Revise shared utilities

client/galaxy/scripts/apps/chart.js

@@ -1,7 +1,7 @@
 import * as _ from "libs/underscore";
 import Client from "mvc/visualization/chart/chart-client";
 import Datasets from "mvc/visualization/chart/utilities/datasets";
-import Helpers from "mvc/visualization/chart/utilities/helpers";
+import Series from "mvc/visualization/chart/utilities/series";
 import Jobs from "mvc/visualization/chart/utilities/jobs";
 
 window.bundleEntries = window.bundleEntries || {};
@@ -12,8 +12,8 @@ export const bundleEntries = {
     },
     chartUtilities: {
         Datasets: Datasets,
-        Helpers: Helpers,
-        Jobs: Jobs
+        Jobs: Jobs,
+        Series: Series
     }
 };
 

client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js

@@ -1,6 +1,50 @@
 /** This class handles, formats and caches datasets. */
 import Utils from "utils/utils";
 
+/** Assists in assigning the viewport panels */
+var requestPanels = function(options) {
+    var self = this;
+    var process = options.process;
+    var chart = options.chart;
+    var render = options.render;
+    var targets = options.targets;
+    var dataset_id = options.dataset_id || options.chart.get("dataset_id");
+    var dataset_groups = options.dataset_groups || options.chart.groups;
+    request({
+        chart: chart,
+        dataset_id: dataset_id,
+        dataset_groups: dataset_groups,
+        success: function(result) {
+            try {
+                if (targets.length == result.length) {
+                    var valid = true;
+                    for (var group_index in result) {
+                        var group = result[group_index];
+                        if (!render(targets[group_index], [group])) {
+                            valid = false;
+                            break;
+                        }
+                    }
+                    if (valid) {
+                        chart.state("ok", "Multi-panel chart drawn.");
+                    }
+                } else if (targets.length == 1) {
+                    if (render(targets[0], result)) {
+                        chart.state("ok", "Chart drawn.");
+                    }
+                } else {
+                    chart.state("failed", "Invalid panel count.");
+                }
+                process.resolve();
+            } catch (err) {
+                console.debug("FAILED: tabular-utilities::panelHelper() - " + err);
+                chart.state("failed", err);
+                process.reject();
+            }
+        }
+    });
+}
+
 /** Fills request dictionary with data from cache/response */
 var _cache = {};
 var request = function(options) {
@@ -124,4 +168,4 @@ var _block_id = function(dataset_id, column) {
     return dataset_id + "_" + "_" + column;
 };
 
-export default { request: request };
+export default { request: request, requestPanels: requestPanels };

