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commit/galaxy-central: dannon: Adjust require order in cloudlaunch controller.
by commits-noreply＠bitbucket.org 05 May '14

05 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/92519a9bfa32/ Changeset: 92519a9bfa32 User: dannon Date: 2014-05-05 15:28:41 Summary: Adjust require order in cloudlaunch controller. Affected #: 1 file diff -r a45f6e57f3d5a4075430a6d460a6caded611b867 -r 92519a9bfa32a42ce47a63fdb72c8e2d717ec52e lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -15,9 +15,9 @@ from galaxy.web.base.controller import BaseUIController from galaxy.util.json import to_json_string +eggs.require('pyyaml') eggs.require('boto') eggs.require('bioblend') -eggs.require('pyyaml') from boto.exception import EC2ResponseError @@ -73,7 +73,7 @@ result = cml.launch(cluster_name, ami, instance_type, password, cfg.kernel_id, cfg.ramdisk_id, cfg.key_name, cfg.security_groups, cfg.placement) - #result is a dict with sg_names, kp_name, kp_material, rs, and instance_id + # result is a dict with sg_names, kp_name, kp_material, rs, and instance_id if not result['rs']: trans.response.status = 400 return "Instance failure, but no specific error was detected. Please check your AWS Console." @@ -86,7 +86,7 @@ pass time.sleep(1) if result['kp_material']: - #We have created a keypair. Save to tempfile for one time retrieval. + # We have created a keypair. Save to tempfile for one time retrieval. (fd, fname) = tempfile.mkstemp(prefix=PKEY_PREFIX, dir=trans.app.config.new_file_path) f = os.fdopen(fd, 'wt') f.write(result['kp_material']) 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: jmchilton: Fix env job metrics plugin for multi-line properties.
by commits-noreply＠bitbucket.org 05 May '14

05 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a45f6e57f3d5/ Changeset: a45f6e57f3d5 User: jmchilton Date: 2014-05-05 01:17:36 Summary: Fix env job metrics plugin for multi-line properties. Thanks to Nicola Soranzo for detailed bug report. Affected #: 1 file diff -r 116d7867f3f8efca5fdc2998bb3bb5df55724529 -r a45f6e57f3d5a4075430a6d460a6caded611b867 lib/galaxy/jobs/metrics/instrumenters/env.py --- a/lib/galaxy/jobs/metrics/instrumenters/env.py +++ b/lib/galaxy/jobs/metrics/instrumenters/env.py @@ -42,6 +42,13 @@ properties = {} for line in open( self.__env_file( job_directory ) ).readlines(): + if "=" not in line: + # Previous line may have had a multiline property value, just + # keep it simple here and only record the first part of + # property. A more robust solution might be to record env -O + # so properties are terminated by null characters instead of + # newlines. + continue var, value = line.split( "=", 1 ) if not variables or var in variables: properties[ var ] = value 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: Implement heatmap sort for sparse data
by commits-noreply＠bitbucket.org 03 May '14

03 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/116d7867f3f8/ Changeset: 116d7867f3f8 User: guerler Date: 2014-05-03 21:39:40 Summary: Charts: Implement heatmap sort for sparse data Affected #: 1 file diff -r fd8cf23297536147d5bbeed5b8b5d501eb8e84bf -r 116d7867f3f8efca5fdc2998bb3bb5df55724529 config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js @@ -20,19 +20,24 @@ // cell size cellSize: 0, + // font size + fontSize: 0, + // color buckets nColors: 0, - + + // margins as cells + margin : { + top : 5, + right : 5, + bottom : 5, + left : 5 + }, + // default settings optionsDefault: { title : '', pace : 1000, - margin : { - top : 50, - right : 10, - bottom : 50, - left : 100 - } }, // initialize @@ -107,20 +112,19 @@ // generate sorted key list for rows for (var i in this.rowLabel) { var row_label = this.rowLabel[i]; - var row_rank = parseInt(i); - this.rowRank[row_label] = row_rank; + var row = parseInt(i); + this.rowRank[row_label] = row; } // generate sorted key list for columns for (var i in this.colLabel) { var col_label = this.colLabel[i]; - var col_rank = parseInt(i); - this.colRank[col_label] = col_rank; + var col = parseInt(i); + this.colRank[col_label] = col; } // // parse indexing from rank dictionary to cells - // identify data range // // min/max @@ -133,8 +137,8 @@ var cell = this.data[i]; // add rank - cell.col_rank = this.colRank[cell.col_label]; - cell.row_rank = this.rowRank[cell.row_label]; + cell.col = this.colRank[cell.col_label]; + cell.row = this.rowRank[cell.row_label]; // identify max/min values if (this.min == undefined || this.min > cell.value) { @@ -199,17 +203,20 @@ // link this var self = this; - // container - var container_width = this.$el.width(); - var container_height = this.$el.height(); + // container (full draw area) + this.widthContainer = this.$el.width(); + this.heightContainer = this.$el.height(); - // get height - this.width = this.$el.width() - this.options.margin.left - this.options.margin.right; - this.height = this.$el.height() - this.options.margin.top - this.options.margin.bottom; + // get grid dimensions + this.width = this.widthContainer; + this.height = this.heightContainer; // calculate cell size - this.cellSize = Math.min(parseInt(this.height / this.rowNumber), - parseInt(this.width / this.colNumber)); + this.cellSize = Math.min(((this.height - 50) / (this.rowNumber + this.margin.top + this.margin.bottom)), + (this.width / (this.colNumber + this.margin.left + this.margin.right))); + + // set font size + this.fontSize = Math.min(this.cellSize, 16); // set width/height for plugin this.width = this.cellSize * this.colNumber; @@ -222,10 +229,9 @@ // add main group and translate this.svg = d3.select(this.$el[0]).append('svg') - .attr('width', width + margin.left + margin.right) - .attr('height', height + margin.top + margin.bottom) .append('g') - .attr('transform', 'translate(' + (container_width - width) / 2 + ',' + (container_height - height) / 2 + ')') + .attr('transform', 'translate(' + (this.widthContainer - width) / 2 + ',' + + (this.heightContainer - height) / 2 + ')') // reset sorting this.rowSortOrder = false; @@ -245,15 +251,17 @@ var self = this; // gather data - var height = this.height; - var width = this.width; - var title = this.options.title; + var height = this.height; + var width = this.width; + var cellSize = this.cellSize; + var fontSize = this.fontSize; + var title = this.options.title; // add title this.svg.append('g') .append('text') .attr('x', width / 2) - .attr('y', height - 10) + .attr('y', height + 3 * cellSize + fontSize + 3) .attr('text-anchor', 'middle') .text(title); }, @@ -265,6 +273,7 @@ // gather data var cellSize = this.cellSize; + var fontSize = this.fontSize; var height = this.height; var legendCellWidth = this.width / this.nColors; @@ -312,8 +321,8 @@ .attr('x', function(d, i) { return legendCellWidth * i; }) - .attr('y', height + cellSize) - .style('font-size', cellSize + 'px'); + .attr('y', height + cellSize - 3) + .style('font-size', fontSize + 'px'); }, // build column labels @@ -323,6 +332,7 @@ // gather data var cellSize = this.cellSize; + var fontSize = this.fontSize; var colIndex = this.colIndex; var colLabel = this.colLabel; @@ -339,7 +349,7 @@ .attr('y', function (d, i) { return colIndex.indexOf(i) * cellSize; }) - .style('font-size', cellSize + 'px') + .style('font-size', fontSize + 'px') .style('text-anchor', 'left') .attr('transform', 'translate(' + cellSize / 2 + ', -17) rotate (-90)') .attr('class', function (d, i) { @@ -347,15 +357,13 @@ }) .on('mouseover', function(d) { d3.select(this).classed('text-hover',true); - d3.select(this).style('font-size', parseInt(cellSize * 1.3) + 'px'); }) .on('mouseout' , function(d) { d3.select(this).classed('text-hover',false); - d3.select(this).style('font-size', parseInt(cellSize) + 'px'); }) .on('click', function(d, i) { self.colSortOrder=!self.colSortOrder; - self._sortByLabel('c', i, self.colSortOrder); + self._sortByLabel('c', 'row', self.rowNumber, i, self.colSortOrder); d3.select('#order').property('selectedIndex', 4).node().focus(); }); }, @@ -367,6 +375,7 @@ // gather data var cellSize = this.cellSize; + var fontSize = this.fontSize; var rowIndex = this.rowIndex; var rowLabel = this.rowLabel; @@ -383,7 +392,7 @@ .attr('y', function (d, i) { return rowIndex.indexOf(i) * cellSize; }) - .style('font-size', cellSize + 'px') + .style('font-size', fontSize + 'px') .style('text-anchor', 'end') .attr('transform', 'translate(-10,' + cellSize / 1.5 + ')') .attr('class', function (d, i) { @@ -391,15 +400,13 @@ } ) .on('mouseover', function(d) { d3.select(this).classed('text-hover',true); - d3.select(this).style('font-size', parseInt(cellSize * 1.3) + 'px'); }) .on('mouseout' , function(d) { d3.select(this).classed('text-hover',false); - d3.select(this).style('font-size', parseInt(cellSize) + 'px'); }) .on('click', function(d, i) { self.rowSortOrder=!self.rowSortOrder; - self._sortByLabel('r', i, self.rowSortOrder); + self._sortByLabel('r', 'col', self.colNumber, i, self.rowSortOrder); d3.select('#order').property('selectedIndex', 4).node().focus(); }); }, @@ -420,18 +427,18 @@ var heatMap = this.svg.append('g').attr('class','g3') .selectAll('.cellg') .data(self.data, function(d) { - return d.row_rank + ':' + d.col_rank; + return d.row + ':' + d.col; }) .enter() .append('rect') .attr('x', function(d) { - return colIndex.indexOf(d.col_rank) * cellSize; + return colIndex.indexOf(d.col) * cellSize; }) .attr('y', function(d) { - return rowIndex.indexOf(d.row_rank) * cellSize; + return rowIndex.indexOf(d.row) * cellSize; }) .attr('class', function(d){ - return 'cell cell-border cr' + d.row_rank + ' cc' + d.col_rank; + return 'cell cell-border cr' + d.row + ' cc' + d.col; }) .attr('width', cellSize) .attr('height', cellSize) @@ -441,15 +448,15 @@ .on('mouseover', function(d){ // highlight text d3.select(this).classed('cell-hover',true); - d3.selectAll('.rowLabel').classed('text-highlight',function(r,ri){ return ri==(d.row_rank);}); - d3.selectAll('.colLabel').classed('text-highlight',function(c,ci){ return ci==(d.col_rank);}); + d3.selectAll('.rowLabel').classed('text-highlight',function(r,ri){ return ri==(d.row);}); + d3.selectAll('.colLabel').classed('text-highlight',function(c,ci){ return ci==(d.col);}); // update the tooltip position and value d3.select('#heatmap-tooltip') .style('left', (d3.event.pageX+10) + 'px') .style('top', (d3.event.pageY-10) + 'px') .select('#value') - .text('Label: ' + rowLabel[d.row_rank] + ' | ' + colLabel[d.col_rank] + ', Value: ' + d.value); + .text('Label: ' + rowLabel[d.row] + ' | ' + colLabel[d.col] + ', Value: ' + d.value); // show the tooltip d3.select('#heatmap-tooltip').classed('hidden', false); }) @@ -462,18 +469,25 @@ }, // change ordering of cells - _sortByLabel: function(rORc, i, sortOrder) { + _sortByLabel: function(rORc, rowORcol, n, index, sortOrder) { // get cell size var cellSize = this.cellSize; // define transition / prepare element var t = this.svg.transition().duration(this.options.pace); + // create cells + var cells=[]; + for (var i = 0; i < n; i++) { + cells[i] = { + value: this.min - 1 + } + cells[i][rowORcol] = i; + } + // collect cells - var cells=[]; - t.selectAll('.c' + rORc + i) - .filter(function(ce){ - cells.push(ce); + t.selectAll('.c' + rORc + index).filter(function(ce) { + cells[ce[rowORcol]].value = ce.value; }); // sort cells @@ -484,19 +498,19 @@ return a.value - b.value; } }); - + + // get sorted key list + var sorted = []; + for (var i in cells) { + sorted.push(cells[i][rowORcol]); + } + // rows or columns if(rORc == 'r') { - // get sorted key list - var sorted = []; - for (var i in cells) { - sorted.push(cells[i].col_rank); - } - // sort cells t.selectAll('.cell') .attr('x', function(d) { - return sorted.indexOf(d.col_rank) * cellSize; + return sorted.indexOf(d.col) * cellSize; }); // sort labels @@ -505,23 +519,17 @@ return sorted.indexOf(i) * cellSize; }); } else { - // get sorted key list - sorted = []; - for (var i in cells) { - sorted.push(cells[i].row_rank); - } - // sort cells t.selectAll('.cell') .attr('y', function(d) { - return sorted.indexOf(d.row_rank) * cellSize; - }); - + return sorted.indexOf(d.row) * cellSize; + }); + // sort labels t.selectAll('.rowLabel') .attr('y', function (d, i) { return sorted.indexOf(i) * cellSize; - }); + }); } }, @@ -542,10 +550,10 @@ if(value=='hclust'){ t.selectAll('.cell') .attr('x', function(d) { - return colIndex.indexOf(d.col_rank) * cellSize; + return colIndex.indexOf(d.col) * cellSize; }) .attr('y', function(d) { - return rowIndex.indexOf(d.row_rank) * cellSize; + return rowIndex.indexOf(d.row) * cellSize; }); t.selectAll('.rowLabel') @@ -561,10 +569,10 @@ } else if (value=='byboth') { t.selectAll('.cell') .attr('x', function(d) { - return d.col_rank * cellSize; + return d.col * cellSize; }) .attr('y', function(d) { - return d.row_rank * cellSize; + return d.row * cellSize; }); t.selectAll('.rowLabel') @@ -579,7 +587,7 @@ } else if (value=='byrow') { t.selectAll('.cell') .attr('y', function(d) { - return d.row_rank * cellSize; + return d.row * cellSize; }); t.selectAll('.rowLabel') @@ -589,7 +597,7 @@ } else if (value=='bycol'){ t.selectAll('.cell') .attr('x', function(d) { - return d.col_rank * cellSize; + return d.col * cellSize; }); t.selectAll('.colLabel') .attr('y', function (d, i) { @@ -666,11 +674,11 @@ .classed('cell-selection', true) .classed('cell-selected', true); - d3.select('.r'+(cell_d.row_rank)) + d3.select('.r' + cell_d.row) .classed('text-selection',true) .classed('text-selected',true); - d3.select('.c'+(cell_d.col_rank)) + d3.select('.c' + cell_d.col) .classed('text-selection',true) .classed('text-selected',true); } 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: Add labels
by commits-noreply＠bitbucket.org 03 May '14

03 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fd8cf2329753/ Changeset: fd8cf2329753 User: guerler Date: 2014-05-03 02:12:26 Summary: Charts: Add labels Affected #: 2 files diff -r 21121d6283a95942061819f5e788ab41cfc1c000 -r fd8cf23297536147d5bbeed5b8b5d501eb8e84bf config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js @@ -25,6 +25,7 @@ // default settings optionsDefault: { + title : '', pace : 1000, margin : { top : 50, @@ -231,12 +232,32 @@ this.colSortOrder = false; // build - this.rowLabels = this._buildRowLabels(); - this.colLabels = this._buildColLabels(); - this.heatMap = this._buildHeatMap(); - this.legend = this._buildLegend(); + this._buildRowLabels(); + this._buildColLabels(); + this._buildHeatMap(); + this._buildLegend(); + this._buildTitle(); }, + // build title + _buildTitle: function() { + // link this + var self = this; + + // gather data + var height = this.height; + var width = this.width; + var title = this.options.title; + + // add title + this.svg.append('g') + .append('text') + .attr('x', width / 2) + .attr('y', height - 10) + .attr('text-anchor', 'middle') + .text(title); + }, + // build legend _buildLegend: function() { // link this diff -r 21121d6283a95942061819f5e788ab41cfc1c000 -r fd8cf23297536147d5bbeed5b8b5d501eb8e84bf config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js @@ -22,12 +22,14 @@ for (var group_index in request_dictionary.groups) { // get group var group = request_dictionary.groups[group_index]; - + var div = self.options.canvas[group_index]; + // draw plot var heatmap = new HeatmapPlugin({ - 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')], - 'data' : group.values, - 'div' : self.options.canvas[group_index] + 'title' : group.key, + 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')], + 'data' : group.values, + 'div' : div }); } 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 color combos, fixes for heatmaps
by commits-noreply＠bitbucket.org 03 May '14

03 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/21121d6283a9/ Changeset: 21121d6283a9 User: guerler Date: 2014-05-03 01:40:37 Summary: Charts: Add color combos, fixes for heatmaps Affected #: 4 files diff -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 -r 21121d6283a95942061819f5e788ab41cfc1c000 config/plugins/visualizations/charts/static/charts/heatmap/config.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/config.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/config.js @@ -17,6 +17,97 @@ value : { title : 'Observations' }, + }, + + settings: { + color_set : { + title : 'Color scheme', + info : 'Select a color scheme for your heatmap', + type : 'select', + init : 'ocean', + data : [ + { + label : 'Cold-to-Hot', + value : 'hot' + }, + { + label : 'Cool', + value : 'cool' + }, + { + label : 'Copper', + value : 'copper' + }, + { + label : 'Gebco', + value : 'gebco' + }, + { + label : 'Globe', + value : 'globe' + }, + { + label : 'Gray scale', + value : 'gray' + }, + { + label : 'Haxby', + value : 'haxby' + }, + { + label : 'Jet', + value : 'jet' + }, + { + label : 'No-Green', + value : 'no_green' + }, + { + label : 'Ocean', + value : 'ocean' + }, + { + label : 'Polar', + value : 'polar' + }, + { + label : 'Rainbow', + value : 'rainbow' + }, + { + label : 'Red-to-Green', + value : 'redgreen' + }, + { + label : 'Red-to-green (saturated)', + value : 'red2green' + }, + { + label : 'Relief', + value : 'relief' + }, + { + label : 'Seismograph', + value : 'seis' + }, + { + label : 'Sealand', + value : 'sealand' + }, + { + label : 'Split', + value : 'split' + }, + { + label : 'Topo', + value : 'topo' + }, + { + label : 'Wysiwyg', + value : 'wysiwyg' + } + ] + } } }; diff -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 -r 21121d6283a95942061819f5e788ab41cfc1c000 config/plugins/visualizations/charts/static/charts/heatmap/heatmap-parameters.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-parameters.js @@ -0,0 +1,52 @@ +// dependencies +define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin'], function(Utils, HeatmapPlugin) { + +// color palettes +var colorSets = { + seis: ['#AA0000', '#D00000', '#F70000', '#FF1D00', '#FF4400', '#FF6A00', '#FF9000', '#FFB700', '#FFDD00', '#FFFF00', '#FFFF00', '#FFFF00', '#BDFF0C', '#73FF1A', '#3FFA36', '#16F45A', '#00D08B', '#0087CD', '#0048FA', '#0024E3'], + + sealand: ['#8C66FF', '#6A66FF', '#6684FF', '#66A7FF', '#66CAFF', '#66ECFF', '#66FFF0', '#66FFCE', '#66FFAB', '#66FF88', '#66FF66', '#88FF66', '#ABFF66', '#CEFF66', '#FFEEA6', '#FFD3A6', '#FFB8A6', '#FFAAB0', '#FFB5CB', '#FFC0E1'], + + redgreen: ['#005824', '#1A693B', '#347B53', '#4F8D6B', '#699F83', '#83B09B', '#9EC2B3', '#B8D4CB', '#D2E6E3', '#EDF8FB', '#FFFFFF', '#F1EEF6', '#E6D3E1','#DBB9CD', '#D19EB9', '#C684A4', '#BB6990', '#B14F7C', '#A63467', '#9B1A53', '#91003F'], + + ocean: ['#000000', '#000209', '#000413', '#00061E', '#000728', '#000932', '#002650', '#00426E', '#005E8C', '#007AAA', '#0096C8', '#22A9C2', '#45BCBB', '#67CFB5', '#8AE2AE', '#ACF6A8', '#BCF8B9', '#CBF9CA', '#DBFBDC', '#EBFDED'], + + cool: ['#00FFFF', '#0DF2FF', '#19E6FF', '#26D9FF', '#33CCFF', '#3FBFFF', '#4CB3FF', '#59A6FF', '#6699FF', '#738CFF', '#7F7FFF', '#8C73FF', '#9966FF', '#A659FF', '#B24DFF', '#BF3FFF', '#CC33FF', '#D926FF', '#E619FF', '#F20DFF'], + + copper: ['#000000', '#100906', '#1F130D', '#301E13', '#40281A', '#50321F', '#603C26', '#70462D', '#805033', '#905A3A', '#A06440', '#B06E46', '#C0784D', '#D08253', '#E08C5A', '#F09660', '#FFA066', '#FFAA6D', '#FFB473', '#FFBE7A'], + + gebco: ['#00F0FF', '#00F0FF', '#00F0FF', '#23FFFF', '#23FFFF', '#23FFFF', '#5AFFFF', '#5AFFFF', '#5AFFFF', '#8CFFE6', '#8CFFE6', '#8CFFE6', '#A5FFD7', '#A5FFD7', '#A5FFD7', '#C3FFD7', '#C3FFD7', '#C3FFD7', '#D2FFD7', '#E6FFF0'], + + globe: ['#9900FF', '#9900FF', '#7722FF', '#5544FF', '#3366FF', '#1188FF', '#1BA4FF', '#51BAFF', '#86D0FF', '#BCE6FF', '#336600', '#F3CA89', '#D9A627', '#A49019', '#9F7B0D', '#996600', '#B27676', '#C2B0B0', '#E5E5E5', '#FFFFFF'], + + gray: ['#000000', '#0D0D0D', '#191919', '#262626', '#333333', '#3F3F3F', '#4C4C4C', '#595959', '#666666', '#737373', '#7F7F7F', '#8C8C8C', '#999999', '#A6A6A6', '#B2B2B2', '#BFBFBF', '#CCCCCC', '#D9D9D9', '#E6E6E6', '#F2F2F2'], + + haxby: ['#090079', '#280096', '#0009C8', '#0019D4', '#1A66F0', '#19AFFF', '#32BEFF', '#61E1F0', '#6AECE1', '#8AECAE', '#CDFFA2', '#DFF68D', '#F8D768', '#FFBD57', '#F4754B', '#FF5A5A', '#FF7C7C', '#F6B3AE', '#FFC4C4', '#FFECEC'], + + hot: ['#000000', '#220000', '#440000', '#660000', '#880000', '#AA0000', '#CC0000', '#EE0000', '#FF1100', '#FF3300', '#FF5500', '#FF7700', '#FF9900', '#FFBB00', '#FFDD00', '#FFFF00', '#FFFF33', '#FFFF66', '#FFFF99', '#FFFFCC'], + + jet: ['#00007F', '#0000B2', '#0000E5', '#0019FF', '#004DFF', '#007FFF', '#00B2FF', '#00E5FF', '#FFFFF2', '#FFFFD9', '#FFFFBF', '#FFFFA5', '#FFFF8C', '#FFE500', '#FFB300', '#FF7F00', '#FF4C00', '#FF1900', '#E50000', '#B20000'], + + no_green: ['#1F60FF', '#1F60FF', '#1F9FFF', '#1FBFFF', '#00CFFF', '#2AFFFF', '#2AFFFF', '#55FFFF', '#7FFFFF', '#AAFFFF', '#FFFF54', '#FFFF54', '#FFF000', '#FFBF00', '#FFA800', '#FF8A00', '#FF8A00', '#FF7000', '#FF4D00', '#FF0000'], + + polar: ['#0000FF', '#1919FF', '#3333FF', '#4C4CFF', '#6666FF', '#7F7FFF', '#9999FF', '#B2B2FF', '#CCCCFF', '#E6E6FF', '#FFFFFF', '#FFE5E5', '#FFCCCC', '#FFB2B2', '#FF9999', '#FF7F7F', '#FF6666', '#FF4C4C', '#FF3333', '#FF1A1A'], + + rainbow: ['#FF00FF', '#BF00FF', '#7F00FF', '#3F00FF', '#0000FF', '#003FFF', '#007FFF', '#00BFFF', '#00FFFF', '#00FFBF', '#00FF7F', '#00FF3F', '#00FF00', '#3FFF00', '#7FFF00', '#BFFF00', '#FFFF00', '#FFBF00', '#FF7F00', '#FF3F00'], + + red2green: ['#FF0000', '#FF1919', '#FF3333', '#FF4C4C', '#FF6666', '#FF7F7F', '#FF9999', '#FFB2B2', '#FFCCCC', '#FFE6E6', '#FFFFFF', '#E5FFE5', '#CCFFCC', '#B2FFB2', '#99FF99', '#7FFF7F', '#66FF66', '#4CFF4C', '#33FF33', '#1AFF1A'], + + relief: ['#000000', '#000413', '#000728', '#002650', '#005E8C', '#0096C8', '#45BCBB', '#8AE2AE', '#BCF8B9', '#DBFBDC', '#467832', '#887438', '#B19D48', '#DBC758', '#FAE769', '#FAEB7E', '#FCED93', '#FCF1A7', '#FCF6C1', '#FDFAE0'], + + split: ['#7F7FFF', '#6666E6', '#4D4DCC', '#3333B3', '#1A1A99', '#00007F', '#000066', '#00004D', '#000033', '#00001A', '#000000', '#1A0000', '#330000', '#4D0000', '#660000', '#7F0000', '#991A1A', '#B33333', '#CC4D4D', '#E66666'], + + topo: ['#C977D9', '#A18AE6', '#8AA2E6', '#8BD1E7', '#8AF3CF', '#85F38E', '#BDF385', '#EDE485', '#F0B086', '#DE9F8B', '#74A3B3', '#99CC70', '#DCD68E', '#EDDFAD', '#F7E8CA', '#FFF9F3', '#FFF9F6', '#FFFBF9', '#FFFCFA', '#FFFEFD'], + + wysiwyg: ['#3F003F', '#3F003F', '#3F00BF', '#003FFF', '#00A0FF', '#3FBFFF', '#3FBFFF', '#40E0FF', '#3FFFBF', '#3FFF3F', '#7FFF3F', '#BFFF3F', '#BFFF3F', '#FFE040', '#FFE040', '#FF6040', '#FF1F40', '#FF60C0', '#FFA0FF', '#FFA0FF'] +} + +// return +return { + colorSets: colorSets +} + +}); \ No newline at end of file diff -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 -r 21121d6283a95942061819f5e788ab41cfc1c000 config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js @@ -1,5 +1,6 @@ // dependencies -define(['utils/utils'], function(Utils) { +define(['utils/utils'], +function(Utils) { // widget return Backbone.View.extend( @@ -30,8 +31,7 @@ right : 10, bottom : 50, left : 100 - }, - colors : ['#005824','#1A693B','#347B53','#4F8D6B','#699F83','#83B09B','#9EC2B3','#B8D4CB','#D2E6E3','#EDF8FB','#FFFFFF','#F1EEF6','#E6D3E1','#DBB9CD','#D19EB9','#C684A4','#BB6990','#B14F7C','#A63467','#9B1A53','#91003F'] + } }, // initialize @@ -43,8 +43,8 @@ this.options = Utils.merge(options, this.optionsDefault) // check requirements - if (!this.options.data || !this.options.div) { - console.debug('FAILED - HeatMapPlugin::initialize() - Parameters (container and/or data) missing.'); + if (!this.options.data || !this.options.div || !this.options.colors) { + console.debug('FAILED - HeatMapPlugin::initialize() - Parameters (container and/or data and/or colors) missing.'); return; } @@ -221,10 +221,10 @@ // add main group and translate this.svg = d3.select(this.$el[0]).append('svg') - .attr("width", width + margin.left + margin.right) - .attr("height", height + margin.top + margin.bottom) - .append("g") - .attr("transform", "translate(" + (container_width - width) / 2 + "," + (container_height - height) / 2 + ")") + .attr('width', width + margin.left + margin.right) + .attr('height', height + margin.top + margin.bottom) + .append('g') + .attr('transform', 'translate(' + (container_width - width) / 2 + ',' + (container_height - height) / 2 + ')') // reset sorting this.rowSortOrder = false; @@ -264,35 +264,35 @@ dataRange[dataRangeMax] = this.max; // create legend - var legend = this.svg.selectAll(".legend") + var legend = this.svg.selectAll('.legend') .data(dataRange) - .enter().append("g") - .attr("class", "legend"); + .enter().append('g') + .attr('class', 'legend'); // add boxes - legend.append("rect") - .attr("x", function(d, i) { + legend.append('rect') + .attr('x', function(d, i) { return legendCellWidth * i; }) - .attr("y", height + cellSize) - .attr("width", legendCellWidth) - .attr("height", cellSize) - .style("fill", function(d, i) { + .attr('y', height + cellSize) + .attr('width', legendCellWidth) + .attr('height', cellSize) + .style('fill', function(d, i) { return self.options.colors[i]; }); // add text - legend.append("text") - .attr("class", "mono") + legend.append('text') + .attr('class', 'mono') .text(function(d) { return d; }) - .attr("width", legendCellWidth) - .attr("x", function(d, i) { + .attr('width', legendCellWidth) + .attr('x', function(d, i) { return legendCellWidth * i; }) - .attr("y", height + cellSize) - .style("font-size", cellSize + "px"); + .attr('y', height + cellSize) + .style('font-size', cellSize + 'px'); }, // build column labels @@ -306,36 +306,36 @@ var colLabel = this.colLabel; // column labels - var colLabels = this.svg.append("g") - .selectAll(".colLabelg") + var colLabels = this.svg.append('g') + .selectAll('.colLabelg') .data(colLabel) .enter() - .append("text") + .append('text') .text(function (d) { return d; }) - .attr("x", 0) - .attr("y", function (d, i) { + .attr('x', 0) + .attr('y', function (d, i) { return colIndex.indexOf(i) * cellSize; }) - .style("font-size", cellSize + "px") - .style("text-anchor", "left") - .attr("transform", "translate(" + cellSize / 2 + ", -17) rotate (-90)") - .attr("class", function (d, i) { - return "colLabel mono c" + i; + .style('font-size', cellSize + 'px') + .style('text-anchor', 'left') + .attr('transform', 'translate(' + cellSize / 2 + ', -17) rotate (-90)') + .attr('class', function (d, i) { + return 'colLabel mono c' + i; }) - .on("mouseover", function(d) { - d3.select(this).classed("text-hover",true); - d3.select(this).style("font-size", parseInt(cellSize * 1.3) + "px"); + .on('mouseover', function(d) { + d3.select(this).classed('text-hover',true); + d3.select(this).style('font-size', parseInt(cellSize * 1.3) + 'px'); }) - .on("mouseout" , function(d) { - d3.select(this).classed("text-hover",false); - d3.select(this).style("font-size", parseInt(cellSize) + "px"); + .on('mouseout' , function(d) { + d3.select(this).classed('text-hover',false); + d3.select(this).style('font-size', parseInt(cellSize) + 'px'); }) - .on("click", function(d, i) { + .on('click', function(d, i) { self.colSortOrder=!self.colSortOrder; - self._sortByLabel("c", i, self.colSortOrder); - d3.select("#order").property("selectedIndex", 4).node().focus(); + self._sortByLabel('c', i, self.colSortOrder); + d3.select('#order').property('selectedIndex', 4).node().focus(); }); }, @@ -350,36 +350,36 @@ var rowLabel = this.rowLabel; // draw labels - var rowLabels = this.svg.append("g") - .selectAll(".rowLabelg") + var rowLabels = this.svg.append('g') + .selectAll('.rowLabelg') .data(rowLabel) .enter() - .append("text") + .append('text') .text(function (d) { return d; }) - .attr("x", 0) - .attr("y", function (d, i) { + .attr('x', 0) + .attr('y', function (d, i) { return rowIndex.indexOf(i) * cellSize; }) - .style("font-size", cellSize + "px") - .style("text-anchor", "end") - .attr("transform", "translate(-10," + cellSize / 1.5 + ")") - .attr("class", function (d, i) { - return "rowLabel mono r" + i; + .style('font-size', cellSize + 'px') + .style('text-anchor', 'end') + .attr('transform', 'translate(-10,' + cellSize / 1.5 + ')') + .attr('class', function (d, i) { + return 'rowLabel mono r' + i; } ) - .on("mouseover", function(d) { - d3.select(this).classed("text-hover",true); - d3.select(this).style("font-size", parseInt(cellSize * 1.3) + "px"); + .on('mouseover', function(d) { + d3.select(this).classed('text-hover',true); + d3.select(this).style('font-size', parseInt(cellSize * 1.3) + 'px'); }) - .on("mouseout" , function(d) { - d3.select(this).classed("text-hover",false); - d3.select(this).style("font-size", parseInt(cellSize) + "px"); + .on('mouseout' , function(d) { + d3.select(this).classed('text-hover',false); + d3.select(this).style('font-size', parseInt(cellSize) + 'px'); }) - .on("click", function(d, i) { + .on('click', function(d, i) { self.rowSortOrder=!self.rowSortOrder; - self._sortByLabel("r", i, self.rowSortOrder); - d3.select("#order").property("selectedIndex", 4).node().focus(); + self._sortByLabel('r', i, self.rowSortOrder); + d3.select('#order').property('selectedIndex', 4).node().focus(); }); }, @@ -396,47 +396,47 @@ var colLabel = this.colLabel; // heat map - var heatMap = this.svg.append("g").attr("class","g3") - .selectAll(".cellg") + var heatMap = this.svg.append('g').attr('class','g3') + .selectAll('.cellg') .data(self.data, function(d) { - return d.row_rank + ":" + d.col_rank; + return d.row_rank + ':' + d.col_rank; }) .enter() - .append("rect") - .attr("x", function(d) { + .append('rect') + .attr('x', function(d) { return colIndex.indexOf(d.col_rank) * cellSize; }) - .attr("y", function(d) { + .attr('y', function(d) { return rowIndex.indexOf(d.row_rank) * cellSize; }) - .attr("class", function(d){ - return "cell cell-border cr" + d.row_rank + " cc" + d.col_rank; + .attr('class', function(d){ + return 'cell cell-border cr' + d.row_rank + ' cc' + d.col_rank; }) - .attr("width", cellSize) - .attr("height", cellSize) - .style("fill", function(d) { + .attr('width', cellSize) + .attr('height', cellSize) + .style('fill', function(d) { return self.colorScale(d.value); }) - .on("mouseover", function(d){ + .on('mouseover', function(d){ // highlight text - d3.select(this).classed("cell-hover",true); - d3.selectAll(".rowLabel").classed("text-highlight",function(r,ri){ return ri==(d.row_rank);}); - d3.selectAll(".colLabel").classed("text-highlight",function(c,ci){ return ci==(d.col_rank);}); + d3.select(this).classed('cell-hover',true); + d3.selectAll('.rowLabel').classed('text-highlight',function(r,ri){ return ri==(d.row_rank);}); + d3.selectAll('.colLabel').classed('text-highlight',function(c,ci){ return ci==(d.col_rank);}); // update the tooltip position and value - d3.select("#heatmap-tooltip") - .style("left", (d3.event.pageX+10) + "px") - .style("top", (d3.event.pageY-10) + "px") - .select("#value") - .text("Label: " + rowLabel[d.row_rank] + " | " + colLabel[d.col_rank] + ", Value: " + d.value); + d3.select('#heatmap-tooltip') + .style('left', (d3.event.pageX+10) + 'px') + .style('top', (d3.event.pageY-10) + 'px') + .select('#value') + .text('Label: ' + rowLabel[d.row_rank] + ' | ' + colLabel[d.col_rank] + ', Value: ' + d.value); // show the tooltip - d3.select("#heatmap-tooltip").classed("hidden", false); + d3.select('#heatmap-tooltip').classed('hidden', false); }) - .on("mouseout", function(){ - d3.select(this).classed("cell-hover",false); - d3.selectAll(".rowLabel").classed("text-highlight",false); - d3.selectAll(".colLabel").classed("text-highlight",false); - d3.select("#heatmap-tooltip").classed("hidden", true); + .on('mouseout', function(){ + d3.select(this).classed('cell-hover',false); + d3.selectAll('.rowLabel').classed('text-highlight',false); + d3.selectAll('.colLabel').classed('text-highlight',false); + d3.select('#heatmap-tooltip').classed('hidden', true); }); }, @@ -450,7 +450,7 @@ // collect cells var cells=[]; - t.selectAll(".c" + rORc + i) + t.selectAll('.c' + rORc + i) .filter(function(ce){ cells.push(ce); }); @@ -465,7 +465,7 @@ }); // rows or columns - if(rORc == "r") { + if(rORc == 'r') { // get sorted key list var sorted = []; for (var i in cells) { @@ -473,14 +473,14 @@ } // sort cells - t.selectAll(".cell") - .attr("x", function(d) { + t.selectAll('.cell') + .attr('x', function(d) { return sorted.indexOf(d.col_rank) * cellSize; }); // sort labels - t.selectAll(".colLabel") - .attr("y", function (d, i) { + t.selectAll('.colLabel') + .attr('y', function (d, i) { return sorted.indexOf(i) * cellSize; }); } else { @@ -491,14 +491,14 @@ } // sort cells - t.selectAll(".cell") - .attr("y", function(d) { + t.selectAll('.cell') + .attr('y', function(d) { return sorted.indexOf(d.row_rank) * cellSize; }); // sort labels - t.selectAll(".rowLabel") - .attr("y", function (d, i) { + t.selectAll('.rowLabel') + .attr('y', function (d, i) { return sorted.indexOf(i) * cellSize; }); } @@ -518,60 +518,60 @@ // set duration / select element var t = this.svg.transition().duration(this.options.pace); - if(value=="hclust"){ - t.selectAll(".cell") - .attr("x", function(d) { + if(value=='hclust'){ + t.selectAll('.cell') + .attr('x', function(d) { return colIndex.indexOf(d.col_rank) * cellSize; }) - .attr("y", function(d) { + .attr('y', function(d) { return rowIndex.indexOf(d.row_rank) * cellSize; }); - t.selectAll(".rowLabel") - .attr("y", function(d, i) { + t.selectAll('.rowLabel') + .attr('y', function(d, i) { return rowIndex.indexOf(i) * cellSize; }); - t.selectAll(".colLabel") - .attr("y", function(d, i) { + t.selectAll('.colLabel') + .attr('y', function(d, i) { return colIndex.indexOf(i) * cellSize; }); - } else if (value=="byboth") { - t.selectAll(".cell") - .attr("x", function(d) { + } else if (value=='byboth') { + t.selectAll('.cell') + .attr('x', function(d) { return d.col_rank * cellSize; }) - .attr("y", function(d) { + .attr('y', function(d) { return d.row_rank * cellSize; }); - t.selectAll(".rowLabel") - .attr("y", function (d, i) { + t.selectAll('.rowLabel') + .attr('y', function (d, i) { return i * cellSize; }); - t.selectAll(".colLabel") - .attr("y", function (d, i) { + t.selectAll('.colLabel') + .attr('y', function (d, i) { return i * cellSize; }); - } else if (value=="byrow") { - t.selectAll(".cell") - .attr("y", function(d) { + } else if (value=='byrow') { + t.selectAll('.cell') + .attr('y', function(d) { return d.row_rank * cellSize; }); - t.selectAll(".rowLabel") - .attr("y", function (d, i) { + t.selectAll('.rowLabel') + .attr('y', function (d, i) { return i * cellSize; }); - } else if (value=="bycol"){ - t.selectAll(".cell") - .attr("x", function(d) { + } else if (value=='bycol'){ + t.selectAll('.cell') + .attr('x', function(d) { return d.col_rank * cellSize; }); - t.selectAll(".colLabel") - .attr("y", function (d, i) { + t.selectAll('.colLabel') + .attr('y', function (d, i) { return i * cellSize; }); } @@ -582,35 +582,35 @@ // // selection // - var sa=d3.select(".g3") - .on("mousedown", function() { + var sa=d3.select('.g3') + .on('mousedown', function() { if( !d3.event.altKey) { - d3.selectAll(".cell-selected").classed("cell-selected", false); - d3.selectAll(".rowLabel").classed("text-selected", false); - d3.selectAll(".colLabel").classed("text-selected", false); + d3.selectAll('.cell-selected').classed('cell-selected', false); + d3.selectAll('.rowLabel').classed('text-selected', false); + d3.selectAll('.colLabel').classed('text-selected', false); } var p = d3.mouse(this); - sa.append("rect") + sa.append('rect') .attr({ rx : 0, ry : 0, - class : "selection", + class : 'selection', x : p[0], y : p[1], width : 1, height : 1 }) }) - .on("mousemove", function() { - var s = sa.select("rect.selection"); + .on('mousemove', function() { + var s = sa.select('rect.selection'); if(!s.empty()) { var p = d3.mouse(this), d = { - x : parseInt(s.attr("x"), 10), - y : parseInt(s.attr("y"), 10), - width : parseInt(s.attr("width"), 10), - height : parseInt(s.attr("height"), 10) + x : parseInt(s.attr('x'), 10), + y : parseInt(s.attr('y'), 10), + width : parseInt(s.attr('width'), 10), + height : parseInt(s.attr('height'), 10) }, move = { x : p[0] - d.x, @@ -633,46 +633,46 @@ s.attr(d); // deselect all temporary selected state objects - d3.selectAll(".cell-selection.cell-selected").classed("cell-selected", false); - d3.selectAll(".text-selection.text-selected").classed("text-selected",false); - d3.selectAll(".cell").filter(function(cell_d, i) { - if(!d3.select(this).classed("cell-selected") && + d3.selectAll('.cell-selection.cell-selected').classed('cell-selected', false); + d3.selectAll('.text-selection.text-selected').classed('text-selected',false); + d3.selectAll('.cell').filter(function(cell_d, i) { + if(!d3.select(this).classed('cell-selected') && // inner circle inside selection frame (this.x.baseVal.value)+cellSize >= d.x && (this.x.baseVal.value)<=d.x+d.width && (this.y.baseVal.value)+cellSize >= d.y && (this.y.baseVal.value)<=d.y+d.height) { d3.select(this) - .classed("cell-selection", true) - .classed("cell-selected", true); + .classed('cell-selection', true) + .classed('cell-selected', true); - d3.select(".r"+(cell_d.row_rank)) - .classed("text-selection",true) - .classed("text-selected",true); + d3.select('.r'+(cell_d.row_rank)) + .classed('text-selection',true) + .classed('text-selected',true); - d3.select(".c"+(cell_d.col_rank)) - .classed("text-selection",true) - .classed("text-selected",true); + d3.select('.c'+(cell_d.col_rank)) + .classed('text-selection',true) + .classed('text-selected',true); } }); } }) - .on("mouseup", function() { + .on('mouseup', function() { // remove selection frame - sa.selectAll("rect.selection").remove(); + sa.selectAll('rect.selection').remove(); // remove temporary selection marker class - d3.selectAll(".cell-selection").classed("cell-selection", false); - d3.selectAll(".text-selection").classed("text-selection",false); + d3.selectAll('.cell-selection').classed('cell-selection', false); + d3.selectAll('.text-selection').classed('text-selection', false); }) - .on("mouseout", function() { + .on('mouseout', function() { if(d3.event.relatedTarget.tagName=='html') { // remove selection frame - sa.selectAll("rect.selection").remove(); + sa.selectAll('rect.selection').remove(); // remove temporary selection marker class - d3.selectAll(".cell-selection").classed("cell-selection", false); - d3.selectAll(".rowLabel").classed("text-selected",false); - d3.selectAll(".colLabel").classed("text-selected",false); + d3.selectAll('.cell-selection').classed('cell-selection', false); + d3.selectAll('.rowLabel').classed('text-selected',false); + d3.selectAll('.colLabel').classed('text-selected',false); } }); }, diff -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 -r 21121d6283a95942061819f5e788ab41cfc1c000 config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js +++ b/config/plugins/visualizations/charts/static/charts/heatmap/heatmap.js @@ -1,5 +1,6 @@ // dependencies -define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin'], function(Utils, HeatmapPlugin) { +define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin', 'plugin/charts/heatmap/heatmap-parameters'], +function(Utils, HeatmapPlugin, HeatmapParameters) { // widget return Backbone.View.extend( @@ -24,8 +25,9 @@ // draw plot var heatmap = new HeatmapPlugin({ - 'data' : group.values, - 'div' : self.options.canvas[group_index] + 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')], + 'data' : group.values, + 'div' : self.options.canvas[group_index] }); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: data libraries: first take on shareable url for datasets
by commits-noreply＠bitbucket.org 03 May '14

03 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9dd03d95b91c/ Changeset: 9dd03d95b91c User: martenson Date: 2014-05-03 00:00:23 Summary: data libraries: first take on shareable url for datasets Affected #: 6 files diff -r b852505038a8c3a05d0320ad7d00dccf7969a864 -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -30,6 +30,7 @@ routes: { "" : "libraries", "folders/:id" : "folder_content", + "folders/:folder_id/datasets/:dataset_id" : "dataset_detail", "folders/:folder_id/download/:format" : "download" } }); @@ -88,6 +89,15 @@ } }); + this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){ + if (Galaxy.libraries.folderToolbarView){ + Galaxy.libraries.folderToolbarView.$el.unbind('click'); + } + Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: folder_id}); + Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id, dataset_id: dataset_id}); + // Galaxy.libraries.folderListView.rowViews.get(dataset_id).showDatasetDetails(); + }); + Backbone.history.start({pushState: false}); } }); diff -r b852505038a8c3a05d0320ad7d00dccf7969a864 -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 static/scripts/mvc/library/library-folderlist-view.js --- a/static/scripts/mvc/library/library-folderlist-view.js +++ b/static/scripts/mvc/library/library-folderlist-view.js @@ -32,10 +32,12 @@ 'click .dataset_row' : 'selectClickedRow', 'click .sort-folder-link' : 'sort_clicked' }, + + // cache of rendered views + rowViews: {}, initialize : function(options){ this.options = _.defaults(this.options || {}, options); - this.fetchFolder(); }, @@ -62,6 +64,9 @@ that.folder_container = folder_container; that.render(); that.addAll(folder_container.get('folder').models); + if (that.options.dataset_id){ + _.findWhere(that.rowViews, {id: that.options.dataset_id}).showDatasetDetails(); + } }, error: function(model, response){ if (typeof response.responseJSON !== "undefined"){ @@ -148,7 +153,12 @@ this.options.contains_file = true; model.set('readable_size', this.size_to_string(model.get('file_size'))); } + model.set('folder_id', this.id); var rowView = new mod_library_folderrow_view.FolderRowView(model); + + // save new rowView to cache + this.rowViews[model.get('id')] = rowView; + this.