 @@ // conditionally execute the original function. _.wrap = function(func, wrapper) { return function() { - var args = [func].concat(slice.call(arguments, 0)); + var args = [func]; + push.apply(args, arguments); return wrapper.apply(this, args); }; }; @@ -600,7 +688,9 @@ _.after = function(times, func) { if (times <= 0) return func(); return function() { - if (--times < 1) { return func.apply(this, arguments); } + if (--times < 1) { + return func.apply(this, arguments); + } }; }; @@ -618,7 +708,23 @@ // Retrieve the values of an object's properties. _.values = function(obj) { - return _.map(obj, _.identity); + var values = []; + for (var key in obj) if (_.has(obj, key)) values.push(obj[key]); + return values; + }; + + // Convert an object into a list of `[key, value]` pairs. + _.pairs = function(obj) { + var pairs = []; + for (var key in obj) if (_.has(obj, key)) pairs.push([key, obj[key]]); + return pairs; + }; + + // Invert the keys and values of an object. The values must be serializable. + _.invert = function(obj) { + var result = {}; + for (var key in obj) if (_.has(obj, key)) result[obj[key]] = key; + return result; }; // Return a sorted list of the function names available on the object. @@ -641,6 +747,26 @@ return obj; }; + // Return a copy of the object only containing the whitelisted properties. + _.pick = function(obj) { + var copy = {}; + var keys = concat.apply(ArrayProto, slice.call(arguments, 1)); + each(keys, function(key) { + if (key in obj) copy[key] = obj[key]; + }); + return copy; + }; + + // Return a copy of the object without the blacklisted properties. + _.omit = function(obj) { + var copy = {}; + var keys = concat.apply(ArrayProto, slice.call(arguments, 1)); + for (var key in obj) { + if (!_.contains(keys, key)) copy[key] = obj[key]; + } + return copy; + }; + // Fill in a given object with default properties. _.defaults = function(obj) { each(slice.call(arguments, 1), function(source) { @@ -665,19 +791,16 @@ return obj; }; - // Internal recursive comparison function. - function eq(a, b, stack) { + // Internal recursive comparison function for `isEqual`. + var eq = function(a, b, aStack, bStack) { // Identical objects are equal. `0 === -0`, but they aren't identical. // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal. if (a === b) return a !== 0 || 1 / a == 1 / b; // A strict comparison is necessary because `null == undefined`. if (a == null || b == null) return a === b; // Unwrap any wrapped objects. - if (a._chain) a = a._wrapped; - if (b._chain) b = b._wrapped; - // Invoke a custom `isEqual` method if one is provided. - if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b); - if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a); + if (a instanceof _) a = a._wrapped; + if (b instanceof _) b = b._wrapped; // Compare `[[Class]]` names. var className = toString.call(a); if (className != toString.call(b)) return false; @@ -707,14 +830,15 @@ if (typeof a != 'object' || typeof b != 'object') return false; // Assume equality for cyclic structures. The algorithm for detecting cyclic // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`. - var length = stack.length; + var length = aStack.length; while (length--) { // Linear search. Performance is inversely proportional to the number of // unique nested structures. - if (stack[length] == a) return true; + if (aStack[length] == a) return bStack[length] == b; } // Add the first object to the stack of traversed objects. - stack.push(a); + aStack.push(a); + bStack.push(b); var size = 0, result = true; // Recursively compare objects and arrays. if (className == '[object Array]') { @@ -724,20 +848,24 @@ if (result) { // Deep compare the contents, ignoring non-numeric properties. while (size--) { - // Ensure commutative equality for sparse arrays. - if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break; + if (!(result = eq(a[size], b[size], aStack, bStack))) break; } } } else { - // Objects with different constructors are not equivalent. - if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false; + // Objects with different constructors are not equivalent, but `Object`s + // from different frames are. + var aCtor = a.constructor, bCtor = b.constructor; + if (aCtor !== bCtor && !(_.isFunction(aCtor) && (aCtor instanceof aCtor) && + _.isFunction(bCtor) && (bCtor instanceof bCtor))) { + return false; + } // Deep compare objects. for (var key in a) { if (_.has(a, key)) { // Count the expected number of properties. size++; // Deep compare each member. - if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break; + if (!(result = _.has(b, key) && eq(a[key], b[key], aStack, bStack))) break; } } // Ensure that both objects contain the same number of properties. @@ -749,18 +877,20 @@ } } // Remove the first object from the stack of traversed objects. - stack.pop(); + aStack.pop(); + bStack.pop(); return result; - } + }; // Perform a deep comparison to check if two objects are equal. _.isEqual = function(a, b) { - return eq(a, b, []); + return eq(a, b, [], []); }; // Is a given array, string, or object empty? // An "empty" object has no enumerable own-properties. _.isEmpty = function(obj) { + if (obj == null) return true; if (_.isArray(obj) || _.isString(obj)) return obj.length === 0; for (var key in obj) if (_.has(obj, key)) return false; return true; @@ -768,7 +898,7 @@ // Is a given value a DOM element? _.isElement = function(obj) { - return !!(obj && obj.nodeType == 1); + return !!(obj && obj.nodeType === 1); }; // Is a given value an array? @@ -782,35 +912,36 @@ return obj === Object(obj); }; - // Is a given variable an arguments object? - _.isArguments = function(obj) { - return toString.call(obj) == '[object Arguments]'; - }; + // Add some isType methods: isArguments, isFunction, isString, isNumber, isDate, isRegExp. + each(['Arguments', 'Function', 'String', 'Number', 'Date', 'RegExp'], function(name) { + _['is' + name] = function(obj) { + return toString.call(obj) == '[object ' + name + ']'; + }; + }); + + // Define a fallback version of the method in browsers (ahem, IE), where + // there isn't any inspectable "Arguments" type. if (!_.isArguments(arguments)) { _.isArguments = function(obj) { return !!(obj && _.has(obj, 'callee')); }; } - // Is a given value a function? - _.isFunction = function(obj) { - return toString.call(obj) == '[object Function]'; + // Optimize `isFunction` if appropriate. + if (typeof (/./) !== 'function') { + _.isFunction = function(obj) { + return typeof obj === 'function'; + }; + } + + // Is a given object a finite number? + _.isFinite = function(obj) { + return _.isNumber(obj) && isFinite(obj); }; - // Is a given value a string? - _.isString = function(obj) { - return toString.call(obj) == '[object String]'; - }; - - // Is a given value a number? - _.isNumber = function(obj) { - return toString.call(obj) == '[object Number]'; - }; - - // Is the given value `NaN`? + // Is the given value `NaN`? (NaN is the only number which does not equal itself). _.isNaN = function(obj) { - // `NaN` is the only value for which `===` is not reflexive. - return obj !