June 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dannon: Correct tools handling of tool.handle_input -- this doesn't always return a successful job.
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6b6c0b985ef3/ Changeset: 6b6c0b985ef3 User: dannon Date: 2014-06-11 17:39:21 Summary: Correct tools handling of tool.handle_input -- this doesn't always return a successful job. Affected #: 1 file diff -r 2f21305e92783303c6254c66678a0d44365f7770 -r 6b6c0b985ef35056b773197354afe83b07d88afa lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -156,7 +156,7 @@ output_dict[ 'output_name' ] = output_name outputs.append( trans.security.encode_dict_ids( output_dict ) ) - for job in vars[ 'jobs' ]: + for job in vars.get('jobs', []): rval[ 'jobs' ].append( self.encode_all_ids( trans, job.to_dict( view='collection' ), recursive=True ) ) for output_name, collection_instance in vars.get( 'implicit_collections', {} ).iteritems(): 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: 2 new changesets
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ef56567006a4/ Changeset: ef56567006a4 Branch: stable User: natefoo Date: 2014-06-11 16:12:54 Summary: Updated tag latest_2014.06.02 for changeset f7dd0060c296 Affected #: 1 file diff -r f7dd0060c2966f2b9c66c5ac739d0e5a9a31faa0 -r ef56567006a42ecfaee303b22f4f379a759c03b8 .hgtags --- a/.hgtags +++ b/.hgtags @@ -9,5 +9,4 @@ 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -7e257c7b10badb65772b1528cb61d58175a42e47 latest_2014.06.02 -fb68af9a775a956fcc397b22d16f2119401d926d latest_2014.06.02 +f7dd0060c2966f2b9c66c5ac739d0e5a9a31faa0 latest_2014.06.02 https://bitbucket.org/galaxy/galaxy-central/commits/2f21305e9278/ Changeset: 2f21305e9278 User: natefoo Date: 2014-06-11 16:26:37 Summary: Merge stable. Affected #: 1 file diff -r a2e6ccecce9d018d9b5ec24d2fc87deab3c74a9a -r 2f21305e92783303c6254c66678a0d44365f7770 .hgtags --- a/.hgtags +++ b/.hgtags @@ -9,5 +9,4 @@ 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -7e257c7b10badb65772b1528cb61d58175a42e47 latest_2014.06.02 -fb68af9a775a956fcc397b22d16f2119401d926d latest_2014.06.02 +f7dd0060c2966f2b9c66c5ac739d0e5a9a31faa0 latest_2014.06.02 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: dannon: Merge stable.
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a2e6ccecce9d/ Changeset: a2e6ccecce9d User: dannon Date: 2014-06-11 16:20:53 Summary: Merge 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: guerler: Charts: Add progress notification
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0fc231c66f8d/ Changeset: 0fc231c66f8d User: guerler Date: 2014-06-11 12:59:41 Summary: Charts: Add progress notification Affected #: 5 files diff -r b62ff72c0d872fd03ed20ffd782a974f7bc0205d -r 0fc231c66f8de637ed9559a7f2d116870edb8dba config/plugins/visualizations/charts/static/app.css --- a/config/plugins/visualizations/charts/static/app.css +++ b/config/plugins/visualizations/charts/static/app.css @@ -48,6 +48,7 @@ margin-left: 5px; top: -1px; font-size: 1.0em; + display: inline-block; } .charts-viewport .icon { diff -r b62ff72c0d872fd03ed20ffd782a974f7bc0205d -r 0fc231c66f8de637ed9559a7f2d116870edb8dba config/plugins/visualizations/charts/static/charts/tools.js --- a/config/plugins/visualizations/charts/static/charts/tools.js +++ b/config/plugins/visualizations/charts/static/charts/tools.js @@ -4,6 +4,9 @@ // render function panelHelper (options) { + // link this + var self = this; + // require parameters var process_id = options.process_id; var chart = options.chart; @@ -15,9 +18,8 @@ // get request size from chart request_dictionary.query_limit = chart.definition.query_limit; - // request data - var self = this; - app.datasets.request(request_dictionary, function() { + // define success function + request_dictionary.success = function() { try { // check if this chart has multiple panels if (!chart.definition.use_panels && chart.settings.get('use_panels') !== 'true') { @@ -52,7 +54,15 @@ // unregister process chart.deferred.done(process_id); } - }); + }; + + // add progress + request_dictionary.progress = function(percentage) { + chart.state('wait', 'Loading data...' + percentage + '%'); + }; + + // request data + app.datasets.request(request_dictionary); }; // get domain boundaries value diff -r b62ff72c0d872fd03ed20ffd782a974f7bc0205d -r 0fc231c66f8de637ed9559a7f2d116870edb8dba 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 @@ -21,18 +21,23 @@ }, // request handler - request: function(request_dictionary, success, error) { + request: function(request_dictionary) { if (request_dictionary.groups) { - this._get_blocks(request_dictionary, success, error); + this._get_blocks(request_dictionary); } else { - this._get_dataset(request_dictionary.id, success, error) + this._get_dataset(request_dictionary.id, request_dictionary.success, request_dictionary.error) } }, // multiple request handler - _get_blocks: function(request_dictionary, success, error) { + _get_blocks: function(request_dictionary) { + // get callbacks + var success = request_dictionary.success; + var progress = request_dictionary.progress; + // query block size - var query_size = this.app.config.get('query_limit'); + var query_size = this.app.config.get('query_limit'); + var query_timeout = this.app.config.get('query_timeout'); // set range var query_start = request_dictionary.start || 0; @@ -51,9 +56,12 @@ // get query dictionary template var query_dictionary_template = $.extend(true, {}, request_dictionary); + // reset query counter + var query_counter = 0; + // fetch blocks var self = this; - function fetch_blocks (query, success, error) { + function fetch_blocks (query) { self._get(query, function() { // copy values from query into request_dictionary var done = false; @@ -78,10 +86,16 @@ } // check if for remaining queries - if (--query_number > 0 && !done) { + if (++query_counter < query_number && !done) { + // report progress + if (progress) { + progress(parseInt((query_counter / query_number) * 100)); + } + + // next query var start = query.start + query_size; query = $.extend(true, query_dictionary_template, {start: start}); - fetch_blocks(query, success, error); + fetch_blocks(query); } else { success(); } @@ -94,7 +108,7 @@ // get dataset meta data this._get_dataset(request_dictionary.id, function() { - fetch_blocks(query, success, error); + fetch_blocks(query); }); }, @@ -197,12 +211,12 @@ // convert _fill_from_cache: function(request_dictionary) { - // log - console.debug('Datasets::_fill_from_cache() - Filling request from cache.'); - // identify start of request var start = request_dictionary.start; + // log + console.debug('Datasets::_fill_from_cache() - Filling request from cache at ' + start + '.'); + // identify end of request var limit = 0; for (var i in request_dictionary.groups) { diff -r b62ff72c0d872fd03ed20ffd782a974f7bc0205d -r 0fc231c66f8de637ed9559a7f2d116870edb8dba 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 @@ -110,19 +110,25 @@ // register process var process_id = this.chart.deferred.register(); + // request dictionary + var request_dictionary = { + id : dataset_id, + success : function(dataset) { + // update select fields + for (var id in select_list) { + self._addRow(id, dataset, select_list, chart_definition.columns[id]) + } + + // loading + self.chart.state('ok', 'Metadata initialized...'); + + // unregister + self.chart.deferred.done(process_id); + } + }; + // get dataset - this.app.datasets.request({id : dataset_id}, function(dataset) { - // update select fields - for (var id in select_list) { - self._addRow(id, dataset, select_list, chart_definition.columns[id]) - } - - // loading - self.chart.state('ok', 'Metadata initialized...'); - - // unregister - self.chart.deferred.done(process_id); - }); + this.app.datasets.request(request_dictionary); }, // add row diff -r b62ff72c0d872fd03ed20ffd782a974f7bc0205d -r 0fc231c66f8de637ed9559a7f2d116870edb8dba config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -50,7 +50,7 @@ // show info $info.show(); $info.find('#text').html(self.chart.get('state_info')); - + // check status var state = self.chart.get('state'); switch (state) { @@ -274,7 +274,7 @@ _template: function() { return '<div class="charts-viewport">' + '<div id="info" class="info">' + - '<span id="icon" class="icon" />' + + '<span id="icon" class="icon"/>' + '<span id="text" class="text" />' + '</div>' + '</div>'; 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: Allow individual chart types to set request limits
