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commit/galaxy-central: greg: Add missing import to the Tool Shed's repository grids utility component.
by commits-noreply＠bitbucket.org 22 May '14

22 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/581e7c8e353e/ Changeset: 581e7c8e353e User: greg Date: 2014-05-22 14:44:18 Summary: Add missing import to the Tool Shed's repository grids utility component. Affected #: 1 file diff -r b38587cb8937d678f2edcd17659fc3ce1724794d -r 581e7c8e353e9348db75d269446651e7122f10ce lib/tool_shed/grids/util.py --- a/lib/tool_shed/grids/util.py +++ b/lib/tool_shed/grids/util.py @@ -5,6 +5,7 @@ from galaxy.web.form_builder import SelectField from tool_shed.util import hg_util +from tool_shed.util import shed_util_common as suc log = logging.getLogger( __name__ ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Charts: Improve options mapping between different chart types
by commits-noreply＠bitbucket.org 22 May '14

22 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b38587cb8937/ Changeset: b38587cb8937 User: guerler Date: 2014-05-22 10:45:43 Summary: Charts: Improve options mapping between different chart types Affected #: 7 files diff -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe -r b38587cb8937d678f2edcd17659fc3ce1724794d 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 @@ -9,11 +9,6 @@ } }, columns : { - x : { - title : 'Values for x-axis', - is_label: true, - is_auto : true - }, y : { title : 'Values for y-axis' } diff -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe -r b38587cb8937d678f2edcd17659fc3ce1724794d 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 @@ -4,11 +4,6 @@ title : 'Stacked', category : 'Bar diagrams', columns : { - x : { - title : 'Values for x-axis', - is_label: true, - is_auto : true - }, y : { title : 'Values for y-axis' } diff -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe -r b38587cb8937d678f2edcd17659fc3ce1724794d 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 @@ -40,7 +40,7 @@ // draw var nvd3 = new NVD3(this.app, this.options); nvd3.draw(process_id, nv.models.multiBarChart(), chart, tmp_dict, function(nvd3_model) { - nvd3_model.options({showControls: true}); + nvd3_model.options({showControls: false}); }); } }); diff -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe -r b38587cb8937d678f2edcd17659fc3ce1724794d 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 @@ -5,7 +5,7 @@ var View = Backbone.View.extend( { // options - optionsDefault: { + optionsDefault : { id : '', cls : '', empty : 'No data available', @@ -21,6 +21,9 @@ // configure options this.options = Utils.merge(options, this.optionsDefault); + // initial value + this.selected = this.options.value; + // create new element this.setElement(this._template(this.options)); @@ -28,10 +31,7 @@ this.$select = this.$el.find('#select'); this.$icon = this.$el.find('#icon'); - // initial value - this.selected = this.options.value; - - // add change event + // add change event. fires only on user activity var self = this; this.$select.on('change', function() { self.value(self.$select.val()); @@ -67,9 +67,9 @@ // get current id/value var after = this.selected; - if(after) { + if (after) { // fire onchange - if ((after != before && this.options.onchange)) { + if (after != before && this.options.onchange) { this.options.onchange(after); } } @@ -78,6 +78,16 @@ return after; }, + // first + first: function() { + var options = this.$select.find('option'); + if (options.length > 0) { + return options.val(); + } else { + return undefined; + } + }, + // label text : function () { return this.$select.find('option:selected').text(); @@ -147,40 +157,17 @@ this.$select.append(this._templateOption(options[key])); } - // select first option if nothing else is selected - if (!this.selected && options.length > 0) { - this.value(options[0].value); - } - // refresh this._refresh(); }, - // force selection to existing value - force: function() { - if (!this._exists(this.selected)) { - // get select options - var options = this.$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) { + setOnChange: function(callback) { this.options.onchange = callback; }, // check if selected value exists - _exists: function(value) { + exists: function(value) { return this.$select.find('option[value=' + value + ']').length > 0; }, @@ -200,11 +187,11 @@ } else { // enable select field this.enable(); - - // update selected value - if (this.selected) { - this.$select.val(this.selected); - } + } + + // update value + if (this.selected) { + this.$select.val(this.selected); } }, diff -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe -r b38587cb8937d678f2edcd17659fc3ce1724794d config/plugins/visualizations/charts/static/library/ui-table-form.js --- a/config/plugins/visualizations/charts/static/library/ui-table-form.js +++ b/config/plugins/visualizations/charts/static/library/ui-table-form.js @@ -40,14 +40,6 @@ for (var id in settings) { this._add(id, settings[id], model); } - - // trigger change - for (var id in this.list) { - var onchange = this.list[id].options.onchange; - if (onchange) { - onchange(); - } - } }, // add table row @@ -66,8 +58,9 @@ field = new Ui.Input({ id : id, placeholder : settings_def.placeholder, - onchange : function() { - model.set(id, field.value()); + value : model.get(id), + onchange : function(value) { + model.set(id, value); } }); break; @@ -76,13 +69,13 @@ field = new Ui.Select.View({ id : id, data : settings_def.data, - onchange : function() { + value : model.get(id), + onchange : function(value) { // set new value - var selected = field.value(); - model.set(id, selected); + model.set(id, value); // find selected dictionary - var dict = _.findWhere(settings_def.data, {value: selected}); + var dict = _.findWhere(settings_def.data, {value: value}); if (dict) { if (dict.show) { self.