== obj; + return _.isNumber(obj) && obj != +obj; }; // Is a given value a boolean? @@ -818,16 +949,6 @@ return obj === true || obj === false || toString.call(obj) == '[object Boolean]'; }; - // Is a given value a date? - _.isDate = function(obj) { - return toString.call(obj) == '[object Date]'; - }; - - // Is the given value a regular expression? - _.isRegExp = function(obj) { - return toString.call(obj) == '[object RegExp]'; - }; - // Is a given value equal to null? _.isNull = function(obj) { return obj === null; @@ -838,7 +959,8 @@ return obj === void 0; }; - // Has own property? + // Shortcut function for checking if an object has a given property directly + // on itself (in other words, not on a prototype). _.has = function(obj, key) { return hasOwnProperty.call(obj, key); }; @@ -859,20 +981,65 @@ }; // Run a function **n** times. - _.times = function (n, iterator, context) { + _.times = function(n, iterator, context) { for (var i = 0; i < n; i++) iterator.call(context, i); }; - // Escape a string for HTML interpolation. - _.escape = function(string) { - return (''+string).replace(/&/g, '&').replace(//g, '>').replace(/"/g, '"').replace(/'/g, ''').replace(/\//g,'/'); + // Return a random integer between min and max (inclusive). + _.random = function(min, max) { + if (max == null) { + max = min; + min = 0; + } + return min + (0 | Math.random() * (max - min + 1)); }; - // Add your own custom functions to the Underscore object, ensuring that - // they're correctly added to the OOP wrapper as well. + // List of HTML entities for escaping. + var entityMap = { + escape: { + '&': '&', + '<': '<', + '>': '>', + '"': '"', + "'": ''', + '/': '/' + } + }; + entityMap.unescape = _.invert(entityMap.escape); + + // Regexes containing the keys and values listed immediately above. + var entityRegexes = { + escape: new RegExp('[' + _.keys(entityMap.escape).join('') + ']', 'g'), + unescape: new RegExp('(' + _.keys(entityMap.unescape).join('|') + ')', 'g') + }; + + // Functions for escaping and unescaping strings to/from HTML interpolation. + _.each(['escape', 'unescape'], function(method) { + _[method] = function(string) { + if (string == null) return ''; + return ('' + string).replace(entityRegexes[method], function(match) { + return entityMap[method][match]; + }); + }; + }); + + // If the value of the named property is a function then invoke it; + // otherwise, return it. + _.result = function(object, property) { + if (object == null) return null; + var value = object[property]; + return _.isFunction(value) ? value.call(object) : value; + }; + + // Add your own custom functions to the Underscore object. _.mixin = function(obj) { each(_.functions(obj), function(name){ - addToWrapper(name, _[name] = obj[name]); + var func = _[name] = obj[name]; + _.prototype[name] = function() { + var args = [this._wrapped]; + push.apply(args, arguments); + return result.call(this, func.apply(_, args)); + }; }); }; @@ -895,41 +1062,72 @@ // When customizing `templateSettings`, if you don't want to define an // interpolation, evaluation or escaping regex, we need one that is // guaranteed not to match. - var noMatch = /.^/; + var noMatch = /(.)^/; - // Within an interpolation, evaluation, or escaping, remove HTML escaping - // that had been previously added. - var unescape = function(code) { - return code.replace(/\\\\/g, '\\').replace(/\\'/g, "'"); + // Certain characters need to be escaped so that they can be put into a + // string literal. + var escapes = { + "'": "'", + '\\': '\\', + '\r': 'r', + '\n': 'n', + '\t': 't', + '\u2028': 'u2028', + '\u2029': 'u2029' }; + var escaper = /\\|'|\r|\n|\t|\u2028|\u2029/g; + // JavaScript micro-templating, similar to John Resig's implementation. // Underscore templating handles arbitrary delimiters, preserves whitespace, // and correctly escapes quotes within interpolated code. - _.template = function(str, data) { - var c = _.templateSettings; - var tmpl = 'var __p=[],print=function(){__p.push.apply(__p,arguments);};' + - 'with(obj||{}){__p.push(\'' + - str.replace(/\\/g, '\\\\') - .replace(/'/g, "\\'") - .replace(c.escape || noMatch, function(match, code) { - return "',_.escape(" + unescape(code) + "),'"; - }) - .replace(c.interpolate || noMatch, function(match, code) { - return "'," + unescape(code) + ",'"; - }) - .replace(c.evaluate || noMatch, function(match, code) { - return "');" + unescape(code).replace(/[\r\n\t]/g, ' ') + ";__p.push('"; - }) - .replace(/\r/g, '\\r') - .replace(/\n/g, '\\n') - .replace(/\t/g, '\\t') - + "');}return __p.join('');"; - var func = new Function('obj', '_', tmpl); - if (data) return func(data, _); - return function(data) { - return func.call(this, data, _); + _.template = function(text, data, settings) { + settings = _.defaults({}, settings, _.templateSettings); + + // Combine delimiters into one regular expression via alternation. + var matcher = new RegExp([ + (settings.escape || noMatch).source, + (settings.interpolate || noMatch).source, + (settings.evaluate || noMatch).source + ].join('|') + '|$', 'g'); + + // Compile the template source, escaping string literals appropriately. + var index = 0; + var source = "__p+='"; + text.replace(matcher, function(match, escape, interpolate, evaluate, offset) { + source += text.slice(index, offset) + .replace(escaper, function(match) { return '\\' + escapes[match]; }); + source += + escape ? "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'" : + interpolate ? "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'" : + evaluate ? "';\n" + evaluate + "\n__p+='" : ''; + index = offset + match.length; + }); + source += "';\n"; + + // If a variable is not specified, place data values in local scope. + if (!settings.variable) source = 'with(obj||{}){\n' + source + '}\n'; + + source = "var __t,__p='',__j=Array.prototype.join," + + "print=function(){__p+=__j.call(arguments,'');};\n" + + source + "return __p;\n"; + + try { + var render = new Function(settings.variable || 'obj', '_', source); + } catch (e) { + e.source = source; + throw e; + } + + if (data) return render(data, _); + var template = function(data) { + return render.call(this, data, _); }; + + // Provide the compiled function source as a convenience for precompilation. + template.source = 'function(' + (settings.variable || 'obj') + '){\n' + source + '}'; + + return template; }; // Add a "chain" function, which will delegate to the wrapper. @@ -937,29 +1135,15 @@ return _(obj).chain(); }; - // The OOP Wrapper + // OOP // --------------- - // If Underscore is called as a function, it returns a wrapped object that // can be used OO-style. This wrapper holds altered versions of all the // underscore functions. Wrapped objects may be chained. - var wrapper = function(obj) { this._wrapped = obj; }; - - // Expose `wrapper.prototype` as `_.prototype` - _.prototype = wrapper.prototype; // Helper function to continue chaining intermediate results. - var result = function(obj, chain) { - return chain ? _(obj).chain() : obj; - }; - - // A method to easily add functions to the OOP wrapper. - var addToWrapper = function(name, func) { - wrapper.prototype[name] = function() { - var args = slice.call(arguments); - unshift.call(args, this._wrapped); - return result(func.apply(_, args), this._chain); - }; + var result = function(obj) { + return this._chain ? _(obj).chain() : obj; }; // Add all of the Underscore functions to the wrapper object. @@ -968,32 +1152,35 @@ // Add all mutator Array functions to the wrapper. each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) { var method = ArrayProto[name]; - wrapper.prototype[name] = function() { - var wrapped = this._wrapped; - method.apply(wrapped, arguments); - var length = wrapped.length; - if ((name == 'shift' || name == 'splice') && length === 0) delete wrapped[0]; - return result(wrapped, this._chain); + _.prototype[name] = function() { + var obj = this._wrapped; + method.apply(obj, arguments); + if ((name == 'shift' || name == 'splice') && obj.length === 0) delete obj[0]; + return result.call(this, obj); }; }); // Add all accessor Array functions to the wrapper. each(['concat', 'join', 'slice'], function(name) { var method = ArrayProto[name]; - wrapper.prototype[name] = function() { - return result(method.apply(this._wrapped, arguments), this._chain); + _.prototype[name] = function() { + return result.call(this, method.apply(this._wrapped, arguments)); }; }); - // Start chaining a wrapped Underscore object. - wrapper.prototype.chain = function() { - this._chain = true; - return this; - }; + _.extend(_.prototype, { - // Extracts the result from a wrapped and chained object. - wrapper.prototype.value = function() { - return this._wrapped; - }; + // Start chaining a wrapped Underscore object. + chain: function() { + this._chain = true; + return this; + }, + + // Extracts the result from a wrapped and chained object. + value: function() { + return this._wrapped; + } + + }); }).call(this); diff --git a/static/scripts/packed/galaxy.base.js b/static/scripts/packed/galaxy.base.js index 44a70bac060..a7d60f5c9c5 100644 --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1 +1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a");var f=b.data("menu_options");if(obj_length(f)<=0){$("