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b62ff72c0d87/ Changeset: b62ff72c0d87 User: guerler Date: 2014-06-11 11:52:01 Summary: Charts: Allow individual chart types to set request limits Affected #: 4 files diff -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 -r b62ff72c0d872fd03ed20ffd782a974f7bc0205d config/plugins/visualizations/charts/static/charts/jqplot/common/config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js @@ -6,6 +6,7 @@ library : 'JqPlot', tag : 'div', keywords : 'default medium', + query_limit : 10000, settings : { separator_label : { title : 'X axis', diff -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 -r b62ff72c0d872fd03ed20ffd782a974f7bc0205d config/plugins/visualizations/charts/static/charts/nvd3/common/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js @@ -6,6 +6,7 @@ library : 'NVD3', tag : 'svg', keywords : 'small', + query_limit : 500, settings : { separator_label : { title : 'X axis', diff -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 -r b62ff72c0d872fd03ed20ffd782a974f7bc0205d config/plugins/visualizations/charts/static/charts/tools.js --- a/config/plugins/visualizations/charts/static/charts/tools.js +++ b/config/plugins/visualizations/charts/static/charts/tools.js @@ -12,6 +12,9 @@ var canvas = options.canvas; var app = options.app; + // get request size from chart + request_dictionary.query_limit = chart.definition.query_limit; + // request data var self = this; app.datasets.request(request_dictionary, function() { diff -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 -r b62ff72c0d872fd03ed20ffd782a974f7bc0205d 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 @@ -20,21 +20,84 @@ this.options = Utils.merge(options, this.optionsDefault); }, - // wait + // request handler request: function(request_dictionary, success, error) { - // link this - var self = this; - - // check if column data is requested if (request_dictionary.groups) { - this._get_dataset(request_dictionary.id, function() { - self._get(request_dictionary, success); - }); + this._get_blocks(request_dictionary, success, error); } else { this._get_dataset(request_dictionary.id, success, error) } }, + // multiple request handler + _get_blocks: function(request_dictionary, success, error) { + // query block size + var query_size = this.app.config.get('query_limit'); + + // set range + var query_start = request_dictionary.start || 0; + var query_end = query_start + request_dictionary.query_limit || query_start + this.app.config.get('query_limit'); + + // get query limit + var query_range = Math.abs(query_end - query_start); + if (query_range <= 0) { + console.debug('FAILED - Datasets::request() - Invalid query range.'); + return; + } + + // get number of required queries + var query_number = Math.ceil(query_range / query_size) || 1; + + // get query dictionary template + var query_dictionary_template = $.extend(true, {}, request_dictionary); + + // fetch blocks + var self = this; + function fetch_blocks (query, success, error) { + self._get(query, function() { + // copy values from query into request_dictionary + var done = false; + for (var group_index in request_dictionary.groups) { + // get source/destination + destination_group = request_dictionary.groups[group_index]; + source_group = query.groups[group_index]; + + // check if value fields already exist + if (!destination_group.values) { + destination_group.values = []; + } + + // concat values + destination_group.values = destination_group.values.concat(source_group.values); + + // validate + if (source_group.values.length == 0) { + done = true; + break; + } + } + + // check if for remaining queries + if (--query_number > 0 && !done) { + var start = query.start + query_size; + query = $.extend(true, query_dictionary_template, {start: start}); + fetch_blocks(query, success, error); + } else { + success(); + } + }); + + }; + + // prepare query + var query = $.extend(true, query_dictionary_template, {start: query_start}); + + // get dataset meta data + this._get_dataset(request_dictionary.id, function() { + fetch_blocks(query, success, error); + }); + }, + // get dataset _get_dataset: function(id, success, error) { // check if dataset is available from cache @@ -62,18 +125,14 @@ // get block id _block_id: function (options, column) { - return options.id + '_' + options.start + '_' + options.end + '_' + column; + return options.id + '_' + options.start + '_' + options.start + this.app.config.get('query_limit') + '_' + column; }, // fills request dictionary with data from cache/response _get: function(request_dictionary, callback) { - // set start/end - if (!request_dictionary.start) { - request_dictionary.start = 0; - } - if (!request_dictionary.end) { - request_dictionary.end = this.app.config.get('query_limit'); - } + // set start + request_dictionary.start = request_dictionary.start || 0; + // get column indices var column_list = []; var column_map = {}; @@ -99,7 +158,7 @@ } } - // check length + // check length of blocks not available in cache if (column_list.length == 0) { // fill dictionary from cache this._fill_from_cache(request_dictionary); @@ -115,7 +174,6 @@ var dataset_request = { dataset_id : request_dictionary.id, start : request_dictionary.start, - end : request_dictionary.end, columns : column_list } @@ -161,7 +219,7 @@ // check length if (limit == 0) { - console.debug('FAILED - Datasets::_fill_from_cache() - Invalid range.'); + console.debug('Datasets::_fill_from_cache() - Reached data range limit.'); } // initialize group values @@ -230,17 +288,13 @@ var offset = dataset_request.start ? dataset_request.start : 0; // set limit - var limit = Math.abs(dataset_request.end - dataset_request.start); - var query_limit = this.app.config.get('query_limit'); - if (!limit || limit > query_limit) { - limit = query_limit; - } + var limit = this.app.config.get('query_limit'); // check length var n_columns = 0; if (dataset_request.columns) { n_columns = dataset_request.columns.length; - console.debug('Datasets::_fetch() - Fetching ' + n_columns + ' column(s)'); + console.debug('Datasets::_fetch() - Fetching ' + n_columns + ' column(s) at ' + offset + '.'); } if (n_columns == 0) { console.debug('Datasets::_fetch() - No columns requested'); 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: Improve axes labeling, formatting options and chart interaction
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/66cfcaf35801/ Changeset: 66cfcaf35801 User: guerler Date: 2014-06-11 08:30:52 Summary: Charts: Improve axes labeling, formatting options and chart interaction Affected #: 22 files diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js @@ -7,7 +7,8 @@ x : { title : 'Values for x-axis', is_label : true, - is_auto : true + is_auto : true, + is_unique : true }, y : { title : 'Values for y-axis', diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js @@ -1,5 +1,5 @@ // dependencies -define(['plugin/charts/jqplot/common/wrapper'], function(Plot) { +define(['plugin/charts/jqplot/common/wrapper', 'plugin/charts/tools'], function(Plot, Tools) { // widget return Backbone.View.extend( @@ -19,8 +19,7 @@ group.columns = null; group.columns = { x: { - index: index++, - is_numeric: true + index : index++ } } } @@ -30,66 +29,67 @@ process_id : process_id, chart : chart, request_dictionary : request_dictionary, - makeConfig : function(plot_config){ + makeConfig : function(plot_config, groups){ + var boundary = Tools.getDomains(groups, 'x'); $.extend(true, plot_config, { seriesDefaults: { renderer: $.jqplot.OHLCRenderer, rendererOptions : { - candleStick : true + candleStick : true, + fillUpBody : true, + fillDownBody : true + } + }, + axes : { + xaxis: { + pad: 1.2 + }, + yaxis: { + min: boundary.x.min, + max: boundary.x.max } } }); }, makeSeries : function (groups) { + /* example data + var catOHLC = [ + [0, 138.7, 139.68, 135.18, 135.4], + [1, 143.46, 144.66, 139.79, 140.02], + [2, 140.67, 143.56, 132.88, 142.44], + [3, 136.01, 139.5, 134.53, 139.48] + ]; + return [catOHLC]; + */ + // plot data var plot_data = []; // check group length - if (groups.length == 0 && groups[0].values.length == 0) { - return; + if (groups.length == 0 || groups[0].values.length < 5) { + chart.state('failed', 'Boxplot data could not be found.'); + return [plot_data]; } - // reset data/categories - var data = []; - - /*/ loop through data groups - for (var key in request_dictionary.groups) { + // loop through data groups + for (var group_index in request_dictionary.groups) { // get group - var group = request_dictionary.groups[key]; - + var group = request_dictionary.groups[group_index]; + // format chart data var point = []; - point.push(group.key); - for (var key in [0, 1, 3, 4]) { - point.push(group.values[key].x); + point.push(parseInt(group_index)); + var indeces = [2, 4, 0, 1]; + for (var key in indeces) { + point.push(group.values[indeces[key]].x); } - + // add to data - data.push (point); - }*/ - - /*/ loop through data groups - for (var key in groups) { - var group = groups[key]; - var point = []; - for (var value_index in group.values) { - point.push(group.values[value_index].x); - } plot_data.push (point); } // return return [plot_data]; - - var catOHLC = [[1, 138.7, 139.68, 135.18, 135.4], - [2, 143.46, 144.66, 139.79, 140.02], - [3, 140.67, 143.56, 132.88, 142.44], - [4, 136.01, 139.5, 134.53, 139.48], - [5, 443.82, 144.56, 136.04, 136.97], - [6, 136.47, 146.4, 136, 144.67], - [7, 124.76, 135.9, 124.55, 135.81], - [8, 223.73, 129.31, 121.57, 122.5]]; - return [catOHLC];*/ } }); } diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js @@ -7,6 +7,7 @@ // get chart settings var settings = chart.settings; var plot_config = { + enablePlugins: true, seriesColors: function() { var colors = []; var colorScale = d3.scale.category20(); @@ -61,30 +62,11 @@ // is specified for each series. series: [], - // Show the legend and put it outside the grid, but inside the - // plot container, shrinking the grid to accomodate the legend. - // A value of "outside" would not shrink the grid and allow - // the legend to overflow the container. - legend: { - renderer : $.jqplot.EnhancedLegendRenderer, - show : chart.settings.get('show_legend') == 'true', - placement : 'outsideGrid', - location : 'n', - rendererOptions: { - textColor : '#000000', - fontSize : '12pt', - border : 'none', - shadowAlpha : 1, - background : 'rgba(255, 255, 255, 0.9)', - fontFamily : 'Arial', - numberRows : 1 - } - }, - axesDefaults: { labelRenderer : $.jqplot.CanvasAxisLabelRenderer, labelOptions: { - fontSize : '12pt' + fontSize : '12pt', + textColor : '#000000' }, tickRenderer : $.jqplot.CanvasAxisTickRenderer , tickOptions: { @@ -108,6 +90,7 @@ // not touch, the grid boundaries. 1.2 is the default padding. yaxis: { label : chart.settings.get('y_axis_label'), + tickOptions : {}, pad : 0 //tickOptions : {formatString: '$%d'}, //padding : 1.2, @@ -116,7 +99,7 @@ }, grid: { - background : '#FFFFFF', // CSS color spec for background color of grid. + background : '#FFFFFF', borderWidth : 0, shadow : false }, @@ -124,11 +107,38 @@ cursor: { show : true, zoom : true, - showTooltip : true, + showTooltip : false, style : 'pointer' + }, + highlighter: { + show : true, + showMarker : false, + tooltipAxes : 'xy' } }; + // Show the legend and put it outside the grid, but inside the + // plot container, shrinking the grid to accomodate the legend. + // A value of "outside" would not shrink the grid and allow + // the legend to overflow the container. + if (chart.settings.get('show_legend') == 'true') { + plot_config.legend = { + renderer : $.jqplot.EnhancedLegendRenderer, + show : true, + placement : 'outsideGrid', + location : 'n', + rendererOptions: { + textColor : '#000000', + fontSize : '12pt', + border : 'none', + shadowAlpha : 1, + background : 'rgba(255, 255, 255, 0.9)', + fontFamily : 'Arial', + numberRows : 1 + } + }; + } + // callback return plot_config; }; diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js @@ -37,35 +37,41 @@ // draw all data into a single canvas render: function(groups, el_canvas) { - // set chart settings - var chart = this.options.chart; - var makeConfig = this.options.makeConfig; - var makeSeries = this.options.makeSeries; + // get parameters + var chart = this.options.chart; + var makeCategories = this.options.makeCategories; + var makeSeries = this.options.makeSeries; + var makeConfig = this.options.makeConfig; // create configuration var plot_config = configmaker(chart); var plot_data = [] - - // identify categories - this._makeCategories(chart, groups, plot_config, true); - - // reset data - if (makeSeries) { - plot_data = makeSeries(groups); - } else { - plot_data = Tools.makeSeries(groups); - } - + // draw plot try { // canvas var canvas = el_canvas[0]; + + // make custom categories call + this._makeAxes(plot_config, groups, chart.settings); - // make custom wrapper callback + // make custom series call + if (makeSeries) { + plot_data = makeSeries(groups); + } else { + plot_data = Tools.makeSeries(groups); + } + + // make custom config call if (makeConfig) { - makeConfig(plot_config); + makeConfig(plot_config, groups); } - + + // check chart state + if (chart.get('state') == 'failed') { + return false; + } + // Draw graph with default options, overwriting with passed options function drawGraph (opts) { el_canvas.empty(); @@ -89,53 +95,54 @@ } }, - // create categories - _makeCategories: function(chart, groups, plot_config) { - - // check length - if (groups.length == 0) { - return; + // create axes formatting + _makeAxes: function(plot_config, groups, settings) { + // result + var makeCategories = this.options.makeCategories; + var categories; + if (makeCategories) { + categories = makeCategories(groups, plot_config); + } else { + categories = Tools.makeCategories(groups); } - - // result - var result = Tools.makeCategories(chart, groups); - - /*/ add categories to plot configuration - for (var key in result.array) { - var axis = key + 'axis'; - if (plot_config.axes[axis]) { - plot_config.axes[axis].ticks = result.array[key]; + + // make axis + function makeAxis (id) { + var axis = plot_config.axes[id + 'axis'].tickOptions; + var type = settings.get(id + '_axis_type'); + var tick = settings.get(id + '_axis_tick'); + var is_category = categories.array[id]; + + // hide axis + if (type == 'hide') { + axis.formatter = function(format, value) { return '' }; + return; } - }*/ - - // add x tick formatter - function axisTickFormatter (axis_char, plot_axis, axis_type, axis_tick) { - // get chart definition from first group - var chart_definition = groups[0]; - /*if (axis_type != 'auto' && axis_type !== undefined) { - plot_axis.tickOptions.formatter = function(format, value) { - if (axis_type == 'hide') { - return ''; - } - var format = d3.format(axis_tick + axis_type); - return format(v); + // format values/labels + if (type == 'auto') { + if (is_category) { + axis.formatter = function(format, value) { + return categories.array[id][value] || ''; + }; } - } else {*/ - if (chart_definition.columns[axis_char] && chart_definition.columns[axis_char].is_label) { - plot_axis.tickOptions.formatter = function(format, value) { - if (result.array[axis_char] !== undefined && - result.array[axis_char][value] !