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

commit/galaxy-central: jmchilton: Fix working directory used for remote metadata command generation.
by commits-noreply＠bitbucket.org 05 Jun '14

05 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3ecffd889d5c/ Changeset: 3ecffd889d5c User: jmchilton Date: 2014-06-05 18:54:58 Summary: Fix working directory used for remote metadata command generation. In short - should fix bam outputs for LWR jobs when setting metadata on remote resource. Thanks to @natefoo for tracking down problem. Affected #: 1 file diff -r dd6fa0b34036d227900c4b92b514ee86aaca60a5 -r 3ecffd889d5c97478630cd127c8ac4681ec49872 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -722,7 +722,7 @@ sa_session.flush() metadata_files_list.append( metadata_files ) #return command required to build - return "%s %s %s %s %s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, tmp_dir, config_root, config_file, datatypes_config, job_metadata, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) ) + return "%s %s %s %s %s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, compute_tmp_dir or tmp_dir, config_root, config_file, datatypes_config, job_metadata, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) ) def external_metadata_set_successfully( self, dataset, sa_session ): metadata_files = self.get_output_filenames_by_dataset( dataset, sa_session ) 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 05 Jun '14

05 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b62f649f1955/ Changeset: b62f649f1955 Branch: stable User: natefoo Date: 2014-06-05 16:13:29 Summary: Updated tag latest_2014.06.02 for changeset fb68af9a775a Affected #: 1 file diff -r fb68af9a775a956fcc397b22d16f2119401d926d -r b62f649f1955f64deb94c7e20093e31f5f411867 .hgtags --- a/.hgtags +++ b/.hgtags @@ -10,3 +10,4 @@ 68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 7e257c7b10badb65772b1528cb61d58175a42e47 latest_2014.06.02 +fb68af9a775a956fcc397b22d16f2119401d926d latest_2014.06.02 https://bitbucket.org/galaxy/galaxy-central/commits/dd6fa0b34036/ Changeset: dd6fa0b34036 User: natefoo Date: 2014-06-05 16:14:36 Summary: Merge stable Affected #: 1 file diff -r 5cd596d49a53974c48c64199d841e8cded05f43e -r dd6fa0b34036d227900c4b92b514ee86aaca60a5 .hgtags --- a/.hgtags +++ b/.hgtags @@ -10,3 +10,4 @@ 68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 7e257c7b10badb65772b1528cb61d58175a42e47 latest_2014.06.02 +fb68af9a775a956fcc397b22d16f2119401d926d 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: natefoo: Upgrade kombu/amqp to fix ssl disconnect on consumer timeout bug: https://github.com/celery/py-amqp/pull/38
by commits-noreply＠bitbucket.org 05 Jun '14

05 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5cd596d49a53/ Changeset: 5cd596d49a53 User: natefoo Date: 2014-06-05 16:07:39 Summary: Upgrade kombu/amqp to fix ssl disconnect on consumer timeout bug: https://github.com/celery/py-amqp/pull/38 Affected #: 1 file diff -r cab2ae91c6a96e133748900e1c203ce864f52052 -r 5cd596d49a53974c48c64199d841e8cded05f43e eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -32,7 +32,7 @@ ; msgpack_python = 0.2.4 [eggs:noplatform] -amqp = 1.4.3 +amqp = 1.4.5 anyjson = 0.3.3 Beaker = 1.4 bioblend = 0.4.2 @@ -44,7 +44,7 @@ Fabric = 1.7.0 GeneTrack = 2.0.0_beta_1 importlib = 1.0.3 -kombu = 3.0.12 +kombu = 3.0.13 lrucache = 0.2 Mako = 0.4.1 mock = 1.0.1 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 zoomable heatmaps, add chart type definition to charts model
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cab2ae91c6a9/ Changeset: cab2ae91c6a9 User: guerler Date: 2014-06-05 00:57:27 Summary: Charts: Add zoomable heatmaps, add chart type definition to charts model Affected #: 19 files diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal_stacked/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal_stacked/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/bar_horizontal_stacked/wrapper.js @@ -15,7 +15,6 @@ { // finalize configuration chart.settings.set('plotoptions_series_stacking', 'normal'); - chart.settings.set('x_axis_categories', []) // draw chart var hc = new Highcharts(this.app, this.options); diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/highcharts/bar_stacked/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/bar_stacked/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/bar_stacked/wrapper.js @@ -15,7 +15,6 @@ { // finalize configuration chart.settings.set('plotoptions_series_stacking', 'normal'); - chart.settings.set('x_axis_categories', []) // draw chart var hc = new Highcharts(this.app, this.options); diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/highcharts/boxplot/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/boxplot/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/boxplot/wrapper.js @@ -11,7 +11,7 @@ }, // render - draw : function(process_id, chart, request_dictionary) + draw : function(process_id, chart, request_dictionary, callback) { // configure request var index = 0; @@ -29,7 +29,7 @@ chart.settings.set('legend_enabled', 'false') // create configuration - this.hc_config = configmaker(chart, chart.settings); + this.hc_config = configmaker(chart, callback); // request data var self = this; diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/common/highcharts-config.js @@ -1,10 +1,14 @@ // dependencies define([], function() { -// widget -return function(chart, settings) { - // highcharts configuration - return { +// highcharts configuration +return function(chart) { + + // get chart settings + var settings = chart.settings; + + // initialize config object + var hc_config = { chart: { type : '', zoomType : 'xy' @@ -23,7 +27,6 @@ }, xAxis: { - categories : settings.get('x_axis_categories'), title: { text : settings.get('x_axis_label') }, @@ -60,7 +63,6 @@ enabled : !