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    ").attr("id","historyItem-"+d).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});var b=a.find("[popupmenu]");b.each(function(e,f){f=$(f);make_popupmenu(f)});this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('
    ');a.append(this._render_titleButtons());a.append('');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('
    ');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display"}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display"});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a={title:"Delete",href:this.model.get("delete_url"),target:"galaxy_main",id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if((this.model.get("deleted")||this.model.get("purged"))&&(!this.model.get("delete_url"))){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("
    "),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=linkHTMLTemplate({title:"Download",href:this.model.get("download_url"),classes:["icon-button","tooltip","disk"]});var d=this.model.get("download_meta_urls");if(!d){return a}var c=$('
    ');c.append(linkHTMLTemplate({text:"Download Dataset",title:"Download",href:this.model.get("download_url"),classes:["icon-button","tooltip","disk"]}));c.append("Additional Files");for(file_type in d){c.append(linkHTMLTemplate({text:"Download "+file_type,href:d[file_type],classes:["action-button"]}))}var b=$((''));b.append(a);c.append(b);return c},_render_errButton:function(){if((this.model.get("state")!==HistoryItem.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_tracksterButton:function(){var a=this.model.get("trackster_urls");if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a)){return null}this.tracksterButton=new IconButtonView({model:new IconButton({title:"View in Trackster",icon_class:"chart_curve"})});this.errButton.render();this.errButton.$el.addClass("trackster-add").attr({"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]});return this.errButton.$el},_render_secondaryActionButtons:function(b){var c=$('
    '),a=this;_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("retag_url"))){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("annotate_url"))){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotate_url"),icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(this.model.get("retag_url")){return null}return $(HistoryItemView.templates.tagArea(this.model.toJSON()))},_render_annotationArea:function(){if(!this.model.get("annotate_url")){return null}return $(HistoryItemView.templates.annotationArea(this.model.toJSON()))},_render_displayApps:function(){if(!this.model.get("display_apps")){return null}var a=this.model.get("displayApps"),c=$("
    "),b=$("");this.log(this+"displayApps:",a);return c},_render_peek:function(){if(!this.model.get("peek")){return null}return $("
    ").append($("
    ").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("
    You do not have permission to view dataset.
    "))},_render_body_uploading:function(a){a.append($("
    Dataset is uploading
    "))},_render_body_queued:function(a){a.append($("
    Job is waiting to run.
    "));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("
    Job is currently running.
    ");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("
    "+this.model.get("misc_blurb")+"
    "))}a.append(("An error occurred running this job: "+$.trim(this.model.get("misc_info"))+""));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("
    The job creating this dataset was cancelled before completion.
    ");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("
    Metadata is being auto-detected.
    "))},_render_body_empty:function(a){a.append($("
    No data: "+this.model.get("misc_blurb")+"
    "));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HistoryItemView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('
    ');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var b=this.model.get("state");var a=$("
    ").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('
    Error: unknown dataset state "'+b+'".
    '))}a.append('
    ');if(this.model.get("bodyIsShown")===false){a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!a.html()){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.model.get("ajax_set_annotation_url");if(d.is(":hidden")){if(!c.html()){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="Describe or add notes to dataset"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(){this.log(this+".toggleBodyVisibility");this.$el.find(".historyItemBody").toggle()},toString:function(){var a=(this.model)?(this.model+""):("");return"HistoryItemView("+a+")"}});HistoryItemView.templates=CompiledTemplateLoader.getTemplates({"common-templates.html":{warningMsg:"template-warningmessagesmall"},"history-templates.html":{messages:"template-history-warning-messages",titleLink:"template-history-titleLink",hdaSummary:"template-history-hdaSummary",failedMetadata:"template-history-failedMetaData",tagArea:"template-history-tagArea",annotationArea:"template-history-annotationArea"}});var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0}},initialize:function(b,a){this.log(this+".initialize",b,a);this.items=new HistoryCollection()},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){a.log("loading dataset: ",f,e);var h=new HistoryItem(_.extend(f,{history_id:b}));a.log("as History:",h);a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize");this.itemViews=[];var a=this;this.model.items.each(function(c){var b=new HistoryItemView({model:c});a.itemViews.push(b)})},render:function(){this.log(this+".render");var a=$("
    ");_.each(this.itemViews,function(b){a.prepend(b.render())});this.$el.append(a.children());a.remove()},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});function createMockHistoryData(){mockHistory={};mockHistory.data={template:{id:"a799d38679e985db",name:"template",data_type:"fastq",file_size:226297533,genome_build:"?",metadata_data_lines:0,metadata_dbkey:"?",metadata_sequences:0,misc_blurb:"215.8 MB",misc_info:"uploaded fastq file (misc_info)",model_class:"HistoryDatasetAssociation",download_url:"",state:"ok",visible:true,deleted:false,purged:false,hid:0,for_editing:true,accessible:true,undelete_url:"",purge_url:"",unhide_url:"",display_url:"example.com/display",edit_url:"example.com/edit",delete_url:"example.com/delete",show_params_url:"example.com/show_params",rerun_url:"example.com/rerun",retag_url:"example.com/retag",annotate_url:"example.com/annotate",peek:['','','','','','','',"
    1.QNAME2.FLAG3.RNAME4.POS5.MAPQ6.CIGAR7.MRNM8.MPOS9.ISIZE10.SEQ11.QUAL12.OPT
    @SQ	SN:gi|87159884|ref|NC_007793.1|	LN:2872769
    @PG	ID:bwa	PN:bwa	VN:0.5.9-r16
    HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968	73	gi|87159884|ref|NC_007793.1|	2720169	37	101M	=	2720169	0	NAATATGACATTATTTTCAAAACAGCTGAAAATTTAGACGTACCGATTTATCTACATCCCGCGCCAGTTAACAGTGACATTTATCAATCATACTATAAAGG	!!!!!!!!!!$!!!$!!!!!$!!!!!!$!$!$$$!!$!!$!!!!!!!!!!!$!