$el.find('#first_folder_item').after(rowView.el); $('.deleted_dataset').hover(function() { diff -r b852505038a8c3a05d0320ad7d00dccf7969a864 -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 static/scripts/mvc/library/library-folderrow-view.js --- a/static/scripts/mvc/library/library-folderrow-view.js +++ b/static/scripts/mvc/library/library-folderrow-view.js @@ -15,7 +15,7 @@ lastSelectedHistory: '', events: { - 'click .library-dataset' : 'showDatasetDetails', + // 'click .library-dataset' : 'showDatasetDetails', 'click .undelete_dataset_btn' : 'undelete_dataset' }, @@ -49,9 +49,10 @@ }, //show modal with current dataset info - showDatasetDetails : function(event){ + // showDatasetDetails : function(event){ + showDatasetDetails : function(){ // prevent default - event.preventDefault(); + // event.preventDefault(); var id = this.id; @@ -270,7 +271,7 @@ tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>'); tmpl_array.push(' </td>'); tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); - tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset + tmpl_array.push(' <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated diff -r b852505038a8c3a05d0320ad7d00dccf7969a864 -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view"],function(e,c,g,k,h,a,f,d,i){var l=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var j=k.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new j({id:"global-lib-prefs"});this.library_router=new l();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new d.LibraryToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:m});Galaxy.libraries.folderListView=new a.FolderListView({id:m})});this.library_router.on("route:download",function(m,n){if($("#folder_list_body").find(":checked").length===0){g.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view"],function(e,c,g,k,h,a,f,d,i){var l=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/download/:format":"download"}});var j=k.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new j({id:"global-lib-prefs"});this.library_router=new l();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new d.LibraryToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:m});Galaxy.libraries.folderListView=new a.FolderListView({id:m})});this.library_router.on("route:download",function(m,n){if($("#folder_list_body").find(":checked").length===0){g.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(n,m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:n});Galaxy.libraries.folderListView=new a.FolderListView({id:n,dataset_id:m})});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}}); \ No newline at end of file diff -r b852505038a8c3a05d0320ad7d00dccf7969a864 -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 static/scripts/packed/mvc/library/library-folderlist-view.js --- a/static/scripts/packed/mvc/library/library-folderlist-view.js +++ b/static/scripts/packed/mvc/library/library-folderlist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},initialize:function(g){this.options=_.defaults(this.options||{},g);this.fetchFolder()},fetchFolder:function(g){var g=g||{};this.options.include_deleted=g.include_deleted;var h=this;this.collection=new d.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(i){h.folder_container=i;h.render();h.addAll(i.get("folder").models)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},render:function(g){this.options=_.defaults(this.options,g);var h=this.templateFolder();var i=this.folderContainer.attributes.metadata.full_path;var j;if(i.length===1){j=0}else{j=i[i.length-2][0]}this.$el.html(h({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:j,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var g=this.folderContainer.attributes.metadata;g.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(g);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(g){_.each(g.reverse(),function(h){Galaxy.libraries.folderListView.collection.add(h)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var g=this;_.each(this.collection.models.reverse(),function(h){g.renderOne(h)});this.postRender()},renderOne:function(h){if(h.get("data_type")!=="folder"){this.options.contains_file=true;h.set("readable_size",this.size_to_string(h.get("file_size")))}var g=new a.FolderRowView(h);this.$el.find("#first_folder_item").after(g.el);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(g){this.$el.find("#"+g.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(g){g.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){return this.collection.sortByNameAsc()}else{if(g==="desc"){return this.collection.sortByNameDesc()}}}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);if(g){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(h){var j="";var g;var i;if(h.target.localName==="input"){j=h.target;g=$(h.target.parentElement.parentElement);i="input"}else{if(h.target.localName==="td"){j=$("#"+h.target.parentElement.id).find(":checkbox")[0];g=$(h.target.parentElement);i="td"}}if(j.checked){if(i==="td"){j.checked="";this.makeWhiteRow(g)}else{if(i==="input"){this.makeDarkRow(g)}}}else{if(i==="td"){j.checked="selected";this.makeDarkRow(g)}else{if(i==="input"){this.makeWhiteRow(g)}}}},makeDarkRow:function(g){g.removeClass("light");g.find("a").removeClass("light");g.addClass("dark");g.find("a").addClass("dark");g.find("span").removeClass("fa-file-o");g.find("span").addClass("fa-file")},makeWhiteRow:function(g){g.removeClass("dark");g.find("a").removeClass("dark");g.addClass("light");g.find("a").addClass("light");g.find("span").addClass("fa-file-o");g.find("span").removeClass("fa-file")},templateFolder:function(){var g=[];g.push('<ol class="breadcrumb">');g.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');g.push(" <% _.each(path, function(path_item) { %>");g.push(" <% if (path_item[0] != id) { %>");g.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');g.push("<% } else { %>");g.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');g.push(" <% } %>");g.push(" <% }); %>");g.push("</ol>");g.push('<table id="folder_table" class="grid table table-condensed">');g.push(" <thead>");g.push(' <th class="button_heading"></th>');g.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');g.push(' <th style="width:30%;"><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');g.push(" <th>data type</th>");g.push(" <th>size</th>");g.push(" <th>time updated (UTC)</th>");g.push(' <th style="width:15%;"></th> ');g.push(" </thead>");g.push(' <tbody id="folder_list_body">');g.push(' <tr id="first_folder_item">');g.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" </tr>");g.push(" </tbody>");g.push("</table>");g.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents.</div>');return _.template(g.join(""))}});return{FolderListView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},rowViews:{},initialize:function(g){this.options=_.defaults(this.options||{},g);this.fetchFolder()},fetchFolder:function(g){var g=g||{};this.options.include_deleted=g.include_deleted;var h=this;this.collection=new d.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(i){h.folder_container=i;h.render();h.addAll(i.get("folder").models);if(h.options.dataset_id){_.findWhere(h.rowViews,{id:h.options.dataset_id}).showDatasetDetails()}},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},render:function(g){this.options=_.defaults(this.options,g);var h=this.templateFolder();var i=this.folderContainer.attributes.metadata.full_path;var j;if(i.length===1){j=0}else{j=i[i.length-2][0]}this.$el.html(h({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:j,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var g=this.folderContainer.attributes.metadata;g.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(g);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(g){_.each(g.reverse(),function(h){Galaxy.libraries.folderListView.collection.add(h)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var g=this;_.each(this.collection.models.reverse(),function(h){g.renderOne(h)});this.postRender()},renderOne:function(h){if(h.get("data_type")!=="folder"){this.options.contains_file=true;h.set("readable_size",this.size_to_string(h.get("file_size")))}h.set("folder_id",this.id);var g=new a.FolderRowView(h);this.rowViews[h.get("id")]=g;this.$el.find("#first_folder_item").after(g.el);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(g){this.$el.find("#"+g.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(g){g.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){return this.collection.sortByNameAsc()}else{if(g==="desc"){return this.collection.sortByNameDesc()}}}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);if(g){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(h){var j="";var g;var i;if(h.target.localName==="input"){j=h.target;g=$(h.target.parentElement.parentElement);i="input"}else{if(h.target.localName==="td"){j=$("#"+h.target.parentElement.id).find(":checkbox")[0];g=$(h.target.parentElement);i="td"}}if(j.checked){if(i==="td"){j.checked="";this.makeWhiteRow(g)}else{if(i==="input"){this.makeDarkRow(g)}}}else{if(i==="td"){j.checked="selected";this.makeDarkRow(g)}else{if(i==="input"){this.makeWhiteRow(g)}}}},makeDarkRow:function(g){g.removeClass("light");g.find("a").removeClass("light");g.addClass("dark");g.find("a").addClass("dark");g.find("span").removeClass("fa-file-o");g.find("span").addClass("fa-file")},makeWhiteRow:function(g){g.removeClass("dark");g.find("a").removeClass("dark");g.addClass("light");g.find("a").addClass("light");g.find("span").addClass("fa-file-o");g.find("span").removeClass("fa-file")},templateFolder:function(){var g=[];g.push('<ol class="breadcrumb">');g.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');g.push(" <% _.each(path, function(path_item) { %>");g.push(" <% if (path_item[0] != id) { %>");g.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');g.push("<% } else { %>");g.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');g.push(" <% } %>");g.push(" <% }); %>");g.push("</ol>");g.push('<table id="folder_table" class="grid table table-condensed">');g.push(" <thead>");g.push(' <th class="button_heading"></th>');g.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');g.push(' <th style="width:30%;"><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');g.push(" <th>data type</th>");g.push(" <th>size</th>");g.push(" <th>time updated (UTC)</th>");g.push(' <th style="width:15%;"></th> ');g.push(" </thead>");g.push(' <tbody id="folder_list_body">');g.push(' <tr id="first_folder_item">');g.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" </tr>");g.push(" </tbody>");g.push("</table>");g.