(settings.get('y_axis_type') == 'hide') } }, - plotOptions: { series: { animation : false, @@ -89,44 +91,10 @@ }, series: [] - }/*, + } - // highcharts stacking - hc_stacklabels: { - enabled: true, - style: { - fontWeight: 'bold', - color: (Highcharts.theme && Highcharts.theme.textColor) || 'gray' - } - }, - - // initialize - initialize: function(settings) { - // stacking - if (settings.get('x_stacked')) { - this.hc_config.xAxis.stackLabels = this.hc_stacklabels; - this.hc_config.plotOptions.column = { - stacking : 'normal', - dataLabels : { - enabled : true, - color: (Highcharts.theme && Highcharts.theme.dataLabelsColor) || 'white', - style: { - textShadow: '0 0 3px black, 0 0 3px black' - } - } - } - } - - // stacking - if (settings.get('y_stacked')) { - this.hc_config.yAxis.stackLabels = this.hc_stacklabels; - this.hc_config.plotOptions.column = { - stacking : 'normal' - } - } - - console.log(this.hc_config); - }*/ + // callback + return hc_config; }; }); \ No newline at end of file diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/highcharts/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/common/wrapper.js @@ -22,15 +22,13 @@ // render draw : function(process_id, hc_type, chart, request_dictionary, callback) { - // create configuration - this.hc_config = configmaker(chart, chart.settings); - // request data var self = this; this.app.datasets.request(request_dictionary, function() { + // check if this chart has multiple panels if (self.options.canvas.length == 1) { // groups - if (self._drawGroups(hc_type, chart, request_dictionary.groups, self.options.canvas[0])) { + if (self._drawGroups(hc_type, chart, request_dictionary.groups, self.options.canvas[0], callback)) { // set chart state chart.state('ok', 'Chart drawn.'); } @@ -40,9 +38,9 @@ for (var group_index in request_dictionary.groups) { // get group var group = request_dictionary.groups[group_index]; - + // draw group - if (!self._drawGroups(hc_type, chart, [group], self.options.canvas[group_index])) { + if (!self._drawGroups(hc_type, chart, [group], self.options.canvas[group_index], callback)) { valid = false; break; } @@ -60,9 +58,17 @@ }, // draw all data into a single canvas - _drawGroups: function(hc_type, chart, groups, canvas) { + _drawGroups: function(hc_type, chart, groups, canvas, callback) { + // create configuration + var hc_config = configmaker(chart); + + // make custom wrapper callback + if (callback) { + callback(hc_config); + } + // reset - this.hc_config.series = []; + hc_config.series = []; // loop through data groups for (var key in groups) { @@ -92,12 +98,12 @@ }; // append series - this.hc_config.series.push(hc_series); + hc_config.series.push(hc_series); } // draw plot try { - canvas.highcharts(this.hc_config); + canvas.highcharts(hc_config); return true; } catch (err) { var regex = /\www\.highcharts\.com([^&]+)/; diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/highcharts/heatmap/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/heatmap/config.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/heatmap/config.js @@ -3,18 +3,21 @@ return $.extend(true, {}, config, { title : 'Heatmap', category : 'Data processing (requires \'charts\' tool from Toolshed)', - execute : 'heatmap', + //execute : 'heatmap', use_panels : true, + keywords : 'default highcharts', columns: { - row_label: { + y: { title : 'Row labels', - is_label : true + is_label : true, + is_numeric : true }, - col_label: { + x: { title : 'Column labels', - is_label : true + is_label : true, + is_numeric : true }, - value: { + z: { title : 'Observations', is_numeric : true } diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/highcharts/heatmap/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts/heatmap/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/highcharts/heatmap/wrapper.js @@ -1,5 +1,5 @@ // dependencies -define(['plugin/charts/highcharts/common/wrapper'], function(Highcharts) { +define(['plugin/charts/highcharts/common/wrapper'], function(HighchartsWrapper) { // widget return Backbone.View.extend( @@ -13,13 +13,14 @@ // render draw : function(process_id, chart, request_dictionary) { - // finalize configuration - chart.settings.set('plotoptions_series_stacking', 'normal'); - chart.settings.set('x_axis_categories', []) - // draw chart - var hc = new Highcharts(this.app, this.options); - hc.draw(process_id, 'heatmap', chart, request_dictionary); + var hc = new HighchartsWrapper(this.app, this.options); + hc.draw(process_id, 'heatmap', chart, request_dictionary, function(model) { + model.colorAxis = { + minColor : '#00FF99', + maxColor : '#000066' + } + }); } }); diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 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 @@ -198,7 +198,7 @@ show_legend : { title : 'Show legend', info : 'Would you like to add a legend?', - type : 'select', + type : 'radiobutton', init : 'true', data : [ { diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/logo.png has changed diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/library/jobs.js --- a/config/plugins/visualizations/charts/static/library/jobs.js +++ b/config/plugins/visualizations/charts/static/library/jobs.js @@ -60,7 +60,7 @@ var chart_type = chart.get('type'); // get chart settings - var chart_settings = this.app.types.get(chart_type); + var chart_definition = chart.definition; // configure tool data = { @@ -70,7 +70,7 @@ 'id' : chart.get('dataset_id'), 'src' : 'hda' }, - 'module' : chart_settings.execute, + 'module' : chart_definition.execute, 'columns' : columns_string, 'settings' : settings_string } diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/library/storage.js --- a/config/plugins/visualizations/charts/static/library/storage.js +++ b/config/plugins/visualizations/charts/static/library/storage.js @@ -114,6 +114,9 @@ // initiating chart console.debug('Storage::load() - Loading chart type ' + chart_type + '.'); + // parse chart definition + this.chart.definition = chart_definition; + // main this.chart.set(chart_dict.attributes); diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/plugins/heatmap/heatmap.css --- a/config/plugins/visualizations/charts/static/plugins/heatmap/heatmap.css +++ /dev/null @@ -1,76 +0,0 @@ -<style> - /* disable text selection */ - svg *::selection { - background : transparent; - } - - svg *::-moz-selection { - background:transparent; - } - - svg *::-webkit-selection { - background:transparent; - } - rect.selection { - stroke : #333; - stroke-dasharray: 4px; - stroke-opacity : 0.5; - fill : transparent; - } - - rect.cell-border { - stroke: #eee; - stroke-width:0.3px; - } - - rect.cell-selected { - stroke: rgb(51,102,153); - stroke-width:0.5px; - } - - rect.cell-hover { - stroke: #F00; - stroke-width:0.3px; - } - - text.mono { - font-size: 9pt; - font-family: Consolas, courier; - fill: #aaa; - } - - text.text-selected { - fill: #000; - } - - text.text-highlight { - fill: #c00; - } - text.text-hover { - fill: #00C; - } - #heatmap-tooltip { - position: absolute; - width: 200px; - height: auto; - padding: 10px; - background-color: white; - -webkit-border-radius: 10px; - -moz-border-radius: 10px; - border-radius: 10px; - -webkit-box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4); - -moz-box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4); - box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4); - pointer-events: none; - } - - #heatmap-tooltip.hidden { - display: none; - } - - #heatmap-tooltip p { - margin: 0; - font-family: sans-serif; - font-size: 12px; - line-height: 20px; - } \ No newline at end of file diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/plugins/highcharts/heatmap.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/plugins/highcharts/heatmap.js @@ -0,0 +1,21 @@ +/* + Highcharts JS v4.0.1 (2014-04-24) + + (c) 2011-2014 Torstein Honsi + + License: www.highcharts.com/license +*/ +(function(g){var j=g.Axis,x=g.Chart,o=g.Color,y=g.Legend,s=g.LegendSymbolMixin,t=g.Series,u=g.getOptions(),k=g.each,p=g.extend,z=g.extendClass,l=g.merge,q=g.pick,v=g.numberFormat,m=g.seriesTypes,w=g.wrap,n=function(){},r=g.ColorAxis=function(){this.isColorAxis=!0;this.init.apply(this,arguments)};p(r.prototype,j.prototype);p(r.prototype,{defaultColorAxisOptions:{lineWidth:0,gridLineWidth:1,tickPixelInterval:72,startOnTick:!0,endOnTick:!0,offset:0,marker:{animation:{duration:50},color:"gray",width:0.01}, +labels:{overflow:"justify"},minColor:"#EFEFFF",maxColor:"#003875",tickLength:5},init:function(b,a){var d=b.options.legend.layout!=="vertical",c;c=l(this.defaultColorAxisOptions,{side:d?2:1,reversed:!d},a,{isX:d,opposite:!d,showEmpty:!1,title:null,isColor:!0});j.prototype.init.call(this,b,c);a.dataClasses&&this.initDataClasses(a);this.initStops(a);this.isXAxis=!0;this.horiz=d;this.zoomEnabled=!1},tweenColors:function(b,a,d){var c=a.rgba[3]!==1||b.rgba[3]!==1;return(c?"rgba(":"rgb(")+Math.round(a.rgba[0]+ +(b.rgba[0]-a.rgba[0])*(1-d))+","+Math.round(a.rgba[1]+(b.rgba[1]-a.rgba[1])*(1-d))+","+Math.round(a.rgba[2]+(b.rgba[2]-a.rgba[2])*(1-d))+(c?","+(a.rgba[3]+(b.rgba[3]-a.rgba[3])*(1-d)):"")+")"},initDataClasses:function(b){var a=this,d=this.chart,c,e=0,h=this.options;this.dataClasses=c=[];k(b.dataClasses,function(f,i){var g,f=l(f);c.push(f);if(!f.color)h.dataClassColor==="category"?