    !!!$!$!$$!!$$!!$!!!!!!!!!!!!!!!!!!!!!!!!!!$!!$!!	XT:A:U	NM:i:1	SM:i:37	AM:i:0	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:0A100
    HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968	133	gi|87159884|ref|NC_007793.1|	2720169	0	*	=	2720169	0	NAAACTGTGGCTTCGTTNNNNNNNNNNNNNNNGTGANNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNCNAANNNNNNNNNNNNNNNNNNNNN	!!!!!!!!!!!!$!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    "].join("")}};_.extend(mockHistory.data,{notAccessible:_.extend(_.clone(mockHistory.data.template),{accessible:false}),deleted:_.extend(_.clone(mockHistory.data.template),{deleted:true,delete_url:"",purge_url:"example.com/purge",undelete_url:"example.com/undelete"}),purgedNotDeleted:_.extend(_.clone(mockHistory.data.template),{purged:true,delete_url:""}),notvisible:_.extend(_.clone(mockHistory.data.template),{visible:false,unhide_url:"example.com/unhide"}),hasDisplayApps:_.extend(_.clone(mockHistory.data.template),{display_apps:{"display in IGB":{Web:"/display_application/63cd3858d057a6d1/igb_bam/Web",Local:"/display_application/63cd3858d057a6d1/igb_bam/Local"}}}),canTrackster:_.extend(_.clone(mockHistory.data.template),{trackster_urls:{"data-url":"example.com/trackster-data","action-url":"example.com/trackster-action","new-url":"example.com/trackster-new"}}),zeroSize:_.extend(_.clone(mockHistory.data.template),{file_size:0}),hasMetafiles:_.extend(_.clone(mockHistory.data.template),{download_meta_urls:{bam_index:"example.com/bam-index"}}),upload:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.UPLOAD}),queued:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.QUEUED}),running:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.RUNNING}),empty:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.EMPTY}),error:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.ERROR,report_error_url:"example.com/report_err"}),discarded:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.DISCARDED}),setting_metadata:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.SETTING_METADATA}),failed_metadata:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.FAILED_METADATA})});$(document).ready(function(){mockHistory.items={};mockHistory.views={};for(key in mockHistory.data){mockHistory.items[key]=new HistoryItem(mockHistory.data[key]);mockHistory.items[key].set("name",key);mockHistory.views[key]=new HistoryItemView({model:mockHistory.items[key]});$("body").append(mockHistory.views[key].render())}})};
\ No newline at end of file
+function linkHTMLTemplate(b,a){if(!b){return""}a=a||"a";var c=["<"+a];for(key in b){var d=b[key];if(d===""){continue}switch(key){case"text":continue;case"classes":key="class";d=(b.classes.join)?(b.classes.join(" ")):(b.classes);default:c.push([" ",key,'="',d,'"'].join(""))}}c.push(">");if("text" in b){c.push(b.text)}c.push("");return c.join("")}var HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryItem.STATES.NOT_VIEWABLE)}},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NOT_VIEWABLE:"not_viewable",NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(){this.log(this+".initialize:",this,this.model)},render:function(){var c=this.model.get("id"),b=this.model.get("state");this.clearReferences();this.$el.attr("id","historyItemContainer-"+c);var a=$("
    ").attr("id","historyItem-"+c).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+b);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});make_popup_menus(a);this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('
    ');a.append(this._render_titleButtons());a.append('');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('
    ');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display"}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display"});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a={title:"Delete",href:this.model.get("delete_url"),target:"galaxy_main",id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if((this.model.get("deleted")||this.model.get("purged"))&&(!this.model.get("delete_url"))){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("
    ").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){var e=d.call(a);b.append(e)});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HistoryItemView.templates.downloadLinks(this.model.toJSON());this.log("_render_downloadButton, downloadLinkHTML:",a);return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryItem.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_tracksterButton:function(){var a=this.model.get("trackster_urls");if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a)){return null}this.tracksterButton=new IconButtonView({model:new IconButton({title:"View in Trackster",icon_class:"chart_curve"})});this.errButton.render();this.errButton.$el.addClass("trackster-add").attr({"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]});return this.errButton.$el},_render_secondaryActionButtons:function(b){var c=$("
    "),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("retag_url"))){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("annotate_url"))){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotate_url"),icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(this.model.get("retag_url")){return null}return $(HistoryItemView.templates.tagArea(this.model.toJSON()))},_render_annotationArea:function(){if(!this.model.get("annotate_url")){return null}return $(HistoryItemView.templates.annotationArea(this.model.toJSON()))},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("
    ").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){this.log(this+"display_types:",this.model.get("display_types"));a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_types}))}if(!_.isEmpty(this.model.get("display_apps"))){this.log(this+"display_apps:",this.model.get("display_apps"));a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_apps}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("
    ").append($("
    ").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("
    You do not have permission to view dataset.
    "))},_render_body_uploading:function(a){a.append($("
    Dataset is uploading
    "))},_render_body_queued:function(a){a.append($("
    Job is waiting to run.
    "));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("
    Job is currently running.
    ");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("
    "+this.model.get("misc_blurb")+"
    "))}a.append(("An error occurred running this job: "+$.trim(this.model.get("misc_info"))+""));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("
    The job creating this dataset was cancelled before completion.
    ");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("
    Metadata is being auto-detected.
    "))},_render_body_empty:function(a){a.append($("
    No data: "+this.model.get("misc_blurb")+"
    "));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HistoryItemView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('
    ');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var b=this.model.get("state");var a=$("
    ").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('
    Error: unknown dataset state "'+b+'".
    '))}a.append('
    ');if(this.model.get("bodyIsShown")===false){a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!a.html()){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.model.get("ajax_set_annotation_url");if(d.is(":hidden")){if(!c.html()){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="Describe or add notes to dataset"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(){this.log(this+".toggleBodyVisibility");this.$el.find(".historyItemBody").toggle()},toString:function(){var a=(this.model)?(this.model+""):("");return"HistoryItemView("+a+")"}});HistoryItemView.templates=CompiledTemplateLoader.getTemplates({"common-templates.html":{warningMsg:"template-warningmessagesmall"},"history-templates.html":{messages:"template-history-warning-messages",titleLink:"template-history-titleLink",hdaSummary:"template-history-hdaSummary",downloadLinks:"template-history-downloadLinks",failedMetadata:"template-history-failedMetaData",tagArea:"template-history-tagArea",annotationArea:"template-history-annotationArea",displayApps:"template-history-displayApps"}});var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0}},initialize:function(b,a){this.log(this+".initialize",b,a);this.items=new HistoryCollection()},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){a.log("loading dataset: ",f,e);var h=new HistoryItem(_.extend(f,{history_id:b}));a.log("as History:",h);a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize");this.itemViews=[];var a=this;this.model.items.each(function(c){var b=new HistoryItemView({model:c});a.itemViews.push(b)})},render:function(){this.log(this+".render");var a=$("
    ");_.each(this.itemViews,function(b){a.prepend(b.render())});this.$el.append(a.children());a.remove()},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/tools.js b/static/scripts/packed/mvc/tools.js
index 1dc259dc52b..e8c89617ce7 100644
--- a/static/scripts/packed/mvc/tools.js
+++ b/static/scripts/packed/mvc/tools.js
@@ -1 +1 @@
-var ServerStateDeferred=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(a){return true}},go:function(){var d=$.Deferred(),c=this,f=c.get("ajax_settings"),e=c.get("success_fn"),b=c.get("interval"),a=function(){$.ajax(f).success(function(g){if(e(g)){d.resolve(g)}else{setTimeout(a,b)}})};a();return d}});var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,inputs:[]},relations:[{type:Backbone.HasMany,key:"inputs",relatedModel:"ToolInput",reverseRelation:{key:"tool",includeInJSON:false}}],urlRoot:galaxy_paths.get("tool_url"),copy:function(b){var c=new Tool(this.toJSON());if(b){var a=new Backbone.Collection();c.get("inputs").each(function(d){if(d.get_samples()){a.push(d)}});c.set("inputs",a)}return c},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(a,b){this.get("inputs").find(function(c){return c.get("name")===a}).set("value",b)},set_input_values:function(b){var a=this;_.each(_.keys(b),function(c){a.set_input_value(c,b[c])})},run:function(){return this._run()},rerun:function(b,a){return this._run({action:"rerun",target_dataset_id:b.id,regions:a})},get_inputs_dict:function(){var a={};this.get("inputs").each(function(b){a[b.get("name")]=b.get("value")});return a},_run:function(c){var d=_.extend({tool_id:this.id,inputs:this.get_inputs_dict()},c);var b=$.Deferred(),a=new ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(d),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(e){return e!=="pending"}});$.when(a.go()).then(function(e){b.resolve(new DatasetCollection().reset(e))});return b}});var ToolInput=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new ToolInput(this.toJSON())},get_samples:function(){var b=this.get("type"),a=null;if(b==="number"){a=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(b==="select"){a=_.map(this.get("options"),function(c){return c[0]})}}return a}});var ToolCollection=Backbone.Collection.extend({model:Tool});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length").text(this.model.attributes.name));return this}});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(a){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===a.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var a=this;var b=new ToolSearchView({model:this.collection.tool_search});b.render();a.$el.append(b.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();a.$el.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();a.$el.append(e.$el)}else{if(d instanceof ToolPanelLabel){var f=new ToolPanelLabelView({model:d});f.render();a.$el.append(f.$el)}}}});a.$el.find("a.tool-link").click(function(f){var d=$(this).attr("class").split(/\s+/)[0],c=a.collection.tools.get(d);a.trigger("tool_link_click",f,c)});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var ToolFormView=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var IntegratedToolMenuAndView=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new ToolPanelView({collection:this.collection});this.tool_form_view=new ToolFormView()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var a=this;this.tool_panel_view.on("tool_link_click",function(c,b){c.preventDefault();a.show_tool(b)})},show_tool:function(b){var a=this;b.fetch().done(function(){a.tool_form_view.model=b;a.tool_form_view.render();a.tool_form_view.$el.show();$("#left").width("650px")})}});
\ No newline at end of file
+define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(q,a,r){var f=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var k=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new k(this.toJSON())},get_samples:function(){var u=this.get("type"),t=null;if(u==="number"){t=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(u==="select"){t=q.map(this.get("options"),function(v){return v[0]})}}return t}});var e=f.extend({defaults:{description:null,target:null,inputs:[]},relations:[{type:Backbone.HasMany,key:"inputs",relatedModel:k,reverseRelation:{key:"tool",includeInJSON:false}}],urlRoot:galaxy_paths.get("tool_url"),copy:function(u){var v=new e(this.toJSON());if(u){var t=new Backbone.Collection();v.get("inputs").each(function(w){if(w.get_samples()){t.push(w)}});v.set("inputs",t)}return v},apply_search_results:function(t){(q.indexOf(t,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(t,u){this.get("inputs").find(function(v){return v.get("name")===t}).set("value",u)},set_input_values:function(u){var t=this;q.each(q.keys(u),function(v){t.set_input_value(v,u[v])})},run:function(){return this._run()},rerun:function(u,t){return this._run({action:"rerun",target_dataset_id:u.id,regions:t})},get_inputs_dict:function(){var t={};this.get("inputs").each(function(u){t[u.get("name")]=u.get("value")});return t},_run:function(v){var w=q.extend({tool_id:this.id,inputs:this.get_inputs_dict()},v);var u=$.Deferred(),t=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(w),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(x){return x!