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents.</div>');return _.template(g.join(""))}});return{FolderListView:b}}); \ No newline at end of file diff -r b852505038a8c3a05d0320ad7d00dccf7969a864 -r 9dd03d95b91c22c1a35aa6328e2d7261705fe454 static/scripts/packed/mvc/library/library-folderrow-view.js --- a/static/scripts/packed/mvc/library/library-folderrow-view.js +++ b/static/scripts/packed/mvc/library/library-folderrow-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .library-dataset":"showDatasetDetails","click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(f){this.render(f)},render:function(f){var g=null;if(f.get("type")==="folder"){this.options.type="folder";g=this.templateRowFolder()}else{this.options.type="file";if(f.get("deleted")){g=this.templateRowDeletedFile()}else{g=this.templateRowFile()}}this.setElement(g({content_item:f}));this.$el.show();return this},showDatasetDetails:function(i){i.preventDefault();var j=this.id;var h=new c.Item();var g=new c.GalaxyHistories();h.id=j;var f=this;h.fetch({success:function(k){g.fetch({success:function(l){f.renderModalAfterFetch(k,l)},error:function(m,l){if(typeof l.responseJSON!=="undefined"){e.error(l.responseJSON.err_msg)}else{e.error("An error occured during fetching histories:(")}f.renderModalAfterFetch(k)}})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){e.error(k.responseJSON.err_msg)}else{e.error("An error occured during loading dataset details :(")}}})},renderModalAfterFetch:function(k,h){var i=this.size_to_string(k.get("file_size"));var j=_.template(this.templateDatasetModal(),{item:k,size:i});var g=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:j,buttons:{Import:function(){g.importCurrentIntoHistory()},Download:function(){g.downloadCurrent()},Close:function(){g.modal.hide()}}});$(".peek").html(k.get("peek"));if(typeof history.models!==undefined){var f=_.template(this.templateHistorySelectInModal(),{histories:h.models});$(this.modal.elMain).find(".buttons").prepend(f);if(g.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(g.lastSelectedHistory)}}},size_to_string:function(f){var g="";if(f>=100000000000){f=f/100000000000;g="TB"}else{if(f>=100000000){f=f/100000000;g="GB"}else{if(f>=100000){f=f/100000;g="MB"}else{if(f>=100){f=f/100;g="KB"}else{f=f*10;g="b"}}}}return(Math.round(f)/10)+g},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var f=[];f.push($("#id_row").attr("data-id"));var g="/api/libraries/datasets/download/uncompressed";var h={ldda_ids:f};this.processDownload(g,h);this.modal.enableButton("Import");this.modal.enableButton("Download")},processDownload:function(g,h,i){if(g&&h){h=typeof h=="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var h=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=h;var f=$("#id_row").attr("data-id");var i=new c.HistoryItem();var g=this;i.url=i.urlRoot+h+"/contents";i.save({content:f,source:"library"},{success:function(){e.success("Dataset imported");g.modal.enableButton("Import");g.modal.enableButton("Download")},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error("Dataset not imported. "+j.responseJSON.err_msg)}else{e.error("An error occured! Dataset not imported. Please try again.")}g.modal.enableButton("Import");g.modal.enableButton("Download")}})},undelete_dataset:function(g){$(".tooltip").hide();var f=$(g.target).closest("tr")[0].id;var h=Galaxy.libraries.folderListView.collection.get(f);h.url=h.urlRoot+h.id+"?undelete=true";h.destroy({success:function(j,i){Galaxy.libraries.folderListView.collection.remove(f);var k=new c.Item(i);Galaxy.libraries.folderListView.collection.add(k);e.success("Dataset undeleted")},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error("Dataset was not undeleted. "+i.responseJSON.err_msg)}else{e.error("An error occured! Dataset was not undeleted. Please try again.")}}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>');tmpl_array.push(" <span>(empty folder)</span>");tmpl_array.push(" <% } %>");tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span></td>');tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(' <td class="right-center"><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateDatasetModal:function(){var f=[];f.push('<div class="modal_table">');f.push(' <table class="grid table table-striped table-condensed">');f.push(" <tr>");f.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');f.push(' <td><%= _.escape(item.get("name")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Data type</th>');f.push(' <td><%= _.escape(item.get("data_type")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Genome build</th>');f.push(' <td><%= _.escape(item.get("genome_build")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Size</th>');f.push(" <td><%= _.escape(size) %></td>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Date uploaded (UTC)</th>');f.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Uploaded by</th>');f.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');f.push(" </tr>");f.push(' <tr scope="row">');f.push(' <th scope="row">Data Lines</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Comment Lines</th>');f.push(' <% if (item.get("metadata_comment_lines") === "") { %>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');f.push(" <% } else { %>");f.push(' <td scope="row">unknown</td>');f.push(" <% } %>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Number of Columns</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Column Types</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Miscellaneous information</th>');f.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');f.push(" </tr>");f.push(" </table>");f.push(' <pre class="peek">');f.push(" </pre>");f.push("</div>");return f.join("")},templateHistorySelectInModal:function(){var f=[];f.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return f.join("")}});return{FolderRowView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(f){this.render(f)},render:function(f){var g=null;if(f.get("type")==="folder"){this.options.type="folder";g=this.templateRowFolder()}else{this.options.type="file";if(f.get("deleted")){g=this.templateRowDeletedFile()}else{g=this.templateRowFile()}}this.setElement(g({content_item:f}));this.$el.show();return this},showDatasetDetails:function(){var i=this.id;var h=new c.Item();var g=new c.GalaxyHistories();h.id=i;var f=this;h.fetch({success:function(j){g.fetch({success:function(k){f.renderModalAfterFetch(j,k)},error:function(l,k){if(typeof k.responseJSON!=="undefined"){e.error(k.responseJSON.err_msg)}else{e.error("An error occured during fetching histories:(")}f.renderModalAfterFetch(j)}})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error occured during loading dataset details :(")}}})},renderModalAfterFetch:function(k,h){var i=this.size_to_string(k.get("file_size"));var j=_.template(this.templateDatasetModal(),{item:k,size:i});var g=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:j,buttons:{Import:function(){g.importCurrentIntoHistory()},Download:function(){g.downloadCurrent()},Close:function(){g.modal.hide()}}});$(".peek").html(k.get("peek"));if(typeof history.models!==undefined){var f=_.template(this.templateHistorySelectInModal(),{histories:h.models});$(this.modal.elMain).find(".buttons").prepend(f);if(g.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(g.lastSelectedHistory)}}},size_to_string:function(f){var g="";if(f>=100000000000){f=f/100000000000;g="TB"}else{if(f>=100000000){f=f/100000000;g="GB"}else{if(f>=100000){f=f/100000;g="MB"}else{if(f>=100){f=f/100;g="KB"}else{f=f*10;g="b"}}}}return(Math.round(f)/10)+g},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var f=[];f.push($("#id_row").attr("data-id"));var g="/api/libraries/datasets/download/uncompressed";var h={ldda_ids:f};this.processDownload(g,h);this.modal.enableButton("Import");this.modal.enableButton("Download")},processDownload:function(g,h,i){if(g&&h){h=typeof h=="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var h=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=h;var f=$("#id_row").attr("data-id");var i=new c.HistoryItem();var g=this;i.url=i.urlRoot+h+"/contents";i.save({content:f,source:"library"},{success:function(){e.success("Dataset imported");g.modal.enableButton("Import");g.modal.enableButton("Download")},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error("Dataset not imported. "+j.responseJSON.err_msg)}else{e.error("An error occured! Dataset not imported. Please try again.")}g.modal.enableButton("Import");g.modal.enableButton("Download")}})},undelete_dataset:function(g){$(".tooltip").hide();var f=$(g.target).closest("tr")[0].id;var h=Galaxy.libraries.folderListView.collection.get(f);h.url=h.urlRoot+h.id+"?undelete=true";h.destroy({success:function(j,i){Galaxy.libraries.folderListView.collection.remove(f);var k=new c.Item(i);Galaxy.libraries.folderListView.collection.add(k);e.success("Dataset undeleted")},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error("Dataset was not undeleted. "+i.responseJSON.err_msg)}else{e.error("An error occured! Dataset was not undeleted. Please try again.")}}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>');tmpl_array.push(" <span>(empty folder)</span>");tmpl_array.push(" <% } %>");tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span></td>');tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(' <td class="right-center"><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateDatasetModal:function(){var f=[];f.push('<div class="modal_table">');f.push(' <table class="grid table table-striped table-condensed">');f.push(" <tr>");f.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');f.push(' <td><%= _.escape(item.get("name")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Data type</th>');f.push(' <td><%= _.escape(item.get("data_type")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Genome build</th>');f.push(' <td><%= _.escape(item.get("genome_build")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Size</th>');f.push(" <td><%= _.escape(size) %></td>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Date uploaded (UTC)</th>');f.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Uploaded by</th>');f.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');f.push(" </tr>");f.push(' <tr scope="row">');f.push(' <th scope="row">Data Lines</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Comment Lines</th>');f.push(' <% if (item.get("metadata_comment_lines") === "") { %>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');f.push(" <% } else { %>");f.push(' <td scope="row">unknown</td>');f.push(" <% } %>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Number of Columns</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Column Types</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Miscellaneous information</th>');f.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');f.push(" </tr>");f.push(" </table>");f.push(' <pre class="peek">');f.push(" </pre>");f.push("</div>");return f.join("")},templateHistorySelectInModal:function(){var f=[];f.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return f.join("")}});return{FolderRowView:a}}); \ No newline at end of file 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: Jeremy Goecks: Put converted datasets in history and add note to merge copied converter code.