(g=d.options.colors,f.color=g[e++],e===g.length&&(e=0)):f.color=a.tweenColors(o(h.minColor),o(h.maxColor),i/(b.dataClasses.length- +1))})},initStops:function(b){this.stops=b.stops||[[0,this.options.minColor],[1,this.options.maxColor]];k(this.stops,function(a){a.color=o(a[1])})},setOptions:function(b){j.prototype.setOptions.call(this,b);this.options.crosshair=this.options.marker;this.coll="colorAxis"},setAxisSize:function(){var b=this.legendSymbol,a=this.chart,d,c,e;if(b)this.left=d=b.attr("x"),this.top=c=b.attr("y"),this.width=e=b.attr("width"),this.height=b=b.attr("height"),this.right=a.chartWidth-d-e,this.bottom=a.chartHeight- +c-b,this.len=this.horiz?e:b,this.pos=this.horiz?d:c},toColor:function(b,a){var d,c=this.stops,e,h=this.dataClasses,f,i;if(h)for(i=h.length;i--;){if(f=h[i],e=f.from,c=f.to,(e===void 0||b>=e)&&(c===void 0||b<=c)){d=f.color;if(a)a.dataClass=i;break}}else{this.isLog&&(b=this.val2lin(b));d=1-(this.max-b)/(this.max-this.min);for(i=c.length;i--;)if(d>c[i][0])break;e=c[i]||c[i+1];c=c[i+1]||e;d=1-(c[0]-d)/(c[0]-e[0]||1);d=this.tweenColors(e.color,c.color,d)}return d},getOffset:function(){var b=this.legendGroup; +if(b&&(j.prototype.getOffset.call(this),!this.axisGroup.parentGroup))this.axisGroup.add(b),this.gridGroup.add(b),this.labelGroup.add(b),this.added=!0},setLegendColor:function(){var b,a=this.options;b=this.horiz?[0,0,1,0]:[0,0,0,1];this.legendColor={linearGradient:{x1:b[0],y1:b[1],x2:b[2],y2:b[3]},stops:a.stops||[[0,a.minColor],[1,a.maxColor]]}},drawLegendSymbol:function(b,a){var d=b.padding,c=b.options,e=this.horiz,h=q(c.symbolWidth,e?200:12),f=q(c.symbolHeight,e?12:200),c=q(c.labelPadding,e?10:30); +this.setLegendColor();a.legendSymbol=this.chart.renderer.rect(0,b.baseline-11,h,f).attr({zIndex:1}).add(a.legendGroup);a.legendSymbol.getBBox();this.legendItemWidth=h+d+(e?0:c);this.legendItemHeight=f+d+(e?c:0)},setState:n,visible:!0,setVisible:n,getSeriesExtremes:function(){var b;if(this.series.length)b=this.series[0],this.dataMin=b.valueMin,this.dataMax=b.valueMax},drawCrosshair:function(b,a){var d=!this.cross,c=a&&a.plotX,e=a&&a.plotY,h,f=this.pos,i=this.len;if(a)h=this.toPixels(a.value),h<f?h= +f-2:h>f+i&&(h=f+i+2),a.plotX=h,a.plotY=this.len-h,j.prototype.drawCrosshair.call(this,b,a),a.plotX=c,a.plotY=e,!d&&this.cross&&this.cross.attr({fill:this.crosshair.color}).add(this.labelGroup)},getPlotLinePath:function(b,a,d,c,e){return e?this.horiz?["M",e-4,this.top-6,"L",e+4,this.top-6,e,this.top,"Z"]:["M",this.left,e,"L",this.left-6,e+6,this.left-6,e-6,"Z"]:j.prototype.getPlotLinePath.call(this,b,a,d,c)},update:function(b,a){k(this.series,function(a){a.isDirtyData=!0});j.prototype.update.call(this, +b,a);this.legendItem&&(this.setLegendColor(),this.chart.legend.colorizeItem(this,!0))},getDataClassLegendSymbols:function(){var b=this,a=this.chart,d=[],c=a.options.legend,e=c.valueDecimals,h=c.valueSuffix||"",f;k(this.dataClasses,function(c,g){var j=!0,l=c.from,m=c.to;f="";l===void 0?f="< ":m===void 0&&(f="> ");l!==void 0&&(f+=v(l,e)+h);l!==void 0&&m!==void 0&&(f+=" - ");m!==void 0&&(f+=v(m,e)+h);d.push(p({chart:a,name:f,options:{},drawLegendSymbol:s.drawRectangle,visible:!0,setState:n,setVisible:function(){j= +this.visible=!j;k(b.series,function(a){k(a.points,function(a){a.dataClass===g&&a.setVisible(j)})});a.legend.colorizeItem(this,j)}},c))});return d},name:""});w(x.prototype,"getAxes",function(b){var a=this.options.colorAxis;b.call(this);this.colorAxis=[];a&&new r(this,a)});w(y.prototype,"getAllItems",function(b){var a=[],d=this.chart.colorAxis[0];d&&(d.options.dataClasses?a=a.concat(d.getDataClassLegendSymbols()):a.push(d),k(d.series,function(a){a.options.showInLegend=!1}));return a.concat(b.call(this))}); +g={pointAttrToOptions:{stroke:"borderColor","stroke-width":"borderWidth",fill:"color",dashstyle:"dashStyle"},pointArrayMap:["value"],axisTypes:["xAxis","yAxis","colorAxis"],optionalAxis:"colorAxis",trackerGroups:["group","markerGroup","dataLabelsGroup"],getSymbol:n,parallelArrays:["x","y","value"],translateColors:function(){var b=this,a=this.options.nullColor,d=this.colorAxis;k(this.data,function(c){var e=c.value;if(e=e===null?a:d?d.toColor(e,c):c.color||b.color)c.color=e})}};u.plotOptions.heatmap= +l(u.plotOptions.scatter,{animation:!1,borderWidth:0,nullColor:"#F8F8F8",dataLabels:{format:"{point.value}",verticalAlign:"middle",crop:!1,overflow:!1,style:{color:"white",fontWeight:"bold",textShadow:"0 0 5px black"}},marker:null,tooltip:{pointFormat:"{point.x}, {point.y}: {point.value}<br/>"},states:{normal:{animation:!0},hover:{brightness:0.2}}});m.heatmap=z(m.scatter,l(g,{type:"heatmap",pointArrayMap:["y","value"],hasPointSpecificOptions:!0,supportsDrilldown:!0,getExtremesFromAll:!0,init:function(){m.scatter.prototype.init.apply(this, +arguments);this.pointRange=this.options.colsize||1;this.yAxis.axisPointRange=this.options.rowsize||1},translate:function(){var b=this.options,a=this.xAxis,d=this.yAxis;this.generatePoints();k(this.points,function(c){var e=(b.colsize||1)/2,h=(b.rowsize||1)/2,f=Math.round(a.len-a.translate(c.x-e,0,1,0,1)),e=Math.round(a.len-a.translate(c.x+e,0,1,0,1)),g=Math.round(d.translate(c.y-h,0,1,0,1)),h=Math.round(d.translate(c.y+h,0,1,0,1));c.plotX=(f+e)/2;c.plotY=(g+h)/2;c.shapeType="rect";c.shapeArgs={x:Math.min(f, +e),y:Math.min(g,h),width:Math.abs(e-f),height:Math.abs(h-g)}});this.translateColors()},drawPoints:m.column.prototype.drawPoints,animate:n,getBox:n,drawLegendSymbol:s.drawRectangle,getExtremes:function(){t.prototype.getExtremes.call(this,this.valueData);this.valueMin=this.dataMin;this.valueMax=this.dataMax;t.prototype.getExtremes.call(this)}}))})(Highcharts); \ No newline at end of file diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 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 @@ -47,7 +47,7 @@ 'back' : new Ui.ButtonIcon({ icon : 'fa-caret-left', tooltip : 'Return to Viewer', - title : 'Return', + title : 'Cancel', onclick : function() { // show viewport self.app.go('viewer'); @@ -63,15 +63,27 @@ // grid with chart types // this.types = new TypesView(app, { - onchange : function(type) { + onchange : function(chart_type) { + // get chart definition + var chart_definition = self.app.types.get(chart_type); + if (!chart_definition) { + console.debug('FAILED - Editor::onchange() - Chart type not supported.'); + } + + // parse chart definition + self.chart.definition = chart_definition; + // reset type relevant chart content self.chart.settings.clear(); // update chart type - self.chart.set({type: type}); + self.chart.set({type: chart_type}); // set modified flag self.chart.set('modified', true); + + // log + console.debug('Editor::onchange() - Switched chart type.'); }, ondblclick : function(chart_id) { self._saveChart(); @@ -230,6 +242,9 @@ // update titles this._refreshGroupKey(); + + // reset + this.chart.set('modified', true); }, // remove group @@ -252,7 +267,7 @@ _resetChart: function() { // reset chart details this.chart.set('id', Utils.uuid()); - this.chart.set('type', 'nvd3_bar'); + this.chart.set('type', 'highcharts_bar'); this.chart.set('dataset_id', this.app.options.config.dataset_id); this.chart.set('title', 'New Chart'); @@ -262,18 +277,30 @@ // create chart _saveChart: function() { - // ensure that data group is available + // update chart data + this.chart.set({ + type : this.types.value(), + title : this.title.value(), + date : Utils.time() + }); + + // make sure that at least one data group is available if (this.chart.groups.length == 0) { + this.message.update({message: 'Please select data columns before drawing the chart.'}); var group = this._addGroupModel(); this.tabs.show(group.id); return; } - // very selected group columns + // make sure that all necessary columns are assigned var self = this; var valid = true; + var chart_def = this.chart.definition; this.chart.groups.each(function(group) { - for (var key in group.attributes) { + if (!valid) { + return; + } + for (var key in chart_def.columns) { if (group.attributes[key] == 'null') { self.message.update({status: 'danger', message: 'This chart type requires column types not found in your tabular file.'}); self.tabs.show(group.id); @@ -290,13 +317,6 @@ // show viewport this.app.go('viewer'); - - // update chart data - this.chart.set({ - type : this.types.value(), - title : this.title.value(), - date : Utils.time() - }); // wait until chart is ready var self = this; diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 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 @@ -74,16 +74,16 @@ var self = this; // configure chart type - var chart_settings = this.app.types.get(chart_type); - + var chart_definition = this.chart.definition; + // reset table this.table.delAll(); // load list for select fields var select_list = {}; - for (var id in chart_settings.columns) { + for (var id in chart_definition.columns) { // get definition - var data_def = chart_settings.columns[id]; + var data_def = chart_definition.columns[id]; if (!data_def) { console.debug('Group::_refreshTable() - Skipping column definition.'); continue; @@ -114,7 +114,7 @@ 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_settings.columns[id]) + self._addRow(id, dataset, select_list, chart_definition.columns[id]) } // loading @@ -126,15 +126,15 @@ }, // add row - _addRow: function(id, dataset, select_list, chart_setting) { + _addRow: function(id, dataset, select_list, column_definition) { // link this var self = this; // is a numeric number required - var is_label = chart_setting.is_label; - var is_auto = chart_setting.is_auto; - var is_numeric = chart_setting.is_numeric; - var is_unique = chart_setting.is_unique; + 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 = []; diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/views/settings.js --- a/config/plugins/visualizations/charts/static/views/settings.js +++ b/config/plugins/visualizations/charts/static/views/settings.js @@ -33,17 +33,14 @@ // update dataset _refresh: function() { - // identify datasets - var chart_type = this.chart.get('type'); + // get settings + var chart_definition = this.chart.definition; // check if dataset is available - if (!chart_type) { + if (!chart_definition) { return; } - // get settings - var chart_definition = this.app.types.get(chart_type); - // set title this.form.title(chart_definition.category + ' - ' + chart_definition.title + ':'); diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/static/views/types.js --- a/config/plugins/visualizations/charts/static/views/types.js +++ b/config/plugins/visualizations/charts/static/views/types.js @@ -32,13 +32,13 @@ // construct chart type subset selection buttons this.library = new Ui.RadioButton({ data : [ { label: 'Default', value: 'default' }, - { label: 'NVD3 (only)', value: 'nvd3' }, - { label: 'Highcharts (only)', value: 'highcharts' }], + { label: 'Classic', value: 'nvd3' }, + { label: 'Zoomable', value: 'highcharts' }], onchange: function(value) { self._filter(value); } }); - $el.append(Utils.wrap(this.library.