$el.find('#' + dict.show).fadeIn('fast'); diff -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe -r b38587cb8937d678f2edcd17659fc3ce1724794d config/plugins/visualizations/charts/static/library/ui.js --- a/config/plugins/visualizations/charts/static/library/ui.js +++ b/config/plugins/visualizations/charts/static/library/ui.js @@ -550,13 +550,13 @@ this.$el.hide(); } - // onchange event handler + // onchange event handler. fires on user activity. var self = this; - if (this.options.onchange) { - this.$el.on('input', function() { - self.options.onchange(); - }); - } + this.$el.on('input', function() { + if (self.options.onchange) { + self.options.onchange(self.$el.val()); + } + }); }, // value diff -r d18b0f6cac6cb7bea6bd66900cc2d119bb733fbe -r b38587cb8937d678f2edcd17659fc3ce1724794d 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 @@ -22,8 +22,8 @@ // ui elements this.group_key = new Ui.Input({ placeholder: 'Data label', - onchange: function() { - self.group.set('key', self.group_key.value()); + onchange: function(value) { + self.group.set('key', value); } }); this.table = new Table.View({content: 'No data column.'}); @@ -92,8 +92,6 @@ // create select field var select = new Ui.Select.View({ id : 'select_' + id, - gid : id, - value : this.group.get(id), wait : true }); @@ -116,48 +114,7 @@ this.app.datasets.request({id : dataset_id}, function(dataset) { // 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_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 - if ((!is_label && (meta[key] == 'int' || meta[key] == 'float')) || is_label) { - // add to selection - columns.push({ - 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', - 'value' : key - }); - } - } - - // add onchange event - select.onchange(function(value) { - self.group.set(this.gid, value); - self.chart.set('modified', true); - }); - - // list - select.update(columns); - select.force(); - select.show(); + self._addRow(id, dataset, list[id], chart_settings.columns[id]) } // loading @@ -168,6 +125,62 @@ }); }, + // add row + _addRow: function(id, dataset, select, chart_setting) { + // is a numeric number required + var is_label = chart_setting.is_label; + var is_auto = chart_setting.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 + if ((!is_label && (meta[key] == 'int' || meta[key] == 'float')) || is_label) { + // add to selection + columns.push({ + 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', + 'value' : key + }); + } + } + + // update selection list + select.update(columns); + select.show(); + + // update current value + if (!select.exists(this.group.get(id))) { + // get first value + var first = select.first(); + + // log + console.debug('Group()::_addRow() - Switching model value from "' + this.group.get(id) + '" to "' + first + '".'); + + // update model value + this.group.set(id, first); + } + select.value(this.group.get(id)); + + // add onchange event + var self = this; + select.setOnChange(function(value) { + // update model value + self.group.set(id, value); + self.chart.set('modified', true); + }); + }, + // update _refreshGroup: function() { this.group.set('date', Utils.time()); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Charts: Adds histograms for string columns/bins and generalizes column selection
by commits-noreply＠bitbucket.org 22 May '14

22 May '14

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/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/316db249f068/ Changeset: 316db249f068 Branch: next-stable User: jmchilton Date: 2014-05-21 22:09:52 Summary: Fix for running workflows with collection inptus. takadonet reported running such workflows were not behaving correctly when copying inputs to new history is enabled. Affected #: 1 file diff -r fc89661b92dcbd9684ac779171235525601d0f4a -r 316db249f068ded4e541415232b480250c7cdd56 lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -203,9 +203,17 @@ # ds_map. if self.copy_inputs_to_history: for input_dataset_hda in out_data.values(): - new_hda = input_dataset_hda.copy( copy_children=True ) - self.target_history.add_dataset( new_hda ) - outputs[ step.id ][ 'input_ds_copy' ] = new_hda + content_type = input_dataset_hda.history_content_type + if content_type == "dataset": + new_hda = input_dataset_hda.copy( copy_children=True ) + self.target_history.add_dataset( new_hda ) + outputs[ step.id ][ 'input_ds_copy' ] = new_hda + elif content_type == "dataset_collection": + new_hdca = input_dataset_hda.copy() + self.target_history.add_dataset_collection( new_hdca ) + outputs[ step.id ][ 'input_ds_copy' ] = new_hdca + else: + raise Exception("Unknown history content encountered") if self.ds_map: outputs[ step.id ][ 'output' ] = self.ds_map[ str( step.id ) ][ 'hda' ] https://bitbucket.org/galaxy/galaxy-central/commits/6c3cc96d1fa7/ Changeset: 6c3cc96d1fa7 User: jmchilton Date: 2014-05-21 22:10:44 Summary: Merge next-stable. Affected #: 1 file diff -r e8f2c4f3e8c8ed63a99254a50ceb18fc33c52080 -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -203,9 +203,17 @@ # ds_map. if self.copy_inputs_to_history: for input_dataset_hda in out_data.values(): - new_hda = input_dataset_hda.copy( copy_children=True ) - self.target_history.add_dataset( new_hda ) - outputs[ step.id ][ 'input_ds_copy' ] = new_hda + content_type = input_dataset_hda.history_content_type + if content_type == "dataset": + new_hda = input_dataset_hda.copy( copy_children=True ) + self.target_history.add_dataset( new_hda ) + outputs[ step.id ][ 'input_ds_copy' ] = new_hda + elif content_type == "dataset_collection": + new_hdca = input_dataset_hda.copy() + self.target_history.add_dataset_collection( new_hdca ) + outputs[ step.id ][ 'input_ds_copy' ] = new_hdca + else: + raise Exception("Unknown history content encountered") if self.ds_map: outputs[ step.id ][ 'output' ] = self.ds_map[ str( step.id ) ][ 'hda' ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Remove appropriate entries from the Tool Shed's new repository registry for repositories that have been marked deprecated or deleted.