by commits-noreply＠bitbucket.org 02 May '14

02 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b852505038a8/ Changeset: b852505038a8 User: Jeremy Goecks Date: 2014-05-02 22:32:38 Summary: Put converted datasets in history and add note to merge copied converter code. Affected #: 2 files diff -r 41bb60076082ea46686a4bb9db8cb593b8f35851 -r b852505038a8c3a05d0320ad7d00dccf7969a864 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1564,8 +1564,7 @@ raise NoConverterException("A dependency (%s) is missing a converter." % dependency) except KeyError: pass # No deps - new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, set_output_history=False ).values()[0] - new_dataset.name = self.name + new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, set_output_history=True ).values()[0] assoc = ImplicitlyConvertedDatasetAssociation( parent=self, file_type=target_ext, dataset=new_dataset, metadata_safe=False ) session = trans.sa_session session.add( new_dataset ) diff -r 41bb60076082ea46686a4bb9db8cb593b8f35851 -r b852505038a8c3a05d0320ad7d00dccf7969a864 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -50,6 +50,7 @@ if converted_dataset: data = converted_dataset else: + # FIXME: merge with hda.get_converted_dataset() mode as it's nearly identical. #run converter here new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output=True, visible=False ).values()[0] new_data.hid = data.hid 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: devteam: Enhance the framework that supports discovery of tool dependencies' scripts that are in the same repository as the tool. This eliminates the requirement for setting a variable _SCRIPT_PATH in the tool_dependencies.xml and requirements tagset in a tool config. Now it only needs to be set in the tool config and it should look like: <requirement type="set_environment">PATH</requirement>
by commits-noreply＠bitbucket.org 02 May '14

02 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/41bb60076082/ Changeset: 41bb60076082 User: devteam Date: 2014-05-02 21:55:45 Summary: Enhance the framework that supports discovery of tool dependencies' scripts that are in the same repository as the tool. This eliminates the requirement for setting a variable _SCRIPT_PATH in the tool_dependencies.xml and requirements tagset in a tool config. Now it only needs to be set in the tool config and it should look like: <requirement type="set_environment">PATH</requirement> Affected #: 5 files diff -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 -r 41bb60076082ea46686a4bb9db8cb593b8f35851 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -289,6 +289,55 @@ raise Exception( message ) return handled_tool_dependencies +def handle_env_vars_for_set_environment_tool_dependency( app, tool_shed_repository, tool_shed_repository_install_dir ): + env_var_name = 'PATH' + install_dir = \ + tool_dependency_util.get_tool_dependency_install_dir( app=app, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + repository_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dependency_type='set_environment', + tool_dependency_name=env_var_name, + tool_dependency_version=None ) + env_var_dict = dict( name=env_var_name, action='prepend_to', value=tool_shed_repository_install_dir ) + if not os.path.exists( install_dir ): + os.makedirs( install_dir ) + status = app.install_model.ToolDependency.installation_status.INSTALLING + tool_dependency = \ + tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=env_var_name, + version=None, + type='set_environment', + status=status, + set_status=True ) + env_file_builder = EnvFileBuilder( install_dir ) + return_code = env_file_builder.append_line( make_executable=True, **env_var_dict ) + if return_code: + error_message = 'Error creating env.sh file for tool dependency %s, return_code: %s' % \ + ( str( tool_dependency.name ), str( return_code ) ) + log.debug( error_message ) + status = app.install_model.ToolDependency.installation_status.ERROR + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=status, + error_message=error_message, + remove_from_disk=False ) + else: + if tool_dependency.status not in [ app.install_model.ToolDependency.installation_status.ERROR, + app.install_model.ToolDependency.installation_status.INSTALLED ]: + status = app.install_model.ToolDependency.installation_status.INSTALLED + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=status, + error_message=None, + remove_from_disk=False ) + log.debug( 'Environment variable %s set in %s for tool dependency %s.' % \ + ( str( env_var_name ), str( install_dir ), str( tool_dependency.name ) ) ) + return tool_dependency + def install_and_build_package_via_fabric( app, tool_shed_repository, tool_dependency, actions_dict ): sa_session = app.install_model.context try: @@ -638,12 +687,20 @@ """ # TODO: Add support for a repository dependency definition within this tool dependency type's tag set. This should look something like # the following. See the implementation of support for this in the tool dependency package type's method above. + # This function is only called for set environment actions as defined below, not within an <install version="1.0"> tool + # dependency type. Here is an example of the tag set this function does handle: + # <action type="set_environment"> + # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + # </action> + # Here is an example of the tag set this function does not handle: # <set_environment version="1.0"> # <repository toolshed="<tool shed>" name="<repository name>" owner="<repository owner>" changeset_revision="<changeset revision>" /> # </set_environment> sa_session = app.install_model.context - tool_dependency = None + tool_dependencies = [] env_var_version = elem.get( 'version', '1.0' ) + tool_shed_repository_install_dir = fabric_util.get_tool_shed_repository_install_dir( app, tool_shed_repository ) + tool_shed_repository_install_dir_added_to_path = False for env_var_elem in elem: # Althoug we're in a loop here, this method will always return only a single ToolDependency or None. env_var_name = env_var_elem.get( 'name', None ) @@ -662,10 +719,10 @@ tool_dependency_type='set_environment', tool_dependency_name=env_var_name, tool_dependency_version=None ) - tool_shed_repository_install_dir = fabric_util.get_tool_shed_repository_install_dir( app, tool_shed_repository ) + install_environment = InstallEnvironment( tool_shed_repository_install_dir=tool_shed_repository_install_dir, + install_dir=install_dir ) env_var_dict = td_common_util.create_env_var_dict( elem=env_var_elem, - tool_dependency_install_dir=install_dir, - tool_shed_repository_install_dir=tool_shed_repository_install_dir ) + install_environment=install_environment ) if env_var_dict: if not os.path.exists( install_dir ): os.makedirs( install_dir ) @@ -714,7 +771,18 @@ status=status, error_message=error_message, remove_from_disk=False ) - return tool_dependency + if tool_dependency.status != app.install_model.ToolDependency.installation_status.ERROR: + if env_var_dict[ 'name' ] == 'PATH' and \ + env_var_dict[ 'action' ] in [ 'prepend_to', 'set_to', 'append_to' ] and \ + env_var_dict[ 'value' ] == install_environment.tool_shed_repository_install_dir: + tool_shed_repository_install_dir_added_to_path = True + tool_dependencies.append( tool_dependency ) + if not tool_shed_repository_install_dir_added_to_path: + tool_dependency = handle_env_vars_for_set_environment_tool_dependency( app, + tool_shed_repository, + tool_shed_repository_install_dir ) + tool_dependencies.append( tool_dependency ) + return tool_dependencies def strip_path( fpath ): if not fpath: diff -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 -r 41bb60076082ea46686a4bb9db8cb593b8f35851 lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -707,17 +707,22 @@ return env_var_dict def prepare_step( self, app, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ): + # This function is only called for set environment actions as defined above, not within a <set_environment> tool + # dependency type. Here is an example of the tag set this function does handle: # <action type="set_environment"> # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> # </action> + # Here is an example of the tag set this function does not handle: + # <action type="set_environment"> + # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + # </action> env_var_dicts = [] for env_elem in action_elem: if env_elem.tag == 'environment_variable': env_var_dict = \ td_common_util.create_env_var_dict( elem=env_elem, - tool_dependency_install_dir=install_environment.install_dir, - tool_shed_repository_install_dir=install_environment.tool_shed_repository_install_dir ) + install_environment=install_environment ) if env_var_dict: env_var_dicts.append( env_var_dict ) if env_var_dicts: diff -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 -r 41bb60076082ea46686a4bb9db8cb593b8f35851 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -168,10 +168,12 @@ return True return False -def create_env_var_dict( elem, tool_dependency_install_dir=None, tool_shed_repository_install_dir=None ): +def create_env_var_dict( elem, install_environment ): env_var_name = elem.get( 'name', 'PATH' ) env_var_action = elem.get( 'action', 'prepend_to' ) env_var_text = None + tool_dependency_install_dir = install_environment.install_dir + tool_shed_repository_install_dir = install_environment.tool_shed_repository_install_dir if elem.text and elem.text.find( 'REPOSITORY_INSTALL_DIR' ) >= 0: if tool_shed_repository_install_dir and elem.text.find( '$REPOSITORY_INSTALL_DIR' ) != -1: env_var_text = elem.text.replace( '$REPOSITORY_INSTALL_DIR', tool_shed_repository_install_dir ) diff -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 -r 41bb60076082ea46686a4bb9db8cb593b8f35851 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 @@ -349,9 +349,15 @@ requirement_dict[ 'status' ] = tool_dependency_status new_val.append( requirement_dict ) if tool_dependency_status in [ trans.install_model.ToolDependency.installation_status.INSTALLED ]: - installed_tool_dependencies[ td_key ] = new_val + if td_key in installed_tool_dependencies: + installed_tool_dependencies[ td_key ].extend( new_val ) + else: + installed_tool_dependencies[ td_key ] = new_val else: - missing_tool_dependencies[ td_key ] = new_val + if td_key in missing_tool_dependencies: + missing_tool_dependencies[ td_key ].extend( new_val ) + else: + missing_tool_dependencies[ td_key ] = new_val else: # The val dictionary looks something like this: # {'repository_name': 'xx', @@ -497,6 +503,7 @@ return installed_tool_dependencies root = tree.getroot() fabric_version_checked = False + set_environment_handled = False for elem in root: if elem.tag == 'package': # Only install the tool_dependency if it is not already installed and it is associated with a database record in the received @@ -556,21 +563,31 @@ # <set_environment version="1.0"> # <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> # </set_environment> + set_environment_handled = True try: - tool_dependency = set_environment( app, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ) + tool_dependencies = set_environment( app, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ) except Exception, e: error_message = "Error setting environment for tool dependency: %s" % str( e ) log.debug( error_message ) - if tool_dependency: - # Since there was an installation error, update the tool dependency status to Error. The remove_installation_path option must - # be left False here. - tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, - tool_dependency, - error_message, - remove_installation_path=False ) - if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED, - app.install_model.ToolDependency.installation_status.ERROR ]: - installed_tool_dependencies.append( tool_dependency ) + for tool_dependency in tool_dependencies: + if tool_dependency and tool_dependency.status == app.install_model.ToolDependency.installation_status.ERROR: + # Since there was an installation error, update the tool dependency status to Error. The remove_installation_path option must + # be left False here. + tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency, + error_message, + remove_installation_path=False ) + for tool_dependency in tool_dependencies: + if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED, + app.install_model.ToolDependency.installation_status.ERROR ]: + installed_tool_dependencies.append( tool_dependency ) + if not set_environment_handled: + element_attributes = dict( name='PATH', action='prepend_to' ) + generated_elem = xml_util.create_element( 'environment_variable', attributes=element_attributes, sub_elements=None ) + generated_elem.text = '$REPOSITORY_INSTALL_DIR' + generated_attr_tups = [ ( 'PATH', None, 'set_environment' ) ] + tool_dependencies = set_environment( app, generated_elem, tool_shed_repository, generated_attr_tups ) + installed_tool_dependencies.extend( tool_dependencies ) return installed_tool_dependencies def repository_dependency_needed_only_for_compiling_tool_dependency( repository, repository_dependency ): diff -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 -r 41bb60076082ea46686a4bb9db8cb593b8f35851 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -23,6 +23,7 @@ from tool_shed.galaxy_install.tool_dependencies import install_util from tool_shed.galaxy_install.tool_dependencies import td_common_util import tool_shed.repository_types.util as rt_util +from xml.etree import ElementTree as XmlET eggs.require( 'mercurial' ) @@ -921,7 +922,28 @@ invalid_tool_dependencies_dict = {} valid_repository_dependency_tups = [] invalid_repository_dependency_tups = [] + needs_set_environment_tool_dependency_for_path = False + tools_metadata = metadata_dict.get( 'tools', None ) + if tools_metadata is not None: + for tools_dict in tools_metadata: + requirements = tools_dict.get( 'requirements', None ) + if requirements is not None: + for requirements_dict in requirements: + if requirements_dict[ 'type' ] == 'set_environment' and requirements_dict[ 'name' ] == 'PATH': + needs_set_environment_tool_dependency_for_path = True + break description = root.get( 'description' ) + if needs_set_environment_tool_dependency_for_path: + # Add this to the in-memory XML tree that is parsed to determine the database tool dependency records. This will not + # modify the on-disk tool dependency definitions, but is needed in order for the tool to correctly source the env.sh + # file that was generated for the PATH variable. + # <set_environment version="1.0"> + # <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + # </set_environment> + env_var_elem_attributes = dict( name='PATH', action='prepend_to' ) + set_environment_elem = xml_util.create_element( 'set_environment', attributes=dict( version='1.0' ) ) + XmlET.SubElement( set_environment_elem, 'environment_variable', attrib=env_var_elem_attributes ) + root.append( set_environment_elem ) for elem in root: if elem.tag == 'package': valid_tool_dependencies_dict, invalid_tool_dependencies_dict, repository_dependency_tup, repository_dependency_is_valid, message = \ 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: carlfeberhard: History: cruft removal from controller and associated javascript
by commits-noreply＠bitbucket.org 02 May '14

02 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f79c07c4438/ Changeset: 2f79c07c4438 User: carlfeberhard Date: 2014-05-02 21:45:25 Summary: History: cruft removal from controller and associated javascript Affected #: 3 files diff -r 3f8e4852623187152ffaea5fd529fac2001c8316 -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -549,6 +549,7 @@ count += 1 return trans.show_ok_message( "%d datasets have been deleted permanently" % count, refresh_frames=['history'] ) + #TODO: use api instead @web.expose def delete_current( self, trans, purge=False ): """Delete just the active history -- this does not require a logged in user.""" @@ -604,6 +605,7 @@ trans.sa_session.add( history ) trans.sa_session.flush() return trans.show_ok_message( "Your datasets have been unhidden.", refresh_frames=refresh_frames ) + #TODO: used in index.mako @web.expose def resume_paused_jobs( self, trans, current=False, ids=None ): @@ -618,6 +620,7 @@ trans.sa_session.add( history ) trans.sa_session.flush() return trans.show_ok_message( "Your jobs have been resumed.", refresh_frames=refresh_frames ) + #TODO: used in index.mako @web.expose @web.require_login( "rate items" ) @@ -630,34 +633,7 @@ # Rate history. history_rating = self.rate_item( trans.sa_session, trans.get_user(), history, rating ) return self.get_ave_item_rating_data( trans.sa_session, history ) - - @web.expose - def rename_async( self, trans, id=None, new_name=None ): - history = self.get_history( trans, id ) - # Check that the history exists, and is either owned by the current - # user (if logged in) or the current history - assert history is not None - if history.user is None: - assert history == trans.get_history() - else: - assert history.user == trans.user - # Rename - new_name = sanitize_html( new_name ) - history.name = new_name - trans.sa_session.add( history ) - trans.sa_session.flush() - return new_name - - @web.expose - @web.require_login( "use Galaxy histories" ) - def annotate_async( self, trans, id, new_annotation=None, **kwargs ): - history = self.get_history( trans, id ) - if new_annotation: - # Sanitize annotation before adding it. - new_annotation = sanitize_html( new_annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), history, new_annotation ) - trans.sa_session.flush() - return new_annotation + #TODO: used in display_base.mako @web.expose # TODO: Remove require_login when users are warned that, if they are not @@ -686,6 +662,7 @@ self.queue_history_import( trans, archive_type=archive_type, archive_source=archive_source ) return trans.show_message( "Importing history from '%s'. \ This history will be visible when the import is complete" % archive_source ) + #TODO: used in this file and index.mako @web.expose def export_archive( self, trans, id=None, gzip=True, include_hidden=False, include_deleted=False ): @@ -719,6 +696,7 @@ return trans.show_message( "Exporting History '%(n)s'. Use this link to download \ the archive or import it to another Galaxy server: \ <a href='%(u)s'>%(u)s</a>" % ( { 'n' : history.name, 'u' : url } ) ) + #TODO: used in this file and index.mako @web.expose @web.json @@ -733,6 +711,7 @@ "link" : url_for(controller='history', action="display_by_username_and_slug", username=history.user.username, slug=history.slug ) } return return_dict + #TODO: used in page/editor.mako @web.expose @web.require_login( "set history's accessible flag" ) @@ -748,6 +727,7 @@ history.importable = importable trans.sa_session.flush() return + #TODO: used in page/editor.mako @web.expose def get_item_content_async( self, trans, id ): @@ -764,6 +744,7 @@ for dataset in datasets: dataset.annotation = self.get_item_annotation_str( trans.sa_session, history.user, dataset ) return trans.stream_template_mako( "/history/item_content.mako", item = history, item_data = datasets ) + #TODO: used in embed_base.mako @web.expose def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ): @@ -773,9 +754,12 @@ return ac_data = "" - for history in trans.sa_session.query( model.History ).filter_by( user=user ).filter( func.lower( model.History.name ) .like(q.lower() + "%") ): + for history in ( trans.sa_session.query( model.History ) + .filter_by( user=user ) + .filter( func.lower( model.History.name ).like(q.lower() + "%") ) ): ac_data = ac_data + history.name + "\n" return ac_data + #TODO: used in grid_base.mako @web.expose def imp( self, trans, id=None, confirm=False, **kwd ): @@ -852,6 +836,7 @@ Warning! If you import this history, you will lose your current history. <br>You can <a href="%s">continue and import this history</a> or %s. """ % ( web.url_for(controller='history', action='imp', id=id, confirm=True, referer=trans.request.referer ), referer_message ), use_panels=True ) + #TODO: used in history/view, display, