[galaxy-commits] commit/galaxy-central: guerler: Charts: Adds histograms for string columns/bins and generalizes column selection

22 May 2014

1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d18b0f6cac6c/
Changeset:   d18b0f6cac6c
User:        guerler
Date:        2014-05-22 04:48:11
Summary:     Charts: Adds histograms for string columns/bins and generalizes column selection
Affected #:  21 files
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/app.css

--- a/config/plugins/visualizations/charts/static/app.css
+++ b/config/plugins/visualizations/charts/static/app.css
@@ -63,5 +63,6 @@
 .charts-viewport .charts-viewport-canvas {
    display: block;
    width:100%;
+	min-height: 100px;
    height: inherit;
 }
\ No newline at end of file
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js
--- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js
+++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js
@@ -285,14 +285,15 @@
         }
// prepare indices
+        dataRangeFormat = d3.format('.3f');
         var dataRangeMin = 0;
-        var dataRangeMid = parseInt((dataRange.length - 1) / 2);
+        var dataRangeMid = '';
         var dataRangeMax = dataRange.length - 1;
// add labels
-        dataRange[dataRangeMin] = this.min;
+        dataRange[dataRangeMin] = dataRangeFormat(this.min);
         dataRange[dataRangeMid] = this.mid;
-        dataRange[dataRangeMax] = this.max;
+        dataRange[dataRangeMax] = dataRangeFormat(this.max);
// create legend
         var legend = this.svg.selectAll('.legend')
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/config.js
@@ -5,12 +5,7 @@
     category    : '',
     library     : 'nvd3.js',
     tag         : 'svg',
-    columns : {
-        y : {
-            title   : 'Values for y-axis'
-        }
-    },
-    settings : {
+    settings    : {
         separator_label  : {
             title       : 'X axis',
             type        : 'separator'
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3/nvd3.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/nvd3.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/nvd3.js
@@ -34,11 +34,13 @@
                 nvd3_model.options({showControls: false});
// legend
-                var legend_visible = true;
-                if (chart.settings.get('show_legend') == 'false') {
-                    legend_visible = false;
+                if (nvd3_model.showLegend) {
+                    var legend_visible = true;
+                    if (chart.settings.get('show_legend') == 'false') {
+                        legend_visible = false;
+                    }
+                    nvd3_model.showLegend(legend_visible);
                 }
-                nvd3_model.showLegend(legend_visible);
// custom callback
                 if (callback) {
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_bar/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_bar/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar/config.js
@@ -2,7 +2,17 @@
return $.extend(true, {}, nvd3_config, {
     title       : 'Regular',
-    category    : 'Bar diagrams'
+    category    : 'Bar diagrams',
+    columns     : {
+        x : {
+            title   : 'Values for x-axis',
+            is_label: true,
+            is_auto : true
+        },
+        y : {
+            title   : 'Values for y-axis'
+        }
+    }
 });
});
\ No newline at end of file
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal/config.js
@@ -3,6 +3,16 @@
 return $.extend(true, {}, nvd3_config, {
     title       : 'Horizontal',
     category    : 'Bar diagrams',
+    columns     : {
+        x : {
+            title   : 'Values for x-axis',
+            is_label: true,
+            is_auto : true
+        },
+        y : {
+            title   : 'Values for y-axis'
+        }
+    },
     settings    : {
         x_axis_type : {
             init : 'hide'
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_horizontal_stacked/config.js
@@ -7,6 +7,16 @@
         x_axis_type : {
             init : 'hide'
         }
+    },
+    columns     : {
+        x : {
+            title   : 'Values for x-axis',
+            is_label: true,
+            is_auto : true
+        },
+        y : {
+            title   : 'Values for y-axis'
+        }
     }
 });
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_bar_stacked/config.js
@@ -2,7 +2,17 @@
return $.extend(true, {}, nvd3_config, {
     title       : 'Stacked',
-    category    : 'Bar diagrams'
+    category    : 'Bar diagrams',
+    columns     : {
+        x : {
+            title   : 'Values for x-axis',
+            is_label: true,
+            is_auto : true
+        },
+        y : {
+            title   : 'Values for y-axis'
+        }
+    }
 });
});
\ No newline at end of file
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/config.js
@@ -5,7 +5,7 @@
     category    : 'Data processing (requires 'charts' tool from Toolshed)',
     execute     : 'histogramdiscrete',
     columns     : {
-        y : {
+        x : {
             title       : 'Observations',
             is_label    : true
         }
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_histogram_discrete/wrapper.js
@@ -15,24 +15,33 @@
     {
         // configure request
         var index = 1;
-        for (var i in request_dictionary.groups) {
-            var group = request_dictionary.groups[i];
-            group.columns = {
-                x: {
-                    index: 0
-                },
-                y: {
-                    index: index++
-                },
-            }
+        var tmp_dict = {
+            id      : request_dictionary.id,
+            groups  : []
+        };
+        
+        // configure groups
+        for (var group_index in request_dictionary.groups) {
+            var group = request_dictionary.groups[group_index];
+            tmp_dict.groups.push({
+                key     : group.key,
+                columns : {
+                    x: {
+                        index       : 0,
+                        is_label    : true
+                    },
+                    y: {
+                        index       : index++
+                    }
+                }
+            });
         }
-        // link this
-        var self = this;
-        
-        // load nvd3
+        // draw
         var nvd3 = new NVD3(this.app, this.options);
-        nvd3.draw(process_id, nv.models.multiBarChart(), chart, request_dictionary);
+        nvd3.draw(process_id, nv.models.multiBarChart(), chart, tmp_dict, function(nvd3_model) {
+            nvd3_model.options({showControls: true});
+        });
     }
 });
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_line/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_line/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_line/config.js
@@ -2,7 +2,16 @@
return $.extend(true, {}, nvd3_config, {
     title       : 'Line chart',
-    category    : 'Others'
+    category    : 'Others',
+    columns     : {
+        x : {
+            title   : 'Values for x-axis',
+            is_auto : true
+        },
+        y : {
+            title   : 'Values for y-axis'
+        }
+    }
 });
});
\ No newline at end of file
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_line_focus/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_line_focus/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_line_focus/config.js
@@ -2,7 +2,12 @@
return $.extend(true, {}, nvd3_config, {
     title       : 'Line with focus',
-    category    : 'Others'
+    category    : 'Others',
+    columns     : {
+        y : {
+            title   : 'Values for y-axis'
+        }
+    }
 });
});
\ No newline at end of file
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_pie/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_pie/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_pie/config.js
@@ -9,7 +9,8 @@
     columns : {
         label : {
             title       : 'Labels',
-            is_label    : true
+            is_label    : true,
+            is_auto     : true
         },
         y : {
             title       : 'Values'
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_scatter/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_scatter/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_scatter/config.js
@@ -6,6 +6,9 @@
     columns     : {
         x : {
             title   : 'Values for x-axis'
+        },
+        y : {
+            title   : 'Values for y-axis'
         }
     }
 });
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea/config.js
@@ -2,7 +2,12 @@
return $.extend(true, {}, nvd3_config, {
     title       : 'Regular',
-    category    : 'Area charts'
+    category    : 'Area charts',
+    columns     : {
+        y : {
+            title   : 'Values for y-axis'
+        }
+    }
 });
});
\ No newline at end of file
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_full/config.js
@@ -2,7 +2,12 @@
return $.extend(true, {}, nvd3_config, {
     title       : 'Expanded',
-    category    : 'Area charts'
+    category    : 'Area charts',
+    columns     : {
+        y : {
+            title   : 'Values for y-axis'
+        }
+    }
 });
});
\ No newline at end of file
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3_stackedarea_stream/config.js
@@ -2,7 +2,12 @@
return $.extend(true, {}, nvd3_config, {
     title       : 'Stream',
-    category    : 'Area charts'
+    category    : 'Area charts',
+    columns     : {
+        y : {
+            title   : 'Values for y-axis'
+        }
+    }
 });
});
\ No newline at end of file
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/charts/types.js
--- a/config/plugins/visualizations/charts/static/charts/types.js
+++ b/config/plugins/visualizations/charts/static/charts/types.js
@@ -48,7 +48,7 @@
         'nvd3_scatter'                      : nvd3_scatter,
         'nvd3_pie'                          : nvd3_pie,
         'nvd3_histogram'                    : nvd3_histogram,
-        //'nvd3_histogram_discrete'           : nvd3_histogram_discrete,
+        'nvd3_histogram_discrete'           : nvd3_histogram_discrete,
         'highcharts_boxplot'                : highcharts_boxplot,
         'heatmap'                           : heatmap
     }
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/library/datasets.js
--- a/config/plugins/visualizations/charts/static/library/datasets.js
+++ b/config/plugins/visualizations/charts/static/library/datasets.js
@@ -27,29 +27,37 @@
// check if column data is requested
         if (request_dictionary.groups) {
-            this._get(request_dictionary, success);
+            this._get_dataset(request_dictionary.id, function() {
+                self._get(request_dictionary, success);
+            });
         } else {
-            // check if dataset is available from cache
-            var dataset = this.list[request_dictionary.id];
-            if (dataset) {
-                success(dataset);
-                return;
+            this._get_dataset(request_dictionary.id, success, error)
+        }
+    },
+    
+    // get dataset
+    _get_dataset: function(id, success, error) {
+        // check if dataset is available from cache
+        var dataset = this.list[id];
+        if (dataset) {
+            success(dataset);
+            return;
+        }
+    
+        // request dataset
+        var self = this;
+        Utils.request('GET', config.root + 'api/datasets/' + id, {}, function(dataset) {
+            switch (dataset.state) {
+                case 'error':
+                    if (error) {
+                        error(dataset);
+                    }
+                    break;
+                default:
+                    self.list[id] = dataset;
+                    success(dataset);
             }
-        
-            // request dataset
-            Utils.request('GET', config.root + 'api/datasets/' + request_dictionary.id, {}, function(dataset) {
-                switch (dataset.state) {
-                    case 'error':
-                        if (error) {
-                            error(dataset);
-                        }
-                        break;
-                    default:
-                        self.list[request_dictionary.id] = dataset;
-                        success(dataset);
-                }
-            });
-        }
+        });
     },
// get block id
@@ -78,7 +86,7 @@
// check if column is in cache
                 var block_id = this._block_id(request_dictionary, column);
-                if (this.cache[block_id]) {
+                if (this.cache[block_id] || column === 'auto') {
                     continue;
                 }
@@ -134,45 +142,74 @@
         // log
         console.debug('Datasets::_fill_from_cache() - Filling request from cache.');
+        // get dataset
+        var dataset = this.list[request_dictionary.id];
+        if (!dataset) {
+            console.debug('FAILED - Datasets::_fill_from_cache() - Dataset not found.');
+        }
+        
+        // identify start/end of request
+        var start = request_dictionary.start;
+        var end   = Math.min(request_dictionary.end, dataset.metadata_data_lines);
+        if (end - start <= 0) {
+            console.debug('FAILED - Datasets::_fill_from_cache() - Invalid range.');
+        }
+        
+        // initialize group values
+        for (var i in request_dictionary.groups) {
+            // get group
+            var group = request_dictionary.groups[i];
+            
+            // reset group
+            group.values = [];
+        
+            // add values
+            for (var j = 0; j < end - start; j++) {
+                // add default x values
+                group.values[j] = {
+                    x : parseInt(j) + start
+                };
+            }
+        }
+        
         // collect all data into the defined groups
         for (var i in request_dictionary.groups) {
             // get group
             var group = request_dictionary.groups[i];
-            // create array for values
-            group.values = [];
-            
             // fill value
             for (var key in group.columns) {
                 // get column
                 var column = group.columns[key];
-                // get block
-                var block_id = this._block_id(request_dictionary, column.index);
-                var column_data = this.cache[block_id];
-            
-                // go through column
-                for (k in column_data) {
-                    // initialize value
-                    var value = group.values[k];
-                    if (value === undefined) {
-                        // create new value field
-                        value = {
-                            x : parseInt(k) + request_dictionary.start
+                // check if auto block is requested
+                if (column.index == 'auto') {
+                    for (var j = start; j < end; j++) {
+                        // get value dictionary
+                        var value = group.values[j];
+                        
+                        // add auto value
+                        value[key] = parseInt(j) + start;
+                    }
+                } else {
+                    // get block
+                    var block_id = this._block_id(request_dictionary, column.index);
+                    var column_data = this.cache[block_id];
+                
+                    // go through column
+                    for (var j = start; j < end; j++) {
+                        // get value dictionary
+                        var value = group.values[j];
+                        
+                        // get/fix value
+                        var v = column_data[j];
+                        if (isNaN(v) && !column.is_label) {
+                            v = 0;
                         }
-                        // add to group
-                        group.values[k] = value;
-                    };
-                    
-                    // get/fix value
-                    var v = column_data[k];
-                    if (isNaN(v) && !column.is_label) {
-                        v = 0;
+                        // add to dict
+                        value[key] = v;
                     }
-                    
-                    // add to dict
-                    value[key] = v;
                 }
             }
         }
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/library/ui-select.js
--- a/config/plugins/visualizations/charts/static/library/ui-select.js
+++ b/config/plugins/visualizations/charts/static/library/ui-select.js
@@ -33,11 +33,9 @@
// add change event
         var self = this;
-        if (this.options.onchange) {
-            this.$select.on('change', function() {
-                self.value(self.$select.val());
-            });
-        }
+        this.$select.on('change', function() {
+            self.value(self.$select.val());
+        });
// refresh
         this._refresh();
@@ -158,6 +156,34 @@
         this._refresh();
     },
+    // force selection to existing value
+    force: function() {
+        if (!this._exists(this.selected)) {
+            // get select options
+            var options = this.$select.find('option');
+            if (options.length > 0) {
+                // get value from options field
+                var value = options.val();
+                
+                // log
+                console.debug('Ui-Select()::force() - Forcing value from "' + this.selected + '" to "' + value + '".');
+
+                // set value
+                this.value(value);
+            }
+        }
+    },
+    
+    // set on change event
+    onchange: function(callback) {
+        this.options.onchange = callback;
+    },
+    
+    // check if selected value exists
+    _exists: function(value) {
+        return this.$select.find('option[value=' + value + ']').length > 0;
+    },
+    
     // refresh
     _refresh: function() {
         // remove placeholder
@@ -166,9 +192,11 @@
         // count remaining entries
         var remaining = this.$select.find('option').length;
         if (remaining == 0) {
+            // disable select field
+            this.disable();
+        
             // append placeholder
             this.$select.append(this._templateOption({value : 'null', label : this.options.empty}));
-            this.disable();
         } else {
             // enable select field
             this.enable();
@@ -180,12 +208,6 @@
         }
     },
-    // exists
-    _exists: function(value) {
-        // check if selected value exists
-        return 0 != this.$select.find('option[value=' + value + ']').length;
-    },
-    
     // option
     _templateOption: function(options) {
         return '<option value="' + options.value + '">' + options.label + '</option>';
diff -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe config/plugins/visualizations/charts/static/views/group.js
--- a/config/plugins/visualizations/charts/static/views/group.js
+++ b/config/plugins/visualizations/charts/static/views/group.js
@@ -82,25 +82,21 @@
         // load list
         var list = {};
         for (var id in chart_settings.columns) {
-            // initialize
-            var value = this.group.get(id);
-            if (!value) {
-                this.group.set(id, 0);
+            // get definition
+            var data_def = chart_settings.columns[id];
+            if (!data_def) {
+                console.debug('Group::_refreshTable() - Skipping column definition.');
+                continue;
             }
+
+            // create select field
+            var select = new Ui.Select.View({
+                id      : 'select_' + id,
+                gid     : id,
+                value   : this.group.get(id),
+                wait    : true
+            });
-            // create select field
-            var data_def = chart_settings.columns[id];
-            var select = new Ui.Select.View({
-                id   : 'select_' + id,
-                gid  : id,
-                onchange : function(value) {
-                    self.group.set(this.gid, value);
-                    self.chart.set('modified', true);
-                },
-                value : value,
-                wait  : true
-            });
-    
             // add row to table
             this.table.add(data_def.title, '25%');
             this.table.add(select.$el);
@@ -121,11 +117,25 @@
             // update select fields
             for (var id in list) {
+                // select
+                var select = list[id];
+                
                 // is a numeric number required
-                var is_label = chart_settings.columns[id].is_label;
-            
+                var is_label    = chart_settings.columns[id].is_label;
+                var is_auto     = chart_settings.columns[id].is_auto;
+                
                 // configure columns
                 var columns = [];
+                
+                // add auto selection column
+                if (is_auto) {
+                    columns.push({
+                        'label' : 'Column: Row Number',
+                        'value' : 'auto'
+                    });
+                }
+                
+                // meta data
                 var meta = dataset.metadata_column_types;
                 for (var key in meta) {
                     // check type
@@ -138,9 +148,16 @@
                     }
                 }
+                // add onchange event
+                select.onchange(function(value) {
+                    self.group.set(this.gid, value);
+                    self.chart.set('modified', true);
+                });
+                
                 // list
-                list[id].update(columns);
-                list[id].show();
+                select.update(columns);
+                select.force();
+                select.show();
             }
// loading
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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[galaxy-commits] commit/galaxy-central: guerler: Charts: Adds histograms for string columns/bins and generalizes column selection