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e8f2c4f3e8c8/ Changeset: e8f2c4f3e8c8 User: greg Date: 2014-05-21 21:57:54 Summary: Remove appropriate entries from the Tool Shed's new repository registry for repositories that have been marked deprecated or deleted. Affected #: 3 files diff -r 155be7ce7910c2effb12fff904390401bdd7976b -r e8f2c4f3e8c8ed63a99254a50ceb18fc33c52080 lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -171,6 +171,8 @@ repository.deleted = True trans.sa_session.add( repository ) trans.sa_session.flush() + # Update the repository registry. + trans.app.repository_registry.remove_entry( repository ) count += 1 deleted_repositories += " %s " % repository.name if count: diff -r 155be7ce7910c2effb12fff904390401bdd7976b -r e8f2c4f3e8c8ed63a99254a50ceb18fc33c52080 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1051,6 +1051,8 @@ trans.sa_session.add( repository ) trans.sa_session.flush() if mark_deprecated: + # Update the repository registry. + trans.app.repository_registry.remove_entry( repository ) message = 'The repository %s has been marked as deprecated.' % repository.name else: # Update the repository registry. diff -r 155be7ce7910c2effb12fff904390401bdd7976b -r e8f2c4f3e8c8ed63a99254a50ceb18fc33c52080 lib/tool_shed/repository_registry.py --- a/lib/tool_shed/repository_registry.py +++ b/lib/tool_shed/repository_registry.py @@ -17,6 +17,7 @@ class Registry( object ): def __init__( self, app ): + log.debug( "Loading the repository registry..." ) self.app = app self.certified_level_one_clause_list = self.get_certified_level_one_clause_list() # The following lists contain tuples like ( repository.name, repository.user.username, changeset_revision ) @@ -164,9 +165,11 @@ if tip_changeset_hash != suc.INITIAL_CHANGELOG_HASH: certified_level_one_tuple = ( name, owner, tip_changeset_hash ) if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: - self.certified_level_one_suite_tuples.append( certified_level_one_tuple ) + if certified_level_one_tuple not in self.certified_level_one_suite_tuples: + self.certified_level_one_suite_tuples.append( certified_level_one_tuple ) else: - self.certified_level_one_repository_and_suite_tuples.append( certified_level_one_tuple ) + if certified_level_one_tuple not in self.certified_level_one_repository_and_suite_tuples: + self.certified_level_one_repository_and_suite_tuples.append( certified_level_one_tuple ) def load_repository_and_suite_tuple( self, repository ): name = str( repository.name ) @@ -174,9 +177,11 @@ for repository_metadata in repository.metadata_revisions: changeset_revision = str( repository_metadata.changeset_revision ) tuple = ( name, owner, changeset_revision ) - self.repository_and_suite_tuples.append( tuple ) + if tuple not in self.repository_and_suite_tuples: + self.repository_and_suite_tuples.append( tuple ) if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: - self.suite_tuples.append( tuple ) + if tuple not in self.suite_tuples: + self.suite_tuples.append( tuple ) def load_repository_and_suite_tuples( self ): # Load self.certified_level_one_repository_and_suite_tuples and self.certified_level_one_suite_tuples. @@ -237,6 +242,55 @@ if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION ]: self.certified_level_one_viewable_suites_by_category[ category_name ] += 1 + def remove_entry( self, repository ): + if repository: + is_valid = self.is_valid( repository ) + for rca in repository.categories: + category = rca.category + category_name = str( category.name ) + self.viewable_repositories_and_suites_by_category[ category_name ] -= 1 + if is_valid: + self.viewable_valid_repositories_and_suites_by_category[ category_name ] -= 1 + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + self.viewable_suites_by_category[ category_name ] -= 1 + if is_valid: + self.viewable_valid_suites_by_category[ category_name ] -= 1 + certified_level_one_tuple = self.get_certified_level_one_tuple( repository ) + latest_installable_changeset_revision, is_level_one_certified = certified_level_one_tuple + if is_level_one_certified: + self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] -= 1 + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + self.certified_level_one_viewable_suites_by_category[ category_name ] -= 1 + self.unload_repository_and_suite_tuple( repository ) + if is_level_one_certified: + self.unload_certified_level_one_repository_and_suite_tuple( repository ) + @property def sa_session( self ): return self.app.model.context.current + + def unload_certified_level_one_repository_and_suite_tuple( self, repository ): + # The received repository has been determined to be level one certified. + name = str( repository.name ) + owner = str( repository.user.username ) + tip_changeset_hash = repository.tip( self.app ) + if tip_changeset_hash != suc.INITIAL_CHANGELOG_HASH: + certified_level_one_tuple = ( name, owner, tip_changeset_hash ) + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + if certified_level_one_tuple in self.certified_level_one_suite_tuples: + self.certified_level_one_suite_tuples.remove( certified_level_one_tuple ) + else: + if certified_level_one_tuple in self.certified_level_one_repository_and_suite_tuples: + self.certified_level_one_repository_and_suite_tuples.remove( certified_level_one_tuple ) + + def unload_repository_and_suite_tuple( self, repository ): + name = str( repository.name ) + owner = str( repository.user.username ) + for repository_metadata in repository.metadata_revisions: + changeset_revision = str( repository_metadata.changeset_revision ) + tuple = ( name, owner, changeset_revision ) + if tuple in self.repository_and_suite_tuples: + self.repository_and_suite_tuples.remove( tuple ) + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + if tuple in self.suite_tuples: + self.suite_tuples.remove( tuple ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add appropriate entries into the Tool Shed's repository registry for newly created repositories and undeleted and undeprecated repositories.