$el).css('text-align', 'center')); + $el.append(Utils.wrap(this.library.$el)); // set element this.setElement($el); @@ -86,7 +86,7 @@ var type = types[id]; var $el = this.$el.find('#' + id); var keywords = type.keywords || ''; - if (keywords.indexOf(value) == -1) { + if (keywords.indexOf(value) == -1 && value != 'all') { $el.hide(); } else { $el.show(); diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 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 @@ -136,10 +136,10 @@ var chart_type = chart.get('type'); // load chart settings - this.chart_settings = this.app.types.get(chart_type); + this.chart_definition = chart.definition; // read settings - var use_panels = this.chart_settings.use_panels; + var use_panels = this.chart_definition.use_panels; // determine number of svg/div-elements to create var n_panels = 1; @@ -148,14 +148,14 @@ } // create canvas element and add to canvas list - this._createContainer(this.chart_settings.tag, n_panels); + this._createContainer(this.chart_definition.tag, n_panels); // set chart state chart.state('wait', 'Please wait...'); // clean up data if there is any from previous jobs - if (!this.chart_settings.execute || - (this.chart_settings.execute && chart.get('modified'))) { + if (!this.chart_definition.execute || + (this.chart_definition.execute && chart.get('modified'))) { // reset jobs this.app.jobs.cleanup(chart); @@ -171,7 +171,7 @@ var view = new ChartView(self.app, {canvas : self.canvas_list}); // request data - if (self.chart_settings.execute) { + if (self.chart_definition.execute) { self.app.jobs.request(chart, self._defaultSettingsString(chart), self._defaultRequestString(chart), function() { view.draw(process_id, chart, self._defaultRequestDictionary(chart)); @@ -203,7 +203,7 @@ group_index++; // add selected columns to column string - for (var key in self.chart_settings.columns) { + for (var key in self.chart_definition.columns) { request_string += key + '_' + group_index + ':' + (parseInt(group.get(key)) + 1) + ', '; } }); @@ -236,7 +236,7 @@ }; // update request dataset id - if (this.chart_settings.execute) { + if (this.chart_definition.execute) { request_dictionary.id = chart.get('dataset_id_job'); } else { request_dictionary.id = chart.get('dataset_id'); @@ -249,9 +249,9 @@ // add columns var columns = {}; - for (var column_key in self.chart_settings.columns) { + for (var column_key in self.chart_definition.columns) { // get settings for column - var column_settings = self.chart_settings.columns[column_key]; + var column_settings = self.chart_definition.columns[column_key]; // add to columns columns[column_key] = { diff -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc -r cab2ae91c6a96e133748900e1c203ce864f52052 config/plugins/visualizations/charts/templates/charts.mako --- a/config/plugins/visualizations/charts/templates/charts.mako +++ b/config/plugins/visualizations/charts/templates/charts.mako @@ -28,10 +28,8 @@ ## install highcharts module ${h.javascript_link( app_root + "plugins/highcharts/highcharts.js" )} ${h.javascript_link( app_root + "plugins/highcharts/highcharts-more.js" )} + ${h.javascript_link( app_root + "plugins/highcharts/heatmap.js" )} - ## install heat map module - ${h.stylesheet_link( app_root + "plugins/heatmap/heatmap.css" )} - ## install boxplot module ##${h.javascript_link( app_root + "plugins/box.js" )} 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.

1 0

commit/galaxy-central: davebgx: Merge bugfix from stable.
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f70167e188f9/ Changeset: f70167e188f9 User: davebgx Date: 2014-06-04 21:15:23 Summary: Merge bugfix from stable. Affected #: 2 files diff -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f -r f70167e188f9ad42d1651ea77a1208ad2fdc9abc lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1694,6 +1694,8 @@ def reset_all_metadata_on_installed_repository( trans, id ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" + invalid_file_tups = [] + metadata_dict = {} repository = suc.get_installed_tool_shed_repository( trans, id ) repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) 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.

1 0

commit/galaxy-central: davebgx: Fix resetting all metadata based on issue found by Nicola Soranzo.
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fb68af9a775a/ Changeset: fb68af9a775a Branch: stable User: davebgx Date: 2014-06-04 21:04:33 Summary: Fix resetting all metadata based on issue found by Nicola Soranzo. Affected #: 1 file diff -r 18777feed30bc0a41e2f46b49e561cd23eb3b564 -r fb68af9a775a956fcc397b22d16f2119401d926d lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1712,6 +1712,8 @@ def reset_all_metadata_on_installed_repository( trans, id ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" + invalid_file_tups = [] + metadata_dict = {} repository = suc.get_installed_tool_shed_repository( trans, id ) repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) 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.

1 0

commit/galaxy-central: jmchilton: Update LWR client throught LWR changeset 860ba9c.