=="pending"}});$.when(t.go()).then(function(x){u.resolve(new r.DatasetCollection().reset(x))});return u}});var i=Backbone.Collection.extend({model:e});var m=f.extend({});var p=f.extend({defaults:{elems:[],open:false},clear_search_results:function(){q.each(this.attributes.elems,function(t){t.show()});this.show();this.set("open",false)},apply_search_results:function(u){var v=true,t;q.each(this.attributes.elems,function(w){if(w instanceof m){t=w;t.hide()}else{if(w instanceof e){if(w.apply_search_results(u)){v=false;if(t){t.show()}}}}});if(v){this.hide()}else{this.show();this.set("open",true)}}});var b=f.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var v=this.attributes.query;if(v.length").text(this.model.attributes.name));return this}});var g=n.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){n.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var t=this.$el.find(".toolSectionBody");q.each(this.model.attributes.elems,function(u){if(u instanceof e){var v=new h({model:u,className:"toolTitle"});v.render();t.append(v.$el)}else{if(u instanceof m){var w=new c({model:u});w.render();t.append(w.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var l=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(t){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===t.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var s=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var t=this;var u=new l({model:this.collection.tool_search});u.render();t.$el.append(u.$el);this.collection.each(function(w){if(w instanceof p){var v=new g({model:w});v.render();t.$el.append(v.$el)}else{if(w instanceof e){var x=new h({model:w,className:"toolTitleNoSection"});x.render();t.$el.append(x.$el)}else{if(w instanceof m){var y=new c({model:w});y.render();t.$el.append(y.$el)}}}});t.$el.find("a.tool-link").click(function(x){var w=$(this).attr("class").split(/\s+/)[0],v=t.collection.tools.get(w);t.trigger("tool_link_click",x,v)});return this},handle_search_results:function(){var t=this.collection.tool_search.attributes.results;if(t&&t.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var o=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var d=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new s({collection:this.collection});this.tool_form_view=new o()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(v,u){v.preventDefault();t.show_tool(u)})},show_tool:function(u){var t=this;u.fetch().done(function(){t.tool_form_view.model=u;t.tool_form_view.render();t.tool_form_view.$el.show();$("#left").width("650px")})}});return{Tool:e,ToolSearch:b,ToolPanel:j,ToolPanelView:s,ToolFormView:o}});
\ No newline at end of file
diff --git a/static/scripts/packed/templates/compiled/helpers-common-templates.js b/static/scripts/packed/templates/compiled/helpers-common-templates.js
index 25d39347cf5..4da393c4955 100644
--- a/static/scripts/packed/templates/compiled/helpers-common-templates.js
+++ b/static/scripts/packed/templates/compiled/helpers-common-templates.js
@@ -1 +1 @@
-Handlebars.registerPartial("clearFloatDiv",function(a){return'
    '});Handlebars.registerPartial("iconButton",function(c,b){var a="";a+=(c.enabled)?(""):(""));return a});Handlebars.registerHelper("warningmessagesmall",function(a){return'
    '+a.fn(this)+"
    "});
\ No newline at end of file
+Handlebars.registerPartial("clearFloatDiv",function(a){return'
    '});Handlebars.registerHelper("warningmessagesmall",function(a){return'
    '+a.fn(this)+"
    "});Handlebars.registerPartial("iconButton",function(c,b){var a="";a+=(c.enabled)?(""):(""));return a});
\ No newline at end of file
diff --git a/static/scripts/packed/templates/compiled/template-history-displayApps.js b/static/scripts/packed/templates/compiled/template-history-displayApps.js
new file mode 100644
index 00000000000..998d92cffaa
--- /dev/null
+++ b/static/scripts/packed/templates/compiled/template-history-displayApps.js
@@ -0,0 +1 @@
+(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-displayApps"]=b(function(g,l,f,k,j){f=f||g.helpers;var c,h="function",i=this.escapeExpression,m=this;function e(r,q){var o="",p,n;o+="\n    ";n=f.label;if(n){p=n.call(r,{hash:{}})}else{p=r.label;p=typeof p===h?p():p}o+=i(p)+"\n    ";p=r.links;p=f.each.call(r,p,{hash:{},inverse:m.noop,fn:m.program(2,d,q)});if(p||p===0){o+=p}o+="\n    
    \n";return o}function d(r,q){var o="",p,n;o+='\n        ';n=f.text;if(n){p=n.call(r,{hash:{}})}else{p=r.text;p=typeof p===h?p():p}o+=i(p)+"\n    ";return o}c=l.displayApps;c=f.each.call(l,c,{hash:{},inverse:m.noop,fn:m.program(1,e,j)});if(c||c===0){return c}else{return""}})})();
\ No newline at end of file
diff --git a/static/scripts/packed/templates/compiled/template-history-downloadLinks.js b/static/scripts/packed/templates/compiled/template-history-downloadLinks.js
new file mode 100644
index 00000000000..68175ea4d2c
--- /dev/null
+++ b/static/scripts/packed/templates/compiled/template-history-downloadLinks.js
@@ -0,0 +1 @@
+(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-downloadLinks"]=b(function(g,l,f,k,j){f=f||g.helpers;var c,h="function",i=this.escapeExpression,m=this;function e(s,r){var p="",q,o;p+='\n
    \n    Download Dataset\n    Additional Files\n    ';q=s.meta_files;q=f.each.call(s,q,{hash:{},inverse:m.noop,fn:m.program(2,d,r)});if(q||q===0){p+=q}p+='\n
    \n\n';return p}function d(s,r){var p="",q,o;p+='\n    Download ';o=f.meta_file_type;if(o){q=o.call(s,{hash:{}})}else{q=s.meta_file_type;q=typeof q===h?q():q}p+=i(q)+"\n    ";return p}function n(p,o){return'\n\n'}c=l.meta_files;c=f["if"].call(l,c,{hash:{},inverse:m.program(4,n,j),fn:m.program(1,e,j)});if(c||c===0){return c}else{return""}})})();
\ No newline at end of file
diff --git a/static/scripts/packed/viz/circster.js b/static/scripts/packed/viz/circster.js
index 0e55a164556..889595bab5c 100644
--- a/static/scripts/packed/viz/circster.js
+++ b/static/scripts/packed/viz/circster.js
@@ -1 +1 @@
-define(["libs/d3","viz/visualization"],function(e,f){var d=function(){this.initialize&&this.initialize.apply(this,arguments)};d.extend=Backbone.Model.extend;var c=Backbone.View.extend({className:"circster",initialize:function(h){this.total_gap=h.total_gap;this.genome=h.genome;this.dataset_arc_height=h.dataset_arc_height;this.track_gap=5},render:function(){var j=this,l=this.dataset_arc_height,m=j.$el.width(),h=j.$el.height(),k=(Math.min(m,h)/2-this.model.get("tracks").length*(this.dataset_arc_height+this.track_gap));var i=e.select(j.$el[0]).append("svg").attr("width",m).attr("height",h).attr("pointer-events","all").append("svg:g").call(e.behavior.zoom().on("zoom",function(){i.attr("transform","translate("+e.event.translate+") scale("+e.event.scale+")")})).attr("transform","translate("+m/2+","+h/2+")").append("svg:g");this.model.get("tracks").each(function(n,p){var q=n.get("genome_wide_data"),s=k+p*(l+j.track_gap),o=(q instanceof f.GenomeWideBigWigData?g:a);var r=new o({track:n,radius_start:s,radius_end:s+l,genome:j.genome,total_gap:j.total_gap});r.render(i)})}});var b=d.extend({initialize:function(h){this.options=h},render:function(m){var h=this.chroms_layout(),k=this.genome_data_layout();var n=this.options.radius_start,j=this.options.radius_end,p=m.append("g").attr("id","inner-arc"),o=e.svg.arc().innerRadius(n).outerRadius(j),i=p.selectAll("#inner-arc>path").data(h).enter().append("path").attr("d",o).