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/155be7ce7910/ Changeset: 155be7ce7910 User: greg Date: 2014-05-21 21:37:27 Summary: Add appropriate entries into the Tool Shed's repository registry for newly created repositories and undeleted and undeprecated repositories. Affected #: 5 files diff -r a769e22480662ec5d1205816bd162b6cfa6649f7 -r 155be7ce7910c2effb12fff904390401bdd7976b lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -31,12 +31,6 @@ from tool_shed.galaxy_install import repository_util import tool_shed.galaxy_install.grids.admin_toolshed_grids as admin_toolshed_grids -import pkg_resources - -pkg_resources.require( 'elementtree' ) -from elementtree import ElementTree -from elementtree.ElementTree import Element - log = logging.getLogger( __name__ ) diff -r a769e22480662ec5d1205816bd162b6cfa6649f7 -r 155be7ce7910c2effb12fff904390401bdd7976b lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -367,6 +367,9 @@ repository.deleted = False trans.sa_session.add( repository ) trans.sa_session.flush() + if not repository.deprecated: + # Update the repository registry. + trans.app.repository_registry.add_entry( repository ) count += 1 undeleted_repositories += " %s" % repository.name if count: diff -r a769e22480662ec5d1205816bd162b6cfa6649f7 -r 155be7ce7910c2effb12fff904390401bdd7976b lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1053,6 +1053,8 @@ if mark_deprecated: message = 'The repository %s has been marked as deprecated.' % repository.name else: + # Update the repository registry. + trans.app.repository_registry.add_entry( repository ) message = 'The repository %s has been marked as not deprecated.' % repository.name trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', diff -r a769e22480662ec5d1205816bd162b6cfa6649f7 -r 155be7ce7910c2effb12fff904390401bdd7976b lib/tool_shed/repository_registry.py --- a/lib/tool_shed/repository_registry.py +++ b/lib/tool_shed/repository_registry.py @@ -40,6 +40,29 @@ self.load_viewable_repositories_and_suites_by_category() self.load_repository_and_suite_tuples() + def add_entry( self, repository ): + if repository: + is_valid = self.is_valid( repository ) + for rca in repository.categories: + category = rca.category + category_name = str( category.name ) + self.viewable_repositories_and_suites_by_category[ category_name ] += 1 + if is_valid: + self.viewable_valid_repositories_and_suites_by_category[ category_name ] += 1 + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + self.viewable_suites_by_category[ category_name ] += 1 + if is_valid: + self.viewable_valid_suites_by_category[ category_name ] += 1 + certified_level_one_tuple = self.get_certified_level_one_tuple( repository ) + latest_installable_changeset_revision, is_level_one_certified = certified_level_one_tuple + if is_level_one_certified: + self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] += 1 + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + self.certified_level_one_viewable_suites_by_category[ category_name ] += 1 + self.load_repository_and_suite_tuple( repository ) + if is_level_one_certified: + self.load_certified_level_one_repository_and_suite_tuple( repository ) + def get_certified_level_one_clause_list( self ): certified_level_one_tuples = [] clause_list = [] @@ -60,7 +83,9 @@ """ Return True if the latest installable changeset_revision of the received repository is level one certified. """ - if repository.deleted: + if repository is None: + return ( None, False ) + if repository.deleted or repository.deprecated: return ( None, False ) repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False ) # Get the latest installable changeset revision since that is all that is currently configured for testing. @@ -126,33 +151,46 @@ return tuple in self.certified_level_one_repository_and_suite_tuples return False + def is_valid( self, repository ): + if repository and not repository.deleted and not repository.deprecated and repository.downloadable_revisions: + return True + return False + + def load_certified_level_one_repository_and_suite_tuple( self, repository ): + # The received repository has been determined to be level one certified. + name = str( repository.name ) + owner = str( repository.user.username ) + tip_changeset_hash = repository.tip( self.app ) + if tip_changeset_hash != suc.INITIAL_CHANGELOG_HASH: + certified_level_one_tuple = ( name, owner, tip_changeset_hash ) + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + self.certified_level_one_suite_tuples.append( certified_level_one_tuple ) + else: + self.certified_level_one_repository_and_suite_tuples.append( certified_level_one_tuple ) + + def load_repository_and_suite_tuple( self, repository ): + name = str( repository.name ) + owner = str( repository.user.username ) + for repository_metadata in repository.metadata_revisions: + changeset_revision = str( repository_metadata.changeset_revision ) + tuple = ( name, owner, changeset_revision ) + self.repository_and_suite_tuples.append( tuple ) + if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: + self.suite_tuples.append( tuple ) + def load_repository_and_suite_tuples( self ): # Load self.certified_level_one_repository_and_suite_tuples and self.certified_level_one_suite_tuples. for repository in self.sa_session.query( model.Repository ) \ .join( model.RepositoryMetadata.table ) \ .filter( or_( *self.certified_level_one_clause_list ) ) \ .join( model.User.table ): - name = str( repository.name ) - owner = str( repository.user.username ) - tip_changeset_hash = repository.tip( self.app ) - certified_level_one_tuple = ( name, owner, tip_changeset_hash ) - if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: - self.certified_level_one_suite_tuples.append( certified_level_one_tuple ) - else: - self.certified_level_one_repository_and_suite_tuples.append( certified_level_one_tuple ) + self.load_certified_level_one_repository_and_suite_tuple( repository ) # Load self.repository_and_suite_tuples and self.suite_tuples for repository in self.sa_session.query( model.Repository ) \ .filter( and_( model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ .join( model.User.table ): - name = str( repository.name ) - owner = str( repository.user.username ) - for repository_metadata in repository.metadata_revisions: - changeset_revision = str( repository_metadata.changeset_revision ) - tuple = ( name, owner, changeset_revision ) - self.repository_and_suite_tuples.append( tuple ) - if repository.type == rt_util.REPOSITORY_SUITE_DEFINITION: - self.suite_tuples.append( tuple ) + self.load_repository_and_suite_tuple( repository ) def load_viewable_repositories_and_suites_by_category( self ): # Clear all dictionaries just in case they were previously loaded. @@ -165,40 +203,39 @@ self.viewable_valid_repositories_and_suites_by_category = {} self.viewable_valid_suites_by_category = {} for category in self.sa_session.query( model.Category ): + category_name = str( category.name ) if category not in self.certified_level_one_viewable_repositories_and_suites_by_category: - self.certified_level_one_viewable_repositories_and_suites_by_category[ str( category.name ) ] = 0 + self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] = 0 if category not in self.certified_level_one_viewable_suites_by_category: - self.certified_level_one_viewable_suites_by_category[ str( category.name ) ] = 0 + self.certified_level_one_viewable_suites_by_category[ category_name ] = 0 if category not in self.viewable_repositories_and_suites_by_category: - self.viewable_repositories_and_suites_by_category[ str( category.name ) ] = 0 + self.viewable_repositories_and_suites_by_category[ category_name ] = 0 if category not in self.viewable_suites_by_category: - self.viewable_suites_by_category[ str( category.name ) ] = 0 + self.viewable_suites_by_category[ category_name ] = 0 if category not in self.viewable_valid_repositories_and_suites_by_category: - self.viewable_valid_repositories_and_suites_by_category[ str( category.name ) ] = 0 + self.viewable_valid_repositories_and_suites_by_category[ category_name ] = 0 if category not in self.viewable_valid_suites_by_category: - self.viewable_valid_suites_by_category[ str( category.name ) ] = 0 + self.viewable_valid_suites_by_category[ category_name ] = 0 for rca in category.repositories: repository = rca.repository - if repository.downloadable_revisions: - is_valid = True - else: - is_valid = False - encoded_repository_id = self.app.security.encode_id( repository.id ) - tip_changeset_hash = repository.tip( self.app ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, - encoded_repository_id, - tip_changeset_hash ) - self.viewable_repositories_and_suites_by_category[ str( category.name ) ] += 1 - if is_valid: - self.viewable_valid_repositories_and_suites_by_category[ str( category.name ) ] += 1 - if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION ]: - self.viewable_suites_by_category[ str( category.name ) ] += 1 + if not repository.deleted and not repository.deprecated: + is_valid = self.is_valid( repository ) + encoded_repository_id = self.app.security.encode_id( repository.id ) + tip_changeset_hash = repository.tip( self.app ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + encoded_repository_id, + tip_changeset_hash ) + self.viewable_repositories_and_suites_by_category[ category_name ] += 1 if is_valid: - self.viewable_valid_suites_by_category[ str( category.name ) ] += 1 - if self.is_level_one_certified( repository_metadata ): - self.certified_level_one_viewable_repositories_and_suites_by_category[ str( category.name ) ] += 1 + self.viewable_valid_repositories_and_suites_by_category[ category_name ] += 1 if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION ]: - self.certified_level_one_viewable_suites_by_category[ str( category.name ) ] += 1 + self.viewable_suites_by_category[ category_name ] += 1 + if is_valid: + self.viewable_valid_suites_by_category[ category_name ] += 1 + if self.is_level_one_certified( repository_metadata ): + self.certified_level_one_viewable_repositories_and_suites_by_category[ category_name ] += 1 + if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION ]: + self.certified_level_one_viewable_suites_by_category[ category_name ] += 1 @property def sa_session( self ): diff -r a769e22480662ec5d1205816bd162b6cfa6649f7 -r 155be7ce7910c2effb12fff904390401bdd7976b lib/tool_shed/util/repository_maintenance_util.py --- a/lib/tool_shed/util/repository_maintenance_util.py +++ b/lib/tool_shed/util/repository_maintenance_util.py @@ -93,6 +93,8 @@ flush_needed = True if flush_needed: trans.sa_session.flush() + # Update the repository registry. + trans.app.repository_registry.add_entry( repository ) message = "Repository %s has been created." % str( repository.name ) return repository, message Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e2fb8fe53e8e/ Changeset: e2fb8fe53e8e Branch: next-stable User: jmchilton Date: 2014-05-21 21:33:24 Summary: Fix admin check in security_check for userless admin keys. ... by removing duplicated check of trans.user, this check is done in trans.user_is_admin if needed. Affected #: 1 file diff -r 65ca3d67f90b6617981cd75663dca2246643c047 -r e2fb8fe53e8ec833881a7e45f7946f09a078c3fd lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -304,7 +304,7 @@ def security_check( self, trans, item, check_ownership=False, check_accessible=False ): """ Security checks for an item: checks if (a) user owns item or (b) item is accessible to user. """ # all items are accessible to an admin - if trans.user and trans.user_is_admin(): + if trans.user_is_admin(): return item # Verify ownership: there is a current user and that user is the same as the item's https://bitbucket.org/galaxy/galaxy-central/commits/fc89661b92dc/ Changeset: fc89661b92dc Branch: next-stable User: jmchilton Date: 2014-05-21 21:33:24 Summary: Fix provenance controller for non-admins. Cannot pass check_accessible=True to get_object with HistoryDatasetAssociations (because item.user is undefined.). Affected #: 2 files diff -r e2fb8fe53e8ec833881a7e45f7946f09a078c3fd -r fc89661b92dcbd9684ac779171235525601d0f4a lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -5,6 +5,7 @@ from galaxy import web from galaxy.web.base.controller import BaseAPIController, UsesHistoryMixin from paste.httpexceptions import HTTPNotImplemented, HTTPBadRequest +from galaxy.managers import hdas log = logging.getLogger( __name__ ) @@ -12,6 +13,10 @@ class BaseProvenanceController( BaseAPIController, UsesHistoryMixin ): """ """ + def __init__( self, app ): + super( BaseProvenanceController, self ).__init__( app ) + self.hdas = hdas.HDAManager() + @web.expose_api def index( self, trans, **kwd ): follow = kwd.get('follow', False) @@ -34,7 +39,11 @@ raise HTTPBadRequest("Cannot Delete Provenance") def _get_provenance(self, trans, item_class_name, item_id, follow=True): - provenance_item = self.get_object( trans, item_id, item_class_name, check_ownership=False, check_accessible=True ) + provenance_item = self.get_object( trans, item_id, item_class_name, check_ownership=False, check_accessible=False) + if item_class_name == "HistoryDatasetAssociation": + self.hdas.check_accessible(trans, provenance_item) + else: + self.security_check(trans, provenance_item, check_accessible=True) out = self._get_record(trans, provenance_item, follow) return out diff -r e2fb8fe53e8ec833881a7e45f7946f09a078c3fd -r fc89661b92dcbd9684ac779171235525601d0f4a test/api/test_history_contents_provenance.py --- /dev/null +++ b/test/api/test_history_contents_provenance.py @@ -0,0 +1,16 @@ +from base import api +from .helpers import DatasetPopulator + + +class TestProvenance( api.ApiTestCase ): + + def setUp( self ): + super( TestProvenance, self ).setUp( ) + self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) + + def test_show_prov( self ): + history_id = self.dataset_populator.new_history() + new_dataset1 = self.dataset_populator.new_dataset( history_id, content='for prov' ) + prov_response = self._get( "histories/%s/contents/%s/provenance" % ( history_id, new_dataset1[ "id" ] ) ) + self._assert_status_code_is( prov_response, 200 ) + self._assert_has_keys( prov_response.json(), "job_id", "id", "stdout", "stderr", "parameters", "tool_id" ) https://bitbucket.org/galaxy/galaxy-central/commits/a769e2248066/ Changeset: a769e2248066 User: jmchilton Date: 2014-05-21 21:33:51 Summary: Merge next-stable. Affected #: 3 files diff -r 2601a535a02267e6af2c43b4a1a3e22ac9e78193 -r a769e22480662ec5d1205816bd162b6cfa6649f7 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -304,7 +304,7 @@ def security_check( self, trans, item, check_ownership=False, check_accessible=False ): """ Security checks for an item: checks if (a) user owns item or (b) item is accessible to user. """ # all items are accessible to an admin - if trans.user and trans.user_is_admin(): + if trans.user_is_admin(): return item # Verify ownership: there is a current user and that user is the same as the item's diff -r 2601a535a02267e6af2c43b4a1a3e22ac9e78193 -r a769e22480662ec5d1205816bd162b6cfa6649f7 lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -5,6 +5,7 @@ from galaxy import web from galaxy.web.base.controller import BaseAPIController, UsesHistoryMixin from paste.httpexceptions import HTTPNotImplemented, HTTPBadRequest +from galaxy.managers import hdas log = logging.getLogger( __name__ ) @@ -12,6 +13,10 @@ class BaseProvenanceController( BaseAPIController, UsesHistoryMixin ): """ """ + def __init__( self, app ): + super( BaseProvenanceController, self ).__init__( app ) + self.hdas = hdas.HDAManager() + @web.expose_api def index( self, trans, **kwd ): follow = kwd.get('follow', False) @@ -34,7 +39,11 @@ raise HTTPBadRequest("Cannot Delete Provenance") def _get_provenance(self, trans, item_class_name, item_id, follow=True): - provenance_item = self.get_object( trans, item_id, item_class_name, check_ownership=False, check_accessible=True ) + provenance_item = self.get_object( trans, item_id, item_class_name, check_ownership=False, check_accessible=False) + if item_class_name == "HistoryDatasetAssociation": + self.hdas.check_accessible(trans, provenance_item) + else: + self.security_check(trans, provenance_item, check_accessible=True) out = self._get_record(trans, provenance_item, follow) return out diff -r 2601a535a02267e6af2c43b4a1a3e22ac9e78193 -r a769e22480662ec5d1205816bd162b6cfa6649f7 test/api/test_history_contents_provenance.py --- /dev/null +++ b/test/api/test_history_contents_provenance.py @@ -0,0 +1,16 @@ +from base import api +from .helpers import DatasetPopulator + + +class TestProvenance( api.ApiTestCase ): + + def setUp( self ): + super( TestProvenance, self ).setUp( ) + self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) + + def test_show_prov( self ): + history_id = self.dataset_populator.new_history() + new_dataset1 = self.dataset_populator.new_dataset( history_id, content='for prov' ) + prov_response = self._get( "histories/%s/contents/%s/provenance" % ( history_id, new_dataset1[ "id" ] ) ) + self._assert_status_code_is( prov_response, 200 ) + self._assert_has_keys( prov_response.json(), "job_id", "id", "stdout", "stderr", "parameters", "tool_id" ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/65ca3d67f90b/ Changeset: 65ca3d67f90b Branch: next-stable User: greg Date: 2014-05-21 21:06:41 Summary: Enhance the Tool Shed API to be able to retrieve an API key for an authenticated user. Affected #: 2 files diff -r a8904f154c5a1d94d8180c75683992a4123caef2 -r 65ca3d67f90b6617981cd75663dca2246643c047 lib/galaxy/webapps/tool_shed/api/authenticate.py --- /dev/null +++ b/lib/galaxy/webapps/tool_shed/api/authenticate.py @@ -0,0 +1,94 @@ +""" +API key retrieval through BaseAuth +Sample usage: + +curl --user zipzap@foo.com:password http://localhost:9009/api/authenticate/baseauth + +Returns: +{ + "api_key": <some api key> +} +""" +import logging +from base64 import b64decode +from paste.httpexceptions import HTTPBadRequest +from urllib import unquote + +from galaxy import web +from galaxy.exceptions import ObjectNotFound +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import CreatesApiKeysMixin + +log = logging.getLogger( __name__ ) + + +class AuthenticationController( BaseAPIController, CreatesApiKeysMixin ): + + @web.expose_api_anonymous + def get_api_key( self, trans, **kwd ): + """ + def get_api_key( self, trans, **kwd ) + * GET /api/authenticate/baseauth + returns an API key for authenticated user based on BaseAuth headers + + :returns: api_key in json format + :rtype: dict + + :raises: ObjectNotFound, HTTPBadRequest + """ + email, password = self._decode_baseauth( trans.environ.get( 'HTTP_AUTHORIZATION' ) ) + user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).all() + if ( len( user ) is not 1 ): + # DB is inconsistent and we have more users with same email + raise ObjectNotFound + else: + user = user[ 0 ] + is_valid_user = user.check_password( password ) + if ( is_valid_user ): + if user.api_keys: + key = user.api_keys[ 0 ].key + else: + key = self.create_api_key( trans, user ) + return dict( api_key=key ) + else: + trans.response.status = 500 + return "invalid password" + + def _decode_baseauth( self, encoded_str ): + """ + Decode an encrypted HTTP basic authentication string. Returns a tuple of + the form (email, password), and raises a HTTPBadRequest exception if + nothing could be decoded. + + :param encoded_str: BaseAuth string encoded base64 + :type encoded_str: string + + :returns: email of the user + :rtype: string + :returns: password of the user + :rtype: string + + :raises: HTTPBadRequest + """ + split = encoded_str.strip().split( ' ' ) + # If split is only one element, try to decode the email and password directly. + if len( split ) == 1: + try: + email, password = b64decode( split[ 0 ] ).split( ':' ) + except: + raise HTTPBadRequest + # If there are only two elements, check the first and ensure it says + # 'basic' so that we know we're about to decode the right thing. If not, + # bail out. + elif len( split ) == 2: + if split[ 0 ].strip().lower() == 'basic': + try: + email, password = b64decode( split[ 1 ] ).split( ':' ) + except: + raise HTTPBadRequest + else: + raise HTTPBadRequest + # If there are more than 2 elements, something crazy must be happening. Bail. + else: + raise HTTPBadRequest + return unquote( email ), unquote( password ) diff -r a8904f154c5a1d94d8180c75683992a4123caef2 -r 65ca3d67f90b6617981cd75663dca2246643c047 lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -80,6 +80,11 @@ webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' ) # Add the web API. # A good resource for RESTful services - http://routes.readthedocs.org/en/latest/restful.html webapp.add_api_controllers( 'galaxy.webapps.tool_shed.api', app ) + webapp.mapper.connect( 'api_key_retrieval', + '/api/authenticate/baseauth/', + controller='authenticate', + action='get_api_key', + conditions=dict( method=[ "GET" ] ) ) webapp.mapper.resource( 'category', 'categories', controller='categories', https://bitbucket.org/galaxy/galaxy-central/commits/2601a535a022/ Changeset: 2601a535a022 User: davebgx Date: 2014-05-21 21:10:01 Summary: Merge with next-stable. Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Enhance the Tool Shed API to be able to retrieve an API key for an authenticated user.