== undefined) { - return result.array[axis_char][value]; - } else { - return ''; - } + } else { + var formatter = d3.format(tick + type); + if (is_category) { + axis.formatter = function(format, value) { + return formatter(categories.array[id][value]); + }; + } else { + axis.formatter = function(format, value) { + return formatter(value); } } - //} - } - //axisTickFormatter ('x', plot_config.axes.xaxis, chart.settings.get('x_axis_type'), chart.settings.get('x_axis_tick')); - //axisTickFormatter ('y', plot_config.axes.yaxis, chart.settings.get('y_axis_type'), chart.settings.get('y_axis_tick')); + } + }; + + // make axes + makeAxis('x'); + makeAxis('y'); }, // handle error diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 config/plugins/visualizations/charts/static/charts/jqplot/line/config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/line/config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/line/config.js @@ -7,7 +7,8 @@ x : { title : 'Values for x-axis', is_label : true, - is_auto : true + is_auto : true, + is_unique : true }, y : { title : 'Values for y-axis', diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 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 @@ -7,10 +7,11 @@ x : { title : 'Values for x-axis', is_label : true, - is_auto : true + is_auto : true, + is_unique : true }, y : { - title : 'Values for y-axis', + title : 'Values for y-axis', is_numeric : true } } diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 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 @@ -4,21 +4,22 @@ title : 'Horizontal', category : 'Bar diagrams', keywords : 'default small', + settings : { + x_axis_type : { + init : 'hide' + } + }, columns : { x : { title : 'Values for x-axis', is_label : true, - is_auto : true + is_auto : true, + is_unique : true }, y : { title : 'Values for y-axis', is_numeric : true } - }, - settings : { - x_axis_type : { - init : 'hide' - } } }); diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 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 @@ -10,8 +10,14 @@ } }, columns : { + x : { + title : 'Values for x-axis', + is_label : true, + is_auto : true, + is_unique : true + }, y : { - title : 'Values for y-axis', + title : 'Values for y-axis', is_numeric : true } } diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 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 @@ -5,8 +5,14 @@ category : 'Bar diagrams', keywords : 'default small', columns : { + x : { + title : 'Values for x-axis', + is_label : true, + is_auto : true, + is_unique : true + }, y : { - title : 'Values for y-axis', + title : 'Values for y-axis', is_numeric : true } } diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js @@ -39,15 +39,9 @@ var self = this; nv.addGraph(function() { try { - // x axis - self._axis(d3chart.xAxis, chart.settings.get('x_axis_type'), chart.settings.get('x_axis_tick')); - // x axis label d3chart.xAxis.axisLabel(chart.settings.get('x_axis_label')); - // y axis - self._axis(d3chart.yAxis, chart.settings.get('y_axis_type'), chart.settings.get('y_axis_tick')); - // y axis label d3chart.yAxis.axisLabel(chart.settings.get('y_axis_label')) .axisLabelDistance(30); @@ -60,14 +54,14 @@ d3chart.showLegend(chart.settings.get('show_legend') == 'true'); } + // make categories + self._makeAxes(d3chart, groups, chart.settings); + // custom callback if (makeConfig) { makeConfig(d3chart); } - // make categories - self._makeCategories(chart, groups, d3chart); - // hide min/max values d3chart.xAxis.showMaxMin(false); d3chart.yAxis.showMaxMin(chart.definition.showmaxmin); @@ -94,6 +88,11 @@ // add zoom handler _addZoom: function(nvd3_model, svg, zoom_mode) { + // clip edges + if (nvd3_model.clipEdge) { + nvd3_model.clipEdge(true); + } + // get canvas dimensions var width = parseInt(svg.style('width')); var height = parseInt(svg.style('height')); @@ -109,63 +108,97 @@ var y = d3.scale.linear() .domain(y_domain) .range([height, 0]); - + + // min/max boundaries + var x_boundary = nvd3_model.xScale().domain().slice(); + var y_boundary = nvd3_model.yScale().domain().slice(); + + // create d3 zoom handler + var d3zoom = d3.behavior.zoom(); + + // fix domain + function fixDomain(domain, boundary) { + domain[0] = Math.max(domain[0], boundary[0]); + domain[1] = Math.min(domain[1], boundary[1]); + return domain; + }; + // zoom event handler function zoomed() { if (zoom_mode == 'axis') { - nvd3_model.xDomain(x.domain()); - nvd3_model.yDomain(y.domain()); + nvd3_model.xDomain(fixDomain(x.domain(), x_boundary)); + nvd3_model.yDomain(fixDomain(y.domain(), y_boundary)); nvd3_model.update(); } else { var translate = d3.event.translate; svg.select('.nvd3').attr("transform", "translate(" + translate + ") scale(" + d3.event.scale + ")"); } - } + }; - // clip edges - if (nvd3_model.clipEdge) { - nvd3_model.clipEdge(true); - } - - // d3 zoom wrapper - var d3zoom = d3.behavior.zoom() - .x(x) - .y(y) - .scaleExtent([1, 10]) - .on("zoom", zoomed); + // zoom event handler + function unzoomed() { + if (zoom_mode == 'axis') { + nvd3_model.xDomain(x_boundary); + nvd3_model.yDomain(y_boundary); + nvd3_model.update(); + d3zoom.scale(1); + d3zoom.translate([0,0]); + } else { + var translate = d3.event.translate; + svg.select('.nvd3').attr("transform", "translate([0,0]) scale(1)"); + } + }; + + // initialize wrapper + d3zoom.x(x) + .y(y) + .scaleExtent([1, 10]) + .on("zoom", zoomed); // add handler - svg.call(d3zoom); + svg.call(d3zoom).on("dblclick.zoom", unzoomed); }, - // create categories - _makeCategories: function(chart, groups, d3chart) { + // create axes formatting + _makeAxes: function(d3chart, groups, settings) { // result - var result = Tools.makeCategories(chart, groups); + var categories = Tools.makeCategories(groups); - // add categories to flot configuration - for (var key in result.array) { - var axis = key + 'Axis'; - if (d3chart[axis]) { - var a = result.array[key]; - d3chart[axis].tickFormat(function(value) { - return a[value]; - }); + // make axis + function makeAxis (id) { + var axis = d3chart[id + 'Axis']; + var type = settings.get(id + '_axis_type'); + var tick = settings.get(id + '_axis_tick'); + var is_category = categories.array[id]; + + // hide axis + if (type == 'hide') { + axis.tickFormat(function() { return '' }); + return; } - } - }, + + // format values/labels + if (type == 'auto') { + if (is_category) { + axis.tickFormat(function(value) { + return categories.array[id][value] + }); + } + } else { + var formatter = d3.format(tick + type); + if (is_category) { + axis.tickFormat(function(value) { + return formatter(categories.array[id][value]); + }); + } else { + axis.tickFormat(formatter); + } + } + }; - // make axis - _axis: function(axis, type, tick) { - switch (type) { - case 'hide': - axis.tickFormat(function() { return '' }); - break; - case 'auto': - break; - default: - axis.tickFormat(d3.format(tick + type)); - } + // make axes + makeAxis('x'); + makeAxis('y'); }, // handle error diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js @@ -1,6 +1,5 @@ define(['plugin/charts/nvd3/common/config'], function(nvd3_config) { - return $.extend(true, {}, nvd3_config, { title : 'Histogram', category : 'Data processing (requires \'charts\' tool from Toolshed)', @@ -8,7 +7,7 @@ keywords : 'small medium large', columns : { y : { - title : 'Observations', + title : 'Observations', is_numeric : true } }, diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js @@ -2,8 +2,7 @@ define(['plugin/charts/nvd3/common/wrapper'], function(NVD3) { // widget -return Backbone.View.extend( -{ +return Backbone.View.extend({ // initialize initialize: function(app, options) { this.app = app; @@ -11,18 +10,18 @@ }, // render - draw : function(process_id, chart, request_dictionary) - { + draw : function(process_id, chart, request_dictionary){ // configure request var index = 1; for (var i in request_dictionary.groups) { var group = request_dictionary.groups[i]; group.columns = { x: { - index: 0 + index : 0, + is_numeric : true }, y: { - index: index++ + index : index++ } } } diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 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 @@ -8,10 +8,11 @@ x : { title : 'Values for x-axis', is_label : true, - is_auto : true + is_auto : true, + is_unique : true }, y : { - title : 'Values for y-axis', + title : 'Values for y-axis', is_numeric : true } } diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 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 @@ -8,7 +8,8 @@ x : { title : 'Values for x-axis', is_label : true, - is_auto : true + is_auto : true, + is_unique : true }, y : { title : 'Values for y-axis', diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 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 @@ -9,7 +9,8 @@ x : { title : 'Values for x-axis', is_label : true, - is_auto : true + is_auto : true, + is_unique : true }, y : { title : 'Values for y-axis', diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 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 @@ -6,6 +6,12 @@ category : 'Area charts', keywords : 'default small', columns : { + x : { + title : 'Values for x-axis', + is_label : true, + is_auto : true, + is_unique : true + }, y : { title : 'Values for y-axis', is_numeric : true diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 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 @@ -7,6 +7,12 @@ keywords : 'default small', showmaxmin : true, columns : { + x : { + title : 'Values for x-axis', + is_label : true, + is_auto : true, + is_unique : true + }, y : { title : 'Values for y-axis', is_numeric : true diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 config/plugins/visualizations/charts/static/charts/tools.js --- a/config/plugins/visualizations/charts/static/charts/tools.js +++ b/config/plugins/visualizations/charts/static/charts/tools.js @@ -81,15 +81,15 @@ return result; }; -// series maker -function makeSeries(groups, order) { +// default series maker +function makeSeries(groups, keys) { // plot data var plot_data = []; // loop through data groups - for (var key in groups) { + for (var group_index in groups) { // get group - var group = groups[key]; + var group = groups[group_index]; // reset data var data = []; @@ -98,9 +98,9 @@ for (var value_index in group.values) { // parse data var point = []; - if (order) { - for (var order_index in order) { - var column_index = order[order_index]; + if (keys) { + for (var key_index in keys) { + var column_index = keys[key_index]; point.push(group.values[value_index][column_index]); } } else { @@ -122,8 +122,50 @@ return plot_data; }; -// category maker -function makeCategories(chart, groups, with_index) { +// default category maker +function makeCategories(groups, with_index) { + // hashkeys, arrays and counter for labeled columns + var array = {}; + + // identify label columns + var chart_definition = groups[0]; + for (var key in chart_definition.columns) { + var column_def = chart_definition.columns[key]; + if (column_def.is_label) { + array[key] = []; + } + } + + // collect string labels in array + if (groups && groups[0]) { + var group = groups[0]; + for (var j in group.values) { + var value_dict = group.values[j]; + for (var key in array) { + array[key].push (String(value_dict[key])); + } + } + } + + // index all values contained in label columns (for all groups) + for (var i in groups) { + var group = groups[i]; + for (var j in group.values) { + var value_dict = group.values[j]; + for (var key in array) { + value_dict[key] = parseInt(j) + } + } + } + + // return dictionary + return { + array : array + } +}; + +// category make for unique category labels +function makeCategoriesUnique(groups, with_index) { // hashkeys, arrays and counter for labeled columns var categories = {}; var array = {}; diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 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 @@ -56,7 +56,7 @@ 'nvd3_histogram_discrete' : nvd3_histogram_discrete, 'jqplot_line' : jqplot_line, 'jqplot_scatter' : jqplot_scatter, - //'jqplot_boxplot' : jqplot_boxplot + 'jqplot_boxplot' : jqplot_boxplot } }); diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.css --- a/config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.css +++ b/config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.css @@ -1,1 +1,261 @@ -.jqplot-target{position:relative;color:#666;font-family:"Trebuchet MS",Arial,Helvetica,sans-serif;font-size:1em}.jqplot-axis{font-size:.75em}.jqplot-xaxis{margin-top:10px}.jqplot-x2axis{margin-bottom:10px}.jqplot-yaxis{margin-right:10px}.jqplot-y2axis,.jqplot-y3axis,.jqplot-y4axis,.jqplot-y5axis,.jqplot-y6axis,.jqplot-y7axis,.jqplot-y8axis,.jqplot-y9axis,.jqplot-yMidAxis{margin-left:10px;margin-right:10px}.jqplot-axis-tick,.jqplot-xaxis-tick,.jqplot-yaxis-tick,.jqplot-x2axis-tick,.jqplot-y2axis-tick,.jqplot-y3axis-tick,.jqplot-y4axis-tick,.jqplot-y5axis-tick,.jqplot-y6axis-tick,.jqplot-y7axis-tick,.jqplot-y8axis-tick,.jqplot-y9axis-tick,.jqplot-yMidAxis-tick{position:absolute;white-space:pre}.jqplot-xaxis-tick{top:0;left:15px;vertical-align:top}.jqplot-x2axis-tick{bottom:0;left:15px;vertical-align:bottom}.jqplot-yaxis-tick{right:0;top:15px;text-align:right}.jqplot-yaxis-tick.jqplot-breakTick{right:-20px;margin-right:0;padding:1px 5px 1px 5px;z-index:2;font-size:1.5em}.jqplot-y2axis-tick,.jqplot-y3axis-tick,.jqplot-y4axis-tick,.jqplot-y5axis-tick,.jqplot-y6axis-tick,.jqplot-y7axis-tick,.jqplot-y8axis-tick,.jqplot-y9axis-tick{left:0;top:15px;text-align:left}.jqplot-yMidAxis-tick{text-align:center;white-space:nowrap}.jqplot-xaxis-label{margin-top:10px;font-size:11pt;position:absolute}.jqplot-x2axis-label{margin-bottom:10px;font-size:11pt;position:absolute}.jqplot-yaxis-label{margin-right:10px;font-size:11pt;position:absolute}.jqplot-yMidAxis-label{font-size:11pt;position:absolute}.jqplot-y2axis-label,.jqplot-y3axis-label,.jqplot-y4axis-label,.jqplot-y5axis-label,.jqplot-y6axis-label,.jqplot-y7axis-label,.jqplot-y8axis-label,.jqplot-y9axis-label{font-size:11pt;margin-left:10px;position:absolute}.jqplot-meterGauge-tick{font-size:.75em;color:#999}.jqplot-meterGauge-label{font-size:1em;color:#999}table.jqplot-table-legend{margin-top:12px;margin-bottom:12px;margin-left:12px;margin-right:12px}table.jqplot-table-legend,table.jqplot-cursor-legend{background-color:rgba(255,255,255,0.6);border:1px solid #ccc;position:absolute;font-size:.75em}td.jqplot-table-legend{vertical-align:middle}td.jqplot-seriesToggle:hover,td.jqplot-seriesToggle:active{cursor:pointer}.jqplot-table-legend .jqplot-series-hidden{text-decoration:line-through}div.jqplot-table-legend-swatch-outline{border:1px solid #ccc;padding:1px}div.jqplot-table-legend-swatch{width:0;height:0;border-top-width:5px;border-bottom-width:5px;border-left-width:6px;border-right-width:6px;border-top-style:solid;border-bottom-style:solid;border-left-style:solid;border-right-style:solid}.jqplot-title{top:0;left:0;padding-bottom:.5em;font-size:1.2em}table.jqplot-cursor-tooltip{border:1px solid #ccc;font-size:.75em}.jqplot-cursor-tooltip{border:1px solid #ccc;font-size:.75em;white-space:nowrap;background:rgba(208,208,208,0.5);padding:1px}.jqplot-highlighter-tooltip,.jqplot-canvasOverlay-tooltip{border:1px solid #ccc;font-size:.75em;white-space:nowrap;background:rgba(208,208,208,0.5);padding:1px}.jqplot-point-label{font-size:.75em;z-index:2}td.jqplot-cursor-legend-swatch{vertical-align:middle;text-align:center}div.jqplot-cursor-legend-swatch{width:1.2em;height:.7em}.jqplot-error{text-align:center}.jqplot-error-message{position:relative;top:46%;display:inline-block}div.jqplot-bubble-label{font-size:.8em;padding-left:2px;padding-right:2px;color:rgb(20%,20%,20%)}div.jqplot-bubble-label.jqplot-bubble-label-highlight{background:rgba(90%,90%,90%,0.7)}div.jqplot-noData-container{text-align:center;background-color:rgba(96%,96%,96%,0.3)} \ No newline at end of file +/*rules for the plot target div. These will be cascaded down to all plot elements according to css rules*/ +.jqplot-target { + position: relative; + color: #666666; + font-family: "Trebuchet MS", Arial, Helvetica, sans-serif; + font-size: 1em; +/* height: 300px; + width: 400px;*/ +} + +/*rules applied to all axes*/ +.jqplot-axis { + font-size: 0.75em; +} + +.jqplot-xaxis { + margin-top: 10px; +} + +.jqplot-x2axis { + margin-bottom: 10px; +} + +.jqplot-yaxis { + margin-right: 10px; +} + +.jqplot-y2axis, .jqplot-y3axis, .jqplot-y4axis, .jqplot-y5axis, .jqplot-y6axis, .jqplot-y7axis, .jqplot-y8axis, .jqplot-y9axis, .jqplot-yMidAxis { + margin-left: 10px; + margin-right: 10px; +} + +/*rules applied to all axis tick divs*/ +.jqplot-axis-tick, .jqplot-xaxis-tick, .jqplot-yaxis-tick, .jqplot-x2axis-tick, .jqplot-y2axis-tick, .jqplot-y3axis-tick, .jqplot-y4axis-tick, .jqplot-y5axis-tick, .jqplot-y6axis-tick, .jqplot-y7axis-tick, .jqplot-y8axis-tick, .jqplot-y9axis-tick, .jqplot-yMidAxis-tick { + position: absolute; + white-space: pre; +} + + +.jqplot-xaxis-tick { + top: 0px; + /* initial position untill tick is drawn in proper place */ + left: 15px; +/* padding-top: 10px;*/ + vertical-align: top; +} + +.jqplot-x2axis-tick { + bottom: 0px; + /* initial position untill tick is drawn in proper place */ + left: 15px; +/* padding-bottom: 10px;*/ + vertical-align: bottom; +} + +.jqplot-yaxis-tick { + right: 0px; + /* initial position untill tick is drawn in proper place */ + top: 15px; +/* padding-right: 10px;*/ + text-align: right; +} + +.jqplot-yaxis-tick.jqplot-breakTick { + right: -20px; + margin-right: 0px; + padding:1px 5px 1px 5px; +/* background-color: white;*/ + z-index: 2; + font-size: 1.5em; +} + +.jqplot-y2axis-tick, .jqplot-y3axis-tick, .jqplot-y4axis-tick, .jqplot-y5axis-tick, .jqplot-y6axis-tick, .jqplot-y7axis-tick, .jqplot-y8axis-tick, .jqplot-y9axis-tick { + left: 0px; + /* initial position untill tick is drawn in proper place */ + top: 15px; +/* padding-left: 10px;*/ +/* padding-right: 15px;*/ + text-align: left; +} + +.jqplot-yMidAxis-tick { + text-align: center; + white-space: nowrap; +} + +.jqplot-xaxis-label { + margin-top: 10px; + font-size: 11pt; + position: absolute; +} + +.jqplot-x2axis-label { + margin-bottom: 10px; + font-size: 11pt; + position: absolute; +} + +.jqplot-yaxis-label { + margin-right: 10px; +/* text-align: center;*/ + font-size: 11pt; + position: absolute; +} + +.jqplot-yMidAxis-label { + font-size: 11pt; + position: absolute; +} + +.jqplot-y2axis-label, .jqplot-y3axis-label, .jqplot-y4axis-label, .jqplot-y5axis-label, .jqplot-y6axis-label, .jqplot-y7axis-label, .jqplot-y8axis-label, .jqplot-y9axis-label { +/* text-align: center;*/ + font-size: 11pt; + margin-left: 10px; + position: absolute; +} + +.jqplot-meterGauge-tick { + font-size: 0.75em; + color: #999999; +} + +.jqplot-meterGauge-label { + font-size: 1em; + color: #999999; +} + +table.jqplot-table-legend { + margin-top: 12px; + margin-bottom: 12px; + margin-left: 12px; + margin-right: 12px; +} + +table.jqplot-table-legend, table.jqplot-cursor-legend { + background-color: rgba(255,255,255,0.6); + border: 1px solid #cccccc; + position: absolute; + font-size: 0.75em; +} + +td.jqplot-table-legend { + vertical-align:middle; +} + +/* +These rules could be used instead of assigning +element styles and relying on js object properties. +*/ + +/* +td.jqplot-table-legend-swatch { + padding-top: 0.5em; + text-align: center; +} + +tr.jqplot-table-legend:first td.jqplot-table-legend-swatch { + padding-top: 0px; +} +*/ + +td.jqplot-seriesToggle:hover, td.jqplot-seriesToggle:active { + cursor: pointer; +} + +.jqplot-table-legend .jqplot-series-hidden { + text-decoration: line-through; +} + +div.jqplot-table-legend-swatch-outline { + border: 1px solid #cccccc; + padding:1px; +} + +div.jqplot-table-legend-swatch { + width:0px; + height:0px; + border-top-width: 5px; + border-bottom-width: 5px; + border-left-width: 6px; + border-right-width: 6px; + border-top-style: solid; + border-bottom-style: solid; + border-left-style: solid; + border-right-style: solid; +} + +.jqplot-title { + top: 0px; + left: 0px; + padding-bottom: 0.5em; + font-size: 1.2em; +} + +table.jqplot-cursor-tooltip { + border: 1px solid #cccccc; + font-size: 0.75em; +} + + +.jqplot-cursor-tooltip { + border: 1px solid #cccccc; + font-size: 0.75em; + white-space: nowrap; + background: rgba(208,208,208,0.5); + padding: 1px; +} + +.jqplot-highlighter-tooltip, .jqplot-canvasOverlay-tooltip { + border: 1px solid #cccccc; + font-size: 1.2em; + font-weight: bold; + white-space: nowrap; + background: rgba(235,235,235,1); + padding: 1px; + border-radius: 5px; +} + +.jqplot-point-label { + font-size: 0.75em; + z-index: 2; +} + +td.jqplot-cursor-legend-swatch { + vertical-align: middle; + text-align: center; +} + +div.jqplot-cursor-legend-swatch { + width: 1.2em; + height: 0.7em; +} + +.jqplot-error { +/* Styles added to the plot target container when there is an error go here.*/ + text-align: center; +} + +.jqplot-error-message { +/* Styling of the custom error message div goes here.*/ + position: relative; + top: 46%; + display: inline-block; +} + +div.jqplot-bubble-label { + font-size: 0.8em; +/* background: rgba(90%, 90%, 90%, 0.15);*/ + padding-left: 2px; + padding-right: 2px; + color: rgb(20%, 20%, 20%); +} + +div.jqplot-bubble-label.jqplot-bubble-label-highlight { + background: rgba(90%, 90%, 90%, 0.7); +} + +div.jqplot-noData-container { + text-align: center; + background-color: rgba(96%, 96%, 96%, 0.3); +} diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 config/plugins/visualizations/charts/static/views/editor.js --- a/config/plugins/visualizations/charts/static/views/editor.js +++ b/config/plugins/visualizations/charts/static/views/editor.js @@ -266,7 +266,7 @@ _resetChart: function() { // reset chart details this.chart.set('id', Utils.uuid()); - this.chart.set('type', 'highcharts_bar'); + this.chart.set('type', 'nvd3_bar'); this.chart.set('dataset_id', this.app.options.config.dataset_id); this.chart.set('title', 'New Chart'); diff -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 -r 66cfcaf35801b8c80491743807ca4d491bfb42e6 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 @@ -134,6 +134,7 @@ var is_label = column_definition.is_label; var is_auto = column_definition.is_auto; var is_numeric = column_definition.is_numeric; + var is_unique = column_definition.is_unique; // configure columns var columns = []; @@ -184,11 +185,31 @@ // update model value this.group.set(id, first); } - select.value(this.group.get(id)); + + // set initial value + if (is_unique) { + select.value(this.chart.groups.first().get(id)); + } else { + select.value(this.group.get(id)); + } + + // link group with select field + this.group.on('change:' + id, function(){ + select.value(self.group.get(id)); + }); // link select field with group select.setOnChange(function(value) { - self.group.set(id, value); + // update model value + if (is_unique) { + // update all groups + self.chart.groups.each(function(group) { + group.set(id, value); + }); + } else { + // only change this group + self.group.set(id, value); + } self.chart.set('modified', true); }); 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: dannon: Set tabular CHUNK_SIZE to ~10kb
by commits-noreply＠bitbucket.org 10 Jun '14

10 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c52cb1f827d4/ Changeset: c52cb1f827d4 User: dannon Date: 2014-06-11 01:24:00 Summary: Set tabular CHUNK_SIZE to ~10kb Affected #: 1 file diff -r e2b761a9b1d6d41db71b28df8b62862c7c300eba -r c52cb1f827d49f0f0ee2c1c97d3626dd1b2cc348 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -25,7 +25,7 @@ # All tabular data is chunkable. CHUNKABLE = True - CHUNK_SIZE = 1000 + CHUNK_SIZE = 10000 """Add metadata elements""" MetadataElement( name="comment_lines", default=0, desc="Number of comment lines", readonly=False, optional=True, no_value=0 ) 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: 4 new changesets
by commits-noreply＠bitbucket.org 10 Jun '14

10 Jun '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f4238cf96afd/ Changeset: f4238cf96afd User: dannon Date: 2014-06-10 22:38:51 Summary: Prevent rendering of sometimes sometimes empty lines in tabular display. Affected #: 1 file diff -r 9a905e98e1550314cf821a99c2adc1b00a4eed83 -r f4238cf96afdc8bf649a660d91b10ecf3f785ef6 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -253,7 +253,9 @@ _renderChunk: function(chunk) { var data_table = this.$el.find('table'); _.each(chunk.ck_data.split('\n'), function(line, index) { - data_table.append(this._renderRow(line)); + if (line !== ''){ + data_table.append(this._renderRow(line)); + } }, this); } }); https://bitbucket.org/galaxy/galaxy-central/commits/2e532a275285/ Changeset: 2e532a275285 User: dannon Date: 2014-06-10 22:39:39 Summary: Pack scripts Affected #: 1 file diff -r f4238cf96afdc8bf649a660d91b10ecf3f785ef6 -r 2e532a2752859580c96b47f5fe0b86550846ec95 static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},render:function(){var s=$("<div/>").attr("id","loading_indicator");this.$el.append(s);var q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var o=this,n=this.model.get("first_data_chunk");if(n){this._renderChunk(n)}else{$.when(o.model.get_next_chunk()).then(function(t){o._renderChunk(t)})}var p=false;this.scroll_elt.scroll(function(){if(!p&&o.scrolled_to_bottom()){p=true;s.show();$.when(o.model.get_next_chunk()).then(function(t){if(t){o._renderChunk(t);p=false}s.hide()})}})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){if(!o.model){o.model=new h(o.dataset_config)}var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el)}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file +define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},render:function(){var s=$("<div/>").attr("id","loading_indicator");this.$el.append(s);var q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var o=this,n=this.model.get("first_data_chunk");if(n){this._renderChunk(n)}else{$.when(o.model.get_next_chunk()).then(function(t){o._renderChunk(t)})}var p=false;this.scroll_elt.scroll(function(){if(!p&&o.scrolled_to_bottom()){p=true;s.show();$.when(o.model.get_next_chunk()).then(function(t){if(t){o._renderChunk(t);p=false}s.hide()})}})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){if(o!==""){n.append(this._renderRow(o))}},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){if(!o.model){o.model=new h(o.dataset_config)}var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el)}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/a8c5c0241015/ Changeset: a8c5c0241015 User: dannon Date: 2014-06-10 22:41:26 Summary: Tabular view -- automatically populate full height page. This handles situations like reported by pjacock where the scroll bars never appear for particularly 'wide' datasets. Affected #: 1 file diff -r 2e532a2752859580c96b47f5fe0b86550846ec95 -r a8c5c02410159295c94b602d44cae2d4549ec7c9 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -122,6 +122,7 @@ initialize: function(options) { // Row count for rendering. this.row_count = 0; + this.loading_chunk = false; // CSS colors used in table. this.header_color = '#AAA'; @@ -134,10 +135,32 @@ }); }, + expand_to_container: function(){ + if (this.$el.height() < this.scroll_elt.height()){ + this.attempt_to_fetch(); + } + }, + + attempt_to_fetch: function( func ){ + var self = this; + if ( !this.loading_chunk && this.scrolled_to_bottom() ) { + this.loading_chunk = true; + this.loading_indicator.show(); + $.when(self.model.get_next_chunk()).then(function(result) { + if (result) { + self._renderChunk(result); + self.loading_chunk = false; + } + self.loading_indicator.hide(); + self.expand_to_container(); + }); + } + }, + render: function() { // Add loading indicator. - var loading_indicator = $('<div/>').attr('id', 'loading_indicator'); - this.$el.append(loading_indicator); + this.loading_indicator = $('<div/>').attr('id', 'loading_indicator'); + this.$el.append(this.loading_indicator); // Add data table and header. var data_table = $('<table/>').attr({ @@ -167,23 +190,9 @@ // -- Show new chunks during scrolling. -- - // Flag to ensure that only one chunk is loaded at a time. - var loading_chunk = false; - // Set up chunk loading when scrolling using the scrolling element. - this.scroll_elt.scroll(function() { - // If not already loading a chunk and have scrolled to the bottom of this element, get next chunk. - if ( !loading_chunk && self.scrolled_to_bottom() ) { - loading_chunk = true; - loading_indicator.show(); - $.when(self.model.get_next_chunk()).then(function(result) { - if (result) { - self._renderChunk(result); - loading_chunk = false; - } - loading_indicator.hide(); - }); - } + this.scroll_elt.scroll(function(){ + self.attempt_to_fetch(); }); }, @@ -641,6 +650,10 @@ if (parent_elt) { parent_elt.append(view.$el); + // If we're sticking this in another element, once it's appended check + // to make sure we've filled enough space. + // Without this, the scroll elements don't work. + view.expand_to_container(); } return view; https://bitbucket.org/galaxy/galaxy-central/commits/e2b761a9b1d6/ Changeset: e2b761a9b1d6 User: dannon Date: 2014-06-10 22:41:53 Summary: Pack scripts. Affected #: 2 files diff -r a8c5c02410159295c94b602d44cae2d4549ec7c9 -r e2b761a9b1d6d41db71b28df8b62862c7c300eba lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -25,7 +25,7 @@ # All tabular data is chunkable. CHUNKABLE = True - CHUNK_SIZE = 50000 + CHUNK_SIZE = 1000 """Add metadata elements""" MetadataElement( name="comment_lines", default=0, desc="Number of comment lines", readonly=False, optional=True, no_value=0 ) diff -r a8c5c02410159295c94b602d44cae2d4549ec7c9 -r e2b761a9b1d6d41db71b28df8b62862c7c300eba static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},render:function(){var s=$("<div/>").attr("id","loading_indicator");this.$el.append(s);var q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var o=this,n=this.model.get("first_data_chunk");if(n){this._renderChunk(n)}else{$.when(o.model.get_next_chunk()).then(function(t){o._renderChunk(t)})}var p=false;this.scroll_elt.scroll(function(){if(!p&&o.scrolled_to_bottom()){p=true;s.show();$.when(o.model.get_next_chunk()).then(function(t){if(t){o._renderChunk(t);p=false}s.hide()})}})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){if(o!==""){n.append(this._renderRow(o))}},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){if(!o.model){o.model=new h(o.dataset_config)}var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el)}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file +define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.loading_chunk=false;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},expand_to_container:function(){if(this.$el.height()<this.scroll_elt.height()){this.attempt_to_fetch()}},attempt_to_fetch:function(n){var m=this;if(!this.loading_chunk&&this.scrolled_to_bottom()){this.loading_chunk=true;this.loading_indicator.show();$.when(m.model.get_next_chunk()).then(function(o){if(o){m._renderChunk(o);m.loading_chunk=false}m.loading_indicator.hide();m.expand_to_container()})}},render:function(){this.loading_indicator=$("<div/>").attr("id","loading_indicator");this.$el.append(this.loading_indicator);var p=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(p);var m=this.model.get_metadata("column_names"),q=$("<tr/>").css("background-color",this.header_color).appendTo(p);if(m){q.append("<th>"+m.join("</th><th>")+"</th>")}var o=this,n=this.model.get("first_data_chunk");if(n){this._renderChunk(n)}else{$.when(o.model.get_next_chunk()).then(function(r){o._renderChunk(r)})}this.scroll_elt.scroll(function(){o.attempt_to_fetch()})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){if(o!==""){n.append(this._renderRow(o))}},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){if(!o.model){o.model=new h(o.dataset_config)}var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el);m.expand_to_container()}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file 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 10 Jun '14