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/72bb9c96a5ba/ Changeset: 72bb9c96a5ba User: jmchilton Date: 2014-06-04 19:16:38 Summary: Update LWR client throught LWR changeset 860ba9c. Allows asynchornous submission of LWR jobs to remote servers without a remote LWR service running. LWR still needs to be configured there and job updates are should be configured to be sent back to Galaxy through AMQP. A long running process will be executed on the remote server to monitor the job - while this will always be needed in some cases - for others it would be great to be able to embedded the update steps into the job to be submitted to the DRM itself so that this long running process can be just a submission. This is one more potential step down the road toward allowing remote execution of Galaxy jobs with ever fewer remote constraints. Extensions to this would include allowing Galaxy job updates via the jobs API (along with staging) so MQ becomes optional, allowing auto-configuration of remote LWR application if unavailable or unconfigured, more transfer options (scp), more CLI shell options (fabric, ansible, etc...). Affected #: 7 files diff -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -402,7 +402,10 @@ def __job_state( self, job, job_wrapper ): job_state = AsynchronousJobState() - job_state.job_id = str( job.get_job_runner_external_id() ) + # TODO: Determine why this is set when using normal message queue updates + # but not CLI submitted MQ updates... + raw_job_id = job.get_job_runner_external_id() or job_wrapper.job_id + job_state.job_id = str( raw_job_id ) job_state.runner_url = job_wrapper.get_job_runner_url() job_state.job_destination = job_wrapper.job_destination job_state.job_wrapper = job_wrapper diff -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -8,6 +8,8 @@ from .decorators import retry from .util import copy from .util import ensure_directory +from .util import to_base64_json + import logging log = logging.getLogger(__name__) @@ -285,16 +287,25 @@ self._raw_execute("download_output", output_params, output_path=output_path) -class MessageJobClient(BaseJobClient): +class BaseMessageJobClient(BaseJobClient): def __init__(self, destination_params, job_id, client_manager): - super(MessageJobClient, self).__init__(destination_params, job_id) + super(BaseMessageJobClient, self).__init__(destination_params, job_id) if not self.job_directory: error_message = "Message-queue based LWR client requires destination define a remote job_directory to stage files into." raise Exception(error_message) self.client_manager = client_manager - def launch(self, command_line, dependencies_description=None, env=[], remote_staging=[], job_config=None): + def clean(self): + del self.client_manager.status_cache[self.job_id] + + def full_status(self): + full_status = self.client_manager.status_cache.get(self.job_id, None) + if full_status is None: + raise Exception("full_status() called before a final status was properly cached with cilent manager.") + return full_status + + def _build_setup_message(self, command_line, dependencies_description, env, remote_staging, job_config): """ """ launch_params = dict(command_line=command_line, job_id=self.job_id) @@ -313,21 +324,54 @@ # before queueing. setup_params = _setup_params_from_job_config(job_config) launch_params["setup_params"] = setup_params + return launch_params + + +class MessageJobClient(BaseMessageJobClient): + + def launch(self, command_line, dependencies_description=None, env=[], remote_staging=[], job_config=None): + """ + """ + launch_params = self._build_setup_message( + command_line, + dependencies_description=dependencies_description, + env=env, + remote_staging=remote_staging, + job_config=job_config + ) response = self.client_manager.exchange.publish("setup", launch_params) log.info("Job published to setup message queue.") return response - def clean(self): - del self.client_manager.status_cache[self.job_id] + def kill(self): + self.client_manager.exchange.publish("kill", dict(job_id=self.job_id)) - def full_status(self): - full_status = self.client_manager.status_cache.get(self.job_id, None) - if full_status is None: - raise Exception("full_status() called before a final status was properly cached with cilent manager.") - return full_status + +class MessageCLIJobClient(BaseMessageJobClient): + + def __init__(self, destination_params, job_id, client_manager, shell): + super(MessageCLIJobClient, self).__init__(destination_params, job_id, client_manager) + self.remote_lwr_path = destination_params["remote_lwr_path"] + self.shell = shell + + def launch(self, command_line, dependencies_description=None, env=[], remote_staging=[], job_config=None): + """ + """ + launch_params = self._build_setup_message( + command_line, + dependencies_description=dependencies_description, + env=env, + remote_staging=remote_staging, + job_config=job_config + ) + base64_message = to_base64_json(launch_params) + submit_command = os.path.join(self.remote_lwr_path, "scripts", "submit.bash") + # TODO: Allow configuration of manager, app, and ini path... + self.shell.execute("nohup %s --base64 %s &" % (submit_command, base64_message)) def kill(self): - self.client_manager.exchange.publish("kill", dict(job_id=self.job_id)) + # TODO + pass class InputCachingJobClient(JobClient): diff -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f lib/galaxy/jobs/runners/lwr_client/interface.py --- a/lib/galaxy/jobs/runners/lwr_client/interface.py +++ b/lib/galaxy/jobs/runners/lwr_client/interface.py @@ -78,8 +78,8 @@ def execute(self, command, args={}, data=None, input_path=None, output_path=None): # If data set, should be unicode (on Python 2) or str (on Python 3). - from lwr import routes - from lwr.framework import build_func_args + from lwr.web import routes + from lwr.web.framework import build_func_args controller = getattr(routes, command) action = controller.func body_args = dict(body=self.__build_body(data, input_path)) diff -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -8,6 +8,7 @@ from .client import JobClient from .client import InputCachingJobClient from .client import MessageJobClient +from .client import MessageCLIJobClient from .interface import HttpLwrInterface from .interface import LocalLwrInterface from .object_client import ObjectStoreClient @@ -71,6 +72,12 @@ pass +try: + from galaxy.jobs.runners.util.cli import factory as cli_factory +except ImportError: + from lwr.managers.util.cli import factory as cli_factory + + class MessageQueueClientManager(object): def __init__(self, **kwds): @@ -90,7 +97,8 @@ def callback_wrapper(body, message): try: if "job_id" in body: - self.status_cache[body["job_id"]] = body + job_id = body["job_id"] + self.status_cache[job_id] = body log.debug("Handling asynchronous status update from remote LWR.") callback(body) except Exception: @@ -116,9 +124,15 @@ return self.active def get_client(self, destination_params, job_id, **kwargs): + if job_id is None: + raise Exception("Cannot generate LWR client for empty job_id.") destination_params = _parse_destination_params(destination_params) destination_params.update(**kwargs) - return MessageJobClient(destination_params, job_id, self) + if 'shell_plugin' in destination_params: + shell = cli_factory.get_shell(destination_params) + return MessageCLIJobClient(destination_params, job_id, self, shell) + else: + return MessageJobClient(destination_params, job_id, self) class ObjectStoreClientManager(object): diff -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f lib/galaxy/jobs/runners/lwr_client/util.py --- a/lib/galaxy/jobs/runners/lwr_client/util.py +++ b/lib/galaxy/jobs/runners/lwr_client/util.py @@ -7,6 +7,8 @@ import os.path import hashlib import shutil +import json +import base64 def unique_path_prefix(path): @@ -70,6 +72,20 @@ if key.startswith(prefix)]) +def to_base64_json(data): + """ + + >>> x = from_base64_json(to_base64_json(dict(a=5))) + >>> x["a"] + 5 + """ + return base64.b64encode(json.dumps(data)) + + +def from_base64_json(data): + return json.loads(base64.b64decode(data)) + + class PathHelper(object): ''' diff -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f lib/galaxy/jobs/runners/util/cli/__init__.py --- a/lib/galaxy/jobs/runners/util/cli/__init__.py +++ b/lib/galaxy/jobs/runners/util/cli/__init__.py @@ -43,11 +43,19 @@ Return shell and job interface defined by and configured via specified params. """ + shell = self.get_shell_plugin(shell_params) + job_interface = self.get_job_interface(job_params) + return shell, job_interface + + def get_shell_plugin(self, shell_params): shell_plugin = shell_params.get('plugin', DEFAULT_SHELL_PLUGIN) + shell = self.cli_shells[shell_plugin](**shell_params) + return shell + + def get_job_interface(self, job_params): job_plugin = job_params['plugin'] - shell = self.cli_shells[shell_plugin](**shell_params) job_interface = self.cli_job_interfaces[job_plugin](**job_params) - return shell, job_interface + return job_interface def split_params(params): diff -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 -r 72bb9c96a5bad59ca79a669ec1d43a87aa06986f lib/galaxy/jobs/runners/util/cli/factory.py --- /dev/null +++ b/lib/galaxy/jobs/runners/util/cli/factory.py @@ -0,0 +1,18 @@ +try: + from galaxy.jobs.runners.util.cli import ( + CliInterface, + split_params + ) + code_dir = 'lib' +except ImportError: + from lwr.managers.util.cli import ( + CliInterface, + split_params + ) + code_dir = '.' + + +def get_shell(params): + cli_interface = CliInterface(code_dir=code_dir) + shell_params, _ = split_params(params) + return cli_interface.get_shell_plugin(shell_params) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for installing from toolshed that uses 307 redirects that are not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided.
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/18777feed30b/ Changeset: 18777feed30b Branch: stable User: dan Date: 2014-06-04 17:05:36 Summary: Fix for installing from toolshed that uses 307 redirects that are not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided. Affected #: 1 file diff -r c68aa8a8e769437473bd23586d1b55fc66cc8c47 -r 18777feed30bc0a41e2f46b49e561cd23eb3b564 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -448,6 +448,8 @@ # Handle secure / insecure Tool Shed URL protocol changes and port changes. tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url ) url = common_util.url_join( tool_shed_url, '/repository/get_required_repo_info_dict' ) + # Fix for handling 307 redirect not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided + url = urllib2.urlopen( urllib2.Request( url ) ).geturl() request = urllib2.Request( url, data=urllib.urlencode( dict( encoded_str=encoded_required_repository_str ) ) ) response = urllib2.urlopen( request ).read() if response: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for installing from toolshed that uses 307 redirects that are not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided.
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3d6b71244ff9/ Changeset: 3d6b71244ff9 User: dan Date: 2014-06-04 17:05:36 Summary: Fix for installing from toolshed that uses 307 redirects that are not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided. Affected #: 1 file diff -r 819818c880b543d9ef32aa61a099235c20937dae -r 3d6b71244ff9a708bd6eda419b50315d7aac4405 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -447,6 +447,8 @@ # Handle secure / insecure Tool Shed URL protocol changes and port changes. tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url ) url = common_util.url_join( tool_shed_url, '/repository/get_required_repo_info_dict' ) + # Fix for handling 307 redirect not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided + url = urllib2.urlopen( urllib2.Request( url ) ).geturl() request = urllib2.Request( url, data=urllib.urlencode( dict( encoded_str=encoded_required_repository_str ) ) ) response = urllib2.urlopen( request ).read() if response: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix the exception handler in the Tool Shed APi submit() function so that an expected dict is returned instead of a string.
by commits-noreply＠bitbucket.org 04 Jun '14

04 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/819818c880b5/ Changeset: 819818c880b5 User: greg Date: 2014-06-04 15:21:18 Summary: Fix the exception handler in the Tool Shed APi submit() function so that an expected dict is returned instead of a string. Affected #: 1 file diff -r 0cb88fa06c32e13c8881ed90af02b239aa574313 -r 819818c880b543d9ef32aa61a099235c20937dae lib/tool_shed/scripts/api/common.py --- a/lib/tool_shed/scripts/api/common.py +++ b/lib/tool_shed/scripts/api/common.py @@ -197,7 +197,7 @@ print e.read( 1024 ) sys.exit( 1 ) else: - return 'Error. '+ str( e.read( 1024 ) ) + return dict( status='error', message=str( e.read( 1024 ) ) ) if not return_formatted: return r print 'Response' 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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