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/55cefad9d53c/ Changeset: 55cefad9d53c User: greg Date: 2014-05-21 21:06:41 Summary: Enhance the Tool Shed API to be able to retrieve an API key for an authenticated user. Affected #: 2 files diff -r ffe1fed76848569754c81c59fdba999d488782c9 -r 55cefad9d53cdb16d0fb04bef60ea43c73e512b0 lib/galaxy/webapps/tool_shed/api/authenticate.py --- /dev/null +++ b/lib/galaxy/webapps/tool_shed/api/authenticate.py @@ -0,0 +1,94 @@ +""" +API key retrieval through BaseAuth +Sample usage: + +curl --user zipzap@foo.com:password http://localhost:9009/api/authenticate/baseauth + +Returns: +{ + "api_key": <some api key> +} +""" +import logging +from base64 import b64decode +from paste.httpexceptions import HTTPBadRequest +from urllib import unquote + +from galaxy import web +from galaxy.exceptions import ObjectNotFound +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import CreatesApiKeysMixin + +log = logging.getLogger( __name__ ) + + +class AuthenticationController( BaseAPIController, CreatesApiKeysMixin ): + + @web.expose_api_anonymous + def get_api_key( self, trans, **kwd ): + """ + def get_api_key( self, trans, **kwd ) + * GET /api/authenticate/baseauth + returns an API key for authenticated user based on BaseAuth headers + + :returns: api_key in json format + :rtype: dict + + :raises: ObjectNotFound, HTTPBadRequest + """ + email, password = self._decode_baseauth( trans.environ.get( 'HTTP_AUTHORIZATION' ) ) + user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).all() + if ( len( user ) is not 1 ): + # DB is inconsistent and we have more users with same email + raise ObjectNotFound + else: + user = user[ 0 ] + is_valid_user = user.check_password( password ) + if ( is_valid_user ): + if user.api_keys: + key = user.api_keys[ 0 ].key + else: + key = self.create_api_key( trans, user ) + return dict( api_key=key ) + else: + trans.response.status = 500 + return "invalid password" + + def _decode_baseauth( self, encoded_str ): + """ + Decode an encrypted HTTP basic authentication string. Returns a tuple of + the form (email, password), and raises a HTTPBadRequest exception if + nothing could be decoded. + + :param encoded_str: BaseAuth string encoded base64 + :type encoded_str: string + + :returns: email of the user + :rtype: string + :returns: password of the user + :rtype: string + + :raises: HTTPBadRequest + """ + split = encoded_str.strip().split( ' ' ) + # If split is only one element, try to decode the email and password directly. + if len( split ) == 1: + try: + email, password = b64decode( split[ 0 ] ).split( ':' ) + except: + raise HTTPBadRequest + # If there are only two elements, check the first and ensure it says + # 'basic' so that we know we're about to decode the right thing. If not, + # bail out. + elif len( split ) == 2: + if split[ 0 ].strip().lower() == 'basic': + try: + email, password = b64decode( split[ 1 ] ).split( ':' ) + except: + raise HTTPBadRequest + else: + raise HTTPBadRequest + # If there are more than 2 elements, something crazy must be happening. Bail. + else: + raise HTTPBadRequest + return unquote( email ), unquote( password ) diff -r ffe1fed76848569754c81c59fdba999d488782c9 -r 55cefad9d53cdb16d0fb04bef60ea43c73e512b0 lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -80,6 +80,11 @@ webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' ) # Add the web API. # A good resource for RESTful services - http://routes.readthedocs.org/en/latest/restful.html webapp.add_api_controllers( 'galaxy.webapps.tool_shed.api', app ) + webapp.mapper.connect( 'api_key_retrieval', + '/api/authenticate/baseauth/', + controller='authenticate', + action='get_api_key', + conditions=dict( method=[ "GET" ] ) ) webapp.mapper.resource( 'category', 'categories', controller='categories', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: merge next-stable
by commits-noreply＠bitbucket.org 21 May '14

21 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ffe1fed76848/ Changeset: ffe1fed76848 User: dan Date: 2014-05-21 20:24:51 Summary: merge next-stable Affected #: 1 file diff -r 6f2455ab4acbce667ff5155fd85fef4d3dacc9cc -r ffe1fed76848569754c81c59fdba999d488782c9 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -16,9 +16,10 @@ self._data_table_name = data_table_name self._static_chrom_info_path = app.config.len_file_path # A dbkey can be listed multiple times, but with different names, so we can't use dictionaries for lookups - self._static_dbkeys = [] if load_old_style: self._static_dbkeys = list( dbnames ) + else: + self._static_dbkeys = [] def get_genome_build_names( self, trans=None ): # FIXME: how to deal with key duplicates? @@ -34,7 +35,7 @@ datasets = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ) \ .filter_by( deleted=False, history_id=trans.history.id, extension="len" ) for dataset in datasets: - rval.append( (dataset.dbkey, dataset.name) ) + rval.append( ( dataset.dbkey, "%s (%s) [History]" % ( dataset.name, dataset.dbkey ) ) ) user = trans.get_user() if user and 'dbkeys' in user.preferences: user_keys = from_json_string( user.preferences['dbkeys'] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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