client/galaxy/scripts/mvc/visualization/chart/utilities/helpers.js

@@ -1,310 +0,0 @@
-import Utils from "utils/utils";
-import Datasets from "mvc/visualization/chart/utilities/datasets";
-
-/** build job dictionary */
-function buildJobDictionary(chart, module) {
-    var settings_string = "";
-    var columns_string = "";
-    var group_index = 0;
-    for (var key in chart.settings.attributes) {
-        var settings_value = chart.settings.get(key);
-        _.each([[" ", " "], [",", ","], [":", ":"]], function(pair) {
-            settings_value = settings_value.replace(new RegExp(pair[0], "g"), pair[1]);
-        });
-        settings_string += key + ":" + settings_value + ", ";
-    }
-    settings_string = settings_string.substring(0, settings_string.length - 2);
-    chart.groups.each(function(group) {
-        group_index++;
-        _.each(group.get("__data_columns"), function(data_columns, name) {
-            columns_string += name + "_" + group_index + ":" + (parseInt(group.get(name)) + 1) + ", ";
-        });
-    });
-    columns_string = columns_string.substring(0, columns_string.length - 2);
-    return {
-        tool_id: "charts",
-        inputs: {
-            input: {
-                id: chart.get("dataset_id"),
-                src: "hda"
-            },
-            module: module,
-            columns: columns_string,
-            settings: settings_string
-        }
-    };
-}
-
-/** Assists in assigning the viewport panels */
-function panelHelper(options) {
-    var self = this;
-    var process = options.process;
-    var chart = options.chart;
-    var render = options.render;
-    var targets = options.targets;
-    var dataset_id = options.dataset_id || options.chart.get("dataset_id");
-    var dataset_groups = options.dataset_groups || options.chart.groups;
-    Datasets.request({
-        chart: chart,
-        dataset_id: dataset_id,
-        dataset_groups: dataset_groups,
-        success: function(result) {
-            try {
-                if (targets.length == result.length) {
-                    var valid = true;
-                    for (var group_index in result) {
-                        var group = result[group_index];
-                        if (!render(targets[group_index], [group])) {
-                            valid = false;
-                            break;
-                        }
-                    }
-                    if (valid) {
-                        chart.state("ok", "Multi-panel chart drawn.");
-                    }
-                } else if (targets.length == 1) {
-                    if (render(targets[0], result)) {
-                        chart.state("ok", "Chart drawn.");
-                    }
-                } else {
-                    chart.state("failed", "Invalid panel count.");
-                }
-                process.resolve();
-            } catch (err) {
-                console.debug("FAILED: tabular-utilities::panelHelper() - " + err);
-                chart.state("failed", err);
-                process.reject();
-            }
-        }
-    });
-}
-
-/** Get domain boundaries value */
-function getDomains(groups, keys) {
-    function _apply(operator, key) {
-        var value = undefined;
-        for (var group_index in groups) {
-            var value_sub = d3[operator](groups[group_index].values, function(d) {
-                return d[key];
-            });
-            value = value === undefined ? value_sub : Math[operator](value, value_sub);
-        }
-        return value;
-    }
-    var result = {};
-    for (var index in keys) {
-        var key = keys[index];
-        result[key] = {
-            min: _apply("min", key),
-            max: _apply("max", key)
-        };
-    }
-    return result;
-}
-
-/** Default series maker */
-function makeSeries(groups, keys) {
-    var plot_data = [];
-    for (var group_index in groups) {
-        var group = groups[group_index];
-        var data = [];
-        for (var value_index in group.values) {
-            var point = [];
-            if (keys) {
-                for (var key_index in keys) {
-                    var column_index = keys[key_index];
-                    point.push(group.values[value_index][column_index]);
-                }
-            } else {
-                for (var column_index in group.values[value_index]) {
-                    point.push(group.values[value_index][column_index]);
-                }
-            }
-            data.push(point);
-        }
-        plot_data.push(data);
-    }
-    return plot_data;
-}
-
-/** Default category maker */
-function makeCategories(groups, column_keys) {
-    var array = {};
-    var data_columns = groups[0].__data_columns;
-    _.each(column_keys, function(key) {
-        if (data_columns[key].is_label) {
-            array[key] = [];
-        }
-    });
-    if (groups && groups[0]) {
-        _.each(groups[0].values, function(value_dict) {
-            for (var key in array) {
-                array[key].push(String(value_dict[key]));
-            }
-        });
-    }
-    mapCategories(array, groups);
-    return { array: array };
-}
-
-/** Apply default mapping index all values contained in label columns (for all groups) */
-function mapCategories(array, groups) {
-    _.each(groups, function(group) {
-        _.each(group.values, function(value_dict, i) {
-            for (var key in array) {
-                value_dict[key] = parseInt(i);
-            }
-        });
-    });
-}
-
-/** Category make for unique category labels */
-function makeUniqueCategories(groups, with_index) {
-    var categories = {};
-    var array = {};
-    var counter = {};
-    var data_columns = groups[0].__data_columns;
-    _.each(data_columns, function(column_def, key) {
-        if (column_def.is_label) {
-            categories[key] = {};
-            array[key] = [];
-            counter[key] = 0;
-        }
-    });
-    // index all values contained in label columns (for all groups)
-    for (var i in groups) {
-        var group = groups[i];
-        for (var j in group.values) {
-            var value_dict = group.values[j];
-            for (var key in categories) {
-                var value = String(value_dict[key]);
-                if (categories[key][value] === undefined) {
-                    categories[key][value] = counter[key];
-                    array[key].push(with_index ? [counter[key], value] : value);
-                    counter[key]++;
-                }
-            }
-        }
-    }
-    // convert group values into category indeces
-    for (var i in groups) {
-        var group = groups[i];
-        for (var j in group.values) {
-            var value_dict = group.values[j];
-            for (var key in categories) {
-                var value = String(value_dict[key]);
-                value_dict[key] = categories[key][value];
-            }
-        }
-    }
-    return {
-        categories: categories,
-        array: array,
-        counter: counter
-    };
-}
-
-/** Make axis */
-function makeTickFormat(options) {
-    var type = options.type;
-    var precision = options.precision;
-    var categories = options.categories;
-    var formatter = options.formatter;
-    if (type == "hide") {
-        formatter(function() {
-            return "";
-        });
-    } else if (type == "auto") {
-        if (categories) {
-            formatter(function(value) {
-                return categories[value] || "";
-            });
-        }
-    } else {
-        var d3format = function(d) {
-            switch (type) {
-                case "s":
-                    var prefix = d3.formatPrefix(d);
-                    return prefix.scale(d).toFixed() + prefix.symbol;
-                default:
-                    return d3.format("." + precision + type)(d);
-            }
-        };
-        if (categories) {
-            formatter(function(value) {
-                var label = categories[value];
-                if (label) {
-                    if (isNaN(label)) {
-                        return label;
-                    } else {
-                        try {
-                            return d3format(label);
-                        } catch (err) {
-                            return label;
-                        }
-                    }
-                } else {
-                    return "";
-                }
-            });
-        } else {
-            formatter(function(value) {
-                return d3format(value);
-            });
-        }
-    }
-}
-
-/** Add zoom handler */
-function addZoom(options) {
-    var scaleExtent = 100;
-    var yAxis = options.yAxis;
-    var xAxis = options.xAxis;
-    var xDomain = options.xDomain || xAxis.scale().domain;
-    var yDomain = options.yDomain || yAxis.scale().domain;
-    var redraw = options.redraw;
-    var svg = options.svg;
-    var xScale = xAxis.scale();
-    var yScale = yAxis.scale();
-    var x_boundary = xScale.domain().slice();
-    var y_boundary = yScale.domain().slice();
-    var d3zoom = d3.behavior.zoom();
-    xScale.nice();
-    yScale.nice();
-    function fixDomain(domain, boundary) {
-        domain[0] = Math.min(Math.max(domain[0], boundary[0]), boundary[1] - boundary[1] / scaleExtent);
-        domain[1] = Math.max(boundary[0] + boundary[1] / scaleExtent, Math.min(domain[1], boundary[1]));
-        return domain;
-    }
-    function zoomed() {
-        yDomain(fixDomain(yScale.domain(), y_boundary));
-        xDomain(fixDomain(xScale.domain(), x_boundary));
-        redraw();
-    }
-    function unzoomed() {
-        xDomain(x_boundary);
-        yDomain(y_boundary);
-        redraw();
-        d3zoom.scale(1);
-        d3zoom.translate([0, 0]);
-    }
-    d3zoom
-        .x(xScale)
-        .y(yScale)
-        .scaleExtent([1, scaleExtent])
-        .on("zoom", zoomed);
-    svg.call(d3zoom).on("dblclick.zoom", unzoomed);
-    return d3zoom;
-}
-
-export default {
-    buildJobDictionary: buildJobDictionary,
-    panelHelper: panelHelper,
-    makeCategories: makeCategories,
-    makeUniqueCategories: makeUniqueCategories,
-    makeSeries: makeSeries,
-    getDomains: getDomains,
-    mapCategories: mapCategories,
-    makeTickFormat: makeTickFormat,
-    addZoom: addZoom
-};