10 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9304293c4eb1/ Changeset: 9304293c4eb1 User: jmchilton Date: 2014-06-10 22:01:38 Summary: Add utility for debugging sqlalchemy queries in db_shell.py. Should aid in interactively building up queries. Affected #: 1 file diff -r 24c5a89db2634fcd5339205164f64e3d7a396003 -r 9304293c4eb1af6b0682dc479923adea5180145f scripts/db_shell.py --- a/scripts/db_shell.py +++ b/scripts/db_shell.py @@ -36,3 +36,72 @@ from galaxy.model.mapping import init sa_session = init( '/tmp/', db_url ).context from galaxy.model import * + +# Helper function for debugging sqlalchemy queries... +# http://stackoverflow.com/questions/5631078/sqlalchemy-print-the-actual-query +import decimal +import datetime + + +def printquery(statement, bind=None): + """ + print a query, with values filled in + for debugging purposes *only* + for security, you should always separate queries from their values + please also note that this function is quite slow + """ + import sqlalchemy.orm + if isinstance(statement, sqlalchemy.orm.Query): + if bind is None: + bind = statement.session.get_bind( + statement._mapper_zero_or_none() + ) + statement = statement.statement + elif bind is None: + bind = statement.bind + + dialect = bind.dialect + compiler = statement._compiler(dialect) + + class LiteralCompiler(compiler.__class__): + def visit_bindparam( + self, bindparam, within_columns_clause=False, + literal_binds=False, **kwargs + ): + return super(LiteralCompiler, self).render_literal_bindparam( + bindparam, + within_columns_clause=within_columns_clause, + literal_binds=literal_binds, + **kwargs + ) + + def render_literal_value(self, value, type_): + """Render the value of a bind parameter as a quoted literal. + + This is used for statement sections that do not accept bind paramters + on the target driver/database. + + This should be implemented by subclasses using the quoting services + of the DBAPI. + + """ + if isinstance(value, basestring): + value = value.replace("'", "''") + return "'%s'" % value + elif value is None: + return "NULL" + elif isinstance(value, (float, int, long)): + return repr(value) + elif isinstance(value, decimal.Decimal): + return str(value) + elif isinstance(value, datetime.datetime): + return "TO_DATE('%s','YYYY-MM-DD HH24:MI:SS')" % value.strftime("%Y-%m-%d %H:%M:%S") + + else: + raise NotImplementedError( + "Don't know how to literal-quote value %r" % value + ) + + compiler = LiteralCompiler(dialect, statement) + print compiler.process(statement) + https://bitbucket.org/galaxy/galaxy-central/commits/9a905e98e155/ Changeset: 9a905e98e155 User: jmchilton Date: 2014-06-10 22:01:38 Summary: Allow injection of high-level helper utility into dynamic destination rules. Helper currently has methods methods for determining users recent usage - job count and sum of job runtime - filterable by user_email, job creation and update time, destination id, job states (only 'ok' job state would make sense for runtime - only way Galaxy has that data). Goal here is to allow dynamic destination to assign higher priorities to users who have not used Galaxy recently. Example usage here : https://gist.github.com/jmchilton/a1b4f0bd3ce7189c0caf. Affected #: 2 files diff -r 9304293c4eb1af6b0682dc479923adea5180145f -r 9a905e98e1550314cf821a99c2adc1b00a4eed83 lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -5,6 +5,7 @@ log = logging.getLogger( __name__ ) import galaxy.jobs.rules +from .rule_helper import RuleHelper DYNAMIC_RUNNER_NAME = "dynamic" DYNAMIC_DESTINATION_ID = "dynamic_legacy_from_url" @@ -56,12 +57,13 @@ def __invoke_expand_function( self, expand_function ): function_arg_names = inspect.getargspec( expand_function ).args - + app = self.job_wrapper.app possible_args = { "job_id" : self.job_wrapper.job_id, "tool" : self.job_wrapper.tool, "tool_id" : self.job_wrapper.tool.id, "job_wrapper" : self.job_wrapper, - "app" : self.job_wrapper.app } + "rule_helper": RuleHelper( app ), + "app" : app } actual_args = {} diff -r 9304293c4eb1af6b0682dc479923adea5180145f -r 9a905e98e1550314cf821a99c2adc1b00a4eed83 lib/galaxy/jobs/rule_helper.py --- /dev/null +++ b/lib/galaxy/jobs/rule_helper.py @@ -0,0 +1,87 @@ +from datetime import datetime + +from sqlalchemy import ( + and_, + func +) + +from galaxy import model + +import logging +log = logging.getLogger( __name__ ) + + +class RuleHelper( object ): + """ Utillity to allow job rules to interface cleanly with the rest of + Galaxy and shield them from low-level details of models, metrics, etc.... + + Currently focus is on figuring out job statistics for a given user, but + could interface with other stuff as well. + """ + + def __init__( self, app ): + self.app = app + + def job_count( + self, + **kwds + ): + query = self.query( model.Job ) + return self._filter_job_query( query, **kwds ).count() + + def sum_job_runtime( + self, + **kwds + ): + # TODO: Consider sum_core_hours or something that scales runtime by + # by calculated cores per job. + query = self.metric_query( + select=func.sum( model.JobMetricNumeric.table.c.metric_value ), + metric_name="runtime_seconds", + plugin="core", + ) + query = query.join( model.Job ) + return float( self._filter_job_query( query, **kwds ).first()[ 0 ] ) + + def metric_query( self, select, metric_name, plugin, numeric=True ): + metric_class = model.JobMetricNumeric if numeric else model.JobMetricText + query = self.query( select ) + query = query.filter( metric_class.table.c.plugin == plugin ) + query = query.filter( metric_class.table.c.metric_name == metric_name ) + return query + + def query( self, select_expression ): + return self.app.model.context.query( select_expression ) + + def _filter_job_query( + self, + query, + for_user_email=None, + for_destination=None, + for_job_states=None, + created_in_last=None, + updated_in_last=None, + ): + query = query.join( model.User ) + if for_user_email is not None: + query = query.filter( model.User.table.c.email == for_user_email ) + + if for_destination is not None: + query = query.filter( model.Job.table.c.destination_id == for_destination ) + + if created_in_last is not None: + end_date = datetime.now() + start_date = end_date - created_in_last + query = query.filter( model.Job.table.c.create_time >= start_date ) + + if updated_in_last is not None: + end_date = datetime.now() + start_date = end_date - updated_in_last + log.info( end_date ) + log.info( start_date ) + query = query.filter( model.Job.table.c.update_time >= start_date ) + + if for_job_states is not None: + query = query.filter( model.Job.table.c.state.in_( for_job_states ) ) + + return query Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: davebgx: Additional fixes for urllib2's 3xx redirects not handling POST requests. This changeset handles httpd proxies that redirect to a secure port before delivering the request to Paste.
by commits-noreply＠bitbucket.org 10 Jun '14

10 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/24c5a89db263/ Changeset: 24c5a89db263 User: davebgx Date: 2014-06-10 17:11:32 Summary: Additional fixes for urllib2's 3xx redirects not handling POST requests. This changeset handles httpd proxies that redirect to a secure port before delivering the request to Paste. Affected #: 1 file diff -r 47e32138de3d0a9debf25cb6b59c967b647af84e -r 24c5a89db2634fcd5339205164f64e3d7a396003 lib/tool_shed/scripts/api/common.py --- a/lib/tool_shed/scripts/api/common.py +++ b/lib/tool_shed/scripts/api/common.py @@ -11,13 +11,25 @@ from tool_shed.util import common_util from tool_shed.util import hg_util + +class HTTPRedirectWithDataHandler( urllib2.HTTPRedirectHandler ): + + def redirect_request( self, request, fp, code, msg, headers, newurl ): + request_method = request.get_method() + if ( code in ( 301, 302, 303, 307 ) and request_method in ( "GET", "HEAD", "POST", "PUT", "DELETE" ) ): + newurl = newurl.replace( ' ', '%20' ) + return urllib2.Request( newurl, + data=request.data, + headers=request.headers, + origin_req_host=request.get_origin_req_host(), + unverifiable=True ) + else: + urllib2.HTTPRedirectHandler.redirect_request( request, fp, code, msg, headers, newurl ) + def build_request_with_data( url, data, api_key, method ): """Build a request with the received method.""" - protocol = common_util.get_protocol_from_tool_shed_url( url ) - if protocol == 'http': - opener = urllib2.build_opener( urllib2.HTTPHandler ) - elif protocol == 'https': - opener = urllib2.build_opener( urllib2.HTTPSHandler ) + opener = urllib2.build_opener( HTTPRedirectWithDataHandler ) + urllib2.install_opener( opener ) url = make_url( url, api_key=api_key, args=None ) request = urllib2.Request( url, headers={ 'Content-Type': 'application/json' }, data=json.dumps( data ) ) request_method = request.get_method() 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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