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(r){return r.data.chrom});var q=this.options.track.get("prefs"),l=q.block_color;_.each(k,function(r){if(!r){return}var u=m.append("g"),t=e.svg.arc().innerRadius(n),s=u.selectAll("path").data(r).enter();s.append("path").attr("d",t).style("stroke",l)})},chroms_layout:function(){var i=this.options.genome.get_chroms_info(),k=e.layout.pie().value(function(m){return m.len}).sort(null),l=k(i),h=this.options.total_gap/i.length,j=_.map(l,function(o,n){var m=o.endAngle-h;o.endAngle=(m>o.startAngle?m:o.startAngle);return o});return j},chrom_data_layout:function(k,j,i,l,h){},genome_data_layout:function(){var i=this,h=this.chroms_layout(),m=this.options.track.get("genome_wide_data"),l=this.options.radius_start,j=this.options.radius_end,k=_.zip(h,m.get("data")),n=_.map(k,function(p){var q=p[0],o=p[1];return i.chrom_data_layout(q,o,l,j,m.get("min"),m.get("max"))});return n}});var a=b.extend({chrom_data_layout:function(r,i,o,n,k,p){if(!i||typeof i==="string"){return null}var l=i[0],q=i[3],j=e.scale.linear().domain([k,p]).range([o,n]),m=e.layout.pie().value(function(s){return q}).startAngle(r.startAngle).endAngle(r.endAngle),h=m(l);_.each(l,function(s,t){h[t].outerRadius=j(s[1])});return h}});var g=b.extend({chrom_data_layout:function(q,i,o,n,k,p){var l=i.data;if(l.length===0){return}var j=e.scale.linear().domain([k,p]).range([o,n]),m=e.layout.pie().value(function(s,r){if(r+1===l.length){return 0}return l[r+1][0]-l[r][0]}).startAngle(q.startAngle).endAngle(q.endAngle),h=m(l);_.each(l,function(r,s){h[s].outerRadius=j(r[1])});return h}});return{CircsterView:c}});
\ No newline at end of file
+define(["libs/underscore","libs/d3","viz/visualization"],function(i,k,j){var e=function(){this.initialize&&this.initialize.apply(this,arguments)};e.extend=Backbone.Model.extend;var l=Backbone.Model.extend({is_visible:function(p,m){var n=p.getBoundingClientRect(),o=$("svg")[0].getBoundingClientRect();if(n.right<0||n.left>o.right||n.bottom<0||n.top>o.bottom){return false}return true}});var f=Backbone.Model.extend({defaults:{prefs:{color:"#ccc"}}});var b=Backbone.View.extend({className:"circster",initialize:function(m){this.total_gap=m.total_gap;this.genome=m.genome;this.dataset_arc_height=m.dataset_arc_height;this.track_gap=5;this.label_arc_height=20},render:function(){var u=this,r=this.dataset_arc_height,m=u.$el.width(),t=u.$el.height(),n=Math.min(m,t)/2-this.model.get("tracks").length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),s=this.model.get("tracks");var p=k.select(u.$el[0]).append("svg").attr("width",m).attr("height",t).attr("pointer-events","all").append("svg:g").call(k.behavior.zoom().on("zoom",function(){p.attr("transform","translate("+k.event.translate+") scale("+k.event.scale+")");var v=new l(),w={};s.each(function(x){w[x.id]=[]});k.selectAll("path.chrom-data").filter(function(y,x){return v.is_visible(this,p)}).each(function(z,x){var y=$.data(this,"chrom_data");w[y.track.id].push(y.chrom)})})).attr("transform","translate("+m/2+","+t/2+")").append("svg:g");s.each(function(v,x){var z=n+x*(r+u.track_gap),w=(v.get("track_type")==="LineTrack"?g:h);var y=new w({track:v,track_index:x,radius_start:z,radius_end:z+r,genome:u.genome,total_gap:u.total_gap});y.render(p)});var q=n+s.length*(r+u.track_gap)+u.track_gap;var o=new a({track:new f(),track_index:s.length,radius_start:q,radius_end:q,genome:u.genome,total_gap:u.total_gap});o.render(p)}});var c=e.extend({initialize:function(m){this.options=m;this.options.bg_stroke="ccc";this.options.bg_fill="ccc"},render:function(r){var o=r.append("g").attr("id","parent-"+this.options.track_index);var m=this._chroms_layout(),s=this.options.radius_start,p=this.options.radius_end,t=k.svg.arc().innerRadius(s).outerRadius(p),n=o.selectAll("g").data(m).enter().append("svg:g");n.append("path").attr("d",t).style("stroke",this.options.bg_stroke).style("fill",this.options.bg_fill).append("title").text(function(v){return v.data.chrom});this.render_data(o);var u=this.options.track.get("prefs"),q=u.block_color;if(!q){q=u.color}o.selectAll("path.chrom-data").style("stroke",q).style("fill",q)},_chroms_layout:function(){var n=this.options.genome.get_chroms_info(),p=k.layout.pie().value(function(r){return r.len}).sort(null),q=p(n),m=this.options.total_gap/n.length,o=i.map(q,function(t,s){var r=t.endAngle-m;t.endAngle=(r>t.startAngle?r:t.startAngle);return t});return o},render_chrom_data:function(o,p,q,n,r,m){},render_data:function(q){var v=this,u=this._chroms_layout(),o=this.options.track,n=this.options.radius_start,s=this.options.radius_end,t=o.get_genome_wide_data(this.options.genome),r=i.zip(u,t),m=this.get_bounds(t),p=i.map(r,function(w){var x=w[0],y=w[1];return v.render_chrom_data(q,x,y,n,s,m.min,m.max)});return p}});var a=c.extend({initialize:function(m){this.options=m;this.options.bg_stroke="fff";this.options.bg_fill="fff"},render_data:function(n){var m=n.selectAll("g");m.selectAll("path").attr("id",function(o){return"label-"+o.data.chrom});m.append("svg:text").filter(function(o){return o.endAngle-o.startAngle>0.08}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(o){return"#label-"+o.data.chrom}).attr("startOffset","25%").text(function(o){return o.data.chrom})}});var d=c.extend({render_quantitative_data:function(q,w,p,t,s,o,u){var r=k.scale.linear().domain([o,u]).range([t,s]);var n=k.scale.linear().domain([0,p.length]).range([w.startAngle,w.endAngle]);var y=k.svg.line.radial().interpolate("linear").radius(function(z){return r(z[1])}).angle(function(A,z){return n(z)});var m=k.svg.area.radial().interpolate(y.interpolate()).innerRadius(r(0)).outerRadius(y.radius()).angle(y.angle());var v=q.datum(p),x=v.append("path").attr("class","chrom-data").attr("d",m);$.data(x[0][0],"chrom_data",{track:this.options.track,chrom:w.data.chrom})},get_bounds:function(){}});var h=d.extend({render_chrom_data:function(o,r,p,n,s,q,m){if(!p||typeof p==="string"){return null}return this.render_quantitative_data(o,r,p.data,n,s,q,m)},get_bounds:function(n){var m=i.map(n,function(o){if(!o||typeof o==="string"){return 0}return o.max});return{min:0,max:(m&&typeof m!=="string"?i.max(m):0)}}});var g=d.extend({render_chrom_data:function(o,r,p,n,t,q,m){var s=p.data;if(s.length===0){return}return this.render_quantitative_data(o,r,s,n,t,q,m)},get_bounds:function(n){var m=i.flatten(i.map(n,function(o){if(o){return i.map(o.data,function(q){return q[1]})}else{return 0}}));return{min:i.min(m),max:i.max(m)}}});return{CircsterView:b}});
\ No newline at end of file
diff --git a/static/scripts/packed/viz/scatterplot.js b/static/scripts/packed/viz/scatterplot.js
new file mode 100644
index 00000000000..69479e9decb
--- /dev/null
+++ b/static/scripts/packed/viz/scatterplot.js
@@ -0,0 +1 @@
+define(["../libs/underscore","../libs/d3","../mvc/base-mvc"],function(){function b(e){var h=this,g=10,f=12,d=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var i=Array.prototype.slice.call(arguments);i.unshift(this.toString());console.debug.apply(null,i)}};this.log("new TwoVarScatterplot:",e);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,bubbleRadius:4,entryAnimDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,e);this.updateConfig=function(i){_.extend(this.config,i)};this.toString=function(){return this.config.id};this.translateStr=function(i,j){return"translate("+i+","+j+")"};this.rotateStr=function(j,i,k){return"rotate("+j+","+i+","+k+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart").style("display","none");this.content=this.svg.append("svg:g").attr("class","content");this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.log("built svg:",d3.selectAll("svg"));this.adjustChartDimensions=function(){this.svg.attr("width",this.config.width+(this.config.marginRight+this.config.marginLeft)).attr("height",this.config.height+(this.config.marginTop+this.config.marginBottom)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft,this.config.marginTop))};this.preprocessData=function(i){return i.slice(0,this.config.maxDataPoints)};this.setUpDomains=function(i,j){this.xMin=this.config.xMin||d3.min(i);this.xMax=this.config.xMax||d3.max(i);this.yMin=this.config.yMin||d3.min(j);this.yMax=this.config.yMax||d3.max(j)};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.log("xAxis:",this.xAxis);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(i){return(String(i)).length}));this.log("xLongestLabel:",this.xLongestLabel);if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel);this.log("xAxisLabel:",this.xAxisLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);this.log("yAxis:",this.yAxis);this.yLongestLabel=d3.max(_.map([this.yMin,this.yMax],function(j){return(String(j)).length}));this.log("yLongestLabel:",this.yLongestLabel);var i=this.yLongestLabel*g+(d);if(this.config.yAxisLabelBumpX>-(i)){this.config.yAxisLabelBumpX=-(i)}if(this.config.marginLeft'+f+""}});e+='
    ';e+='";e+="
    ";e+='
    ';e+='";e+="
    ";e+='';e+='
    ';this.$el.append(e);this.$el.find("#render-button");return this},renderScatterplot:function(){var d=this,e=this.apiDatasetsURL+"/"+this.dataset.id+"?data_type=raw_data&",i=this.$el.find('[name="x-column"]'),j=i.val(),g=i.children('[value="'+j+'"]').text(),h=this.$el.find('[name="y-column"]'),f=h.val(),c=h.children('[value="'+f+'"]').text();this.log(g,c);this.chartConfig.xLabel=g;this.chartConfig.yLabel=c;d.plot.updateConfig(this.chartConfig);e+=jQuery.param({columns:"["+[j,f]+"]"});this.log("url:",e);jQuery.ajax({url:e,dataType:"json",success:function(k){d.endpoint=k.endpoint;d.plot.render(_.map(k.data,function(l){return l[0]}),_.map(k.data,function(l){return l[1]}))},error:function(m,k,l){alert("ERROR:"+k+"\n"+l)}})}});return{ScatterplotView:a}});
\ No newline at end of file
diff --git a/static/scripts/packed/viz/sweepster.js b/static/scripts/packed/viz/sweepster.js
index 0b28b22acc9..58136d5287c 100644
--- a/static/scripts/packed/viz/sweepster.js
+++ b/static/scripts/packed/viz/sweepster.js
@@ -1 +1 @@
-define(["libs/d3","viz/trackster/util","viz/visualization","viz/trackster/tracks"],function(m,e,l,f){var k=Backbone.Model.extend({defaults:{inputs:null,values:null}});var n=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(p){var o=this;this.get("tool").get("inputs").each(function(q){if(!q.get_samples()){return}q.on("change:min change:max change:num_samples",function(r){if(r.get("in_ptree")){o.set_tree_data()}},o);q.on("change:in_ptree",function(r){if(r.get("in_ptree")){o.add_param(r)}else{o.remove_param(r)}o.set_tree_data()},o)});if(p.config){_.each(p.config,function(r){var q=o.get("tool").get("inputs").find(function(s){return s.get("name")===r.name});o.add_param(q);q.set(r)})}},add_param:function(o){if(o.get("ptree_index")){return}o.set("in_ptree",true);o.set("ptree_index",this.get_tree_params().length)},remove_param:function(o){o.set("in_ptree",false);o.set("ptree_index",null);_(this.get_tree_params()).each(function(p,q){p.set("ptree_index",q+1)})},set_tree_data:function(){var p=_.map(this.get_tree_params(),function(r){return{param:r,samples:r.get_samples()}});var o=0,q=function(u,r){var w=u[r],v=w.param,t=v.get("label"),s=w.samples;if(u.length-1===r){return _.map(s,function(x){return{id:o++,name:x,param:v,value:x}})}return _.map(s,function(x){return{id:o++,name:x,param:v,value:x,children:q(u,r+1)}})};this.set("tree_data",{name:"Root",id:o++,children:(p.length!==0?q(p,0):null)})},get_tree_params:function(){return _(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(o){return o.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(o,p){return o*p.get_samples().length},1)},get_node_settings:function(s){var q=this.get("tool").get_inputs_dict();var t=s.parent;if(t){while(t.depth!==0){q[t.param.get("name")]=t.value;t=t.parent}}var o=this,p=function(v,u){if(v.param){u[v.param.get("name")]=v.value}if(!v.children){return new k({inputs:o.get("tool").get("inputs"),values:u})}else{return _.flatten(_.map(v.children,function(w){return p(w,_.clone(u))}))}},r=p(s,q);if(!_.isArray(r)){r=[r]}return r},get_connected_nodes:function(q){var r=function(s){if(!s.children){return s}else{return _.flatten([s,_.map(s.children,function(t){return r(t)})])}};var p=[],o=q.parent;while(o){p.push(o);o=o.parent}return _.flatten([p,r(q)])},get_leaf:function(p){var q=this.get("tree_data"),o=function(r){return _.find(r,function(s){return p[s.param.get("name")]===s.value})};while(q.children){q=o(q.children)}return q},toJSON:function(){return this.get_tree_params().map(function(o){return{name:o.get("name"),min:o.get("min"),max:o.get("max"),num_samples:o.get("num_samples")}})}});var c=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:l.GenomeRegion}],initialize:function(o){if(o.track){var p=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},o.track);this.set("track",f.object_from_template(p,{},null))}},same_settings:function(o){var p=this.get("settings"),q=o.get("settings");for(var r in p){if(!q[r]||p[r]!==q[r]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var a=Backbone.Collection.extend({model:c});var g=l.Visualization.extend({defaults:_.extend({},l.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:Dataset},{type:Backbone.HasOne,key:"tool",relatedModel:Tool},{type:Backbone.HasMany,key:"regions",relatedModel:l.GenomeRegion},{type:Backbone.HasMany,key:"tracks",relatedModel:c}],initialize:function(o){var p=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",p);this.set("parameter_tree",new n({tool:p,config:o.tree_config}))},add_track:function(o){this.get("tracks").add(o)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var j=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(o){this.canvas_manager=o.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var t=this.model.get("settings"),p=t.get("values"),r=$("").addClass("settings").appendTo(this.$el),q=$("
    ").addClass("track-info").hide().appendTo(r);q.append($("
    ").css("font-weight","bold").text("Track Settings"));t.get("inputs").each(function(v){q.append(v.get("label")+": "+p[v.get("name")]+"
    ")});var o=this,u=$("