client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js

@@ -4,6 +4,40 @@ import Utils from "utils/utils";
 /** Time to wait before refreshing to check if job has completed */
 var WAITTIME = 1000;
 
+/** build job dictionary */
+var requestCharts = function(chart, module) {
+    var settings_string = "";
+    var columns_string = "";
+    var group_index = 0;
+    for (var key in chart.settings.attributes) {
+        var settings_value = chart.settings.get(key);
+        _.each([[" ", " "], [",", ","], [":", ":"]], function(pair) {
+            settings_value = settings_value.replace(new RegExp(pair[0], "g"), pair[1]);
+        });
+        settings_string += key + ":" + settings_value + ", ";
+    }
+    settings_string = settings_string.substring(0, settings_string.length - 2);
+    chart.groups.each(function(group) {
+        group_index++;
+        _.each(group.get("__data_columns"), function(data_columns, name) {
+            columns_string += name + "_" + group_index + ":" + (parseInt(group.get(name)) + 1) + ", ";
+        });
+    });
+    columns_string = columns_string.substring(0, columns_string.length - 2);
+    return {
+        tool_id: "charts",
+        inputs: {
+            input: {
+                id: chart.get("dataset_id"),
+                src: "hda"
+            },
+            module: module,
+            columns: columns_string,
+            settings: settings_string
+        }
+    };
+}
+
 /** Submit job request to charts tool */
 var request = function(chart, parameters, success, error) {
     chart.state("wait", "Requesting job results...");
@@ -113,4 +147,4 @@ var refreshHdas = function() {
     Galaxy && Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.refreshContents();
 };
 
-export default { request: request };
+export default { request: request, requestCharts: requestCharts };

config/plugins/visualizations/nvd3_bar/src/nvd3.js

@@ -3,7 +3,8 @@ import * as d3 from "d3";
 import * as nv from "nvd3";
 import "../node_modules/nvd3/build/nv.d3.css";
 
-var Utilities = window.bundleEntries.chartUtilities.Helpers;
+var Series = window.bundleEntries.chartUtilities.Series;
+var Datasets = window.bundleEntries.chartUtilities.Datasets;
 
 var CommonWrapper = Backbone.View.extend({
     initialize: function(options) {
@@ -12,7 +13,7 @@ var CommonWrapper = Backbone.View.extend({
         options.render = function(canvas_id, groups) {
             return self.render(canvas_id, groups);
         };
-        Utilities.panelHelper(options);
+        Datasets.requestPanels(options);
     },
     render: function(canvas_id, groups) {
         var self = this;
@@ -48,7 +49,7 @@ var CommonWrapper = Backbone.View.extend({
                         if (d3chart.clipEdge) {
                             d3chart.clipEdge(true);
                         }
-                        Utilities.addZoom({
+                        Series.addZoom({
                             xAxis: d3chart.xAxis,
                             yAxis: d3chart.yAxis,
                             yDomain: d3chart.yDomain,
@@ -70,9 +71,9 @@ var CommonWrapper = Backbone.View.extend({
 
     /** Format axes ticks */
     _makeAxes: function(d3chart, groups, settings) {
-        var categories = Utilities.makeCategories(groups, ["x", "y"]);
+        var categories = Series.makeCategories(groups, ["x", "y"]);
         function makeTickFormat(id) {
-            Utilities.makeTickFormat({
+            Series.makeTickFormat({
                 categories: categories.array[id],
                 type: settings.get(id + "_axis_type|type"),
                 precision: settings.get(id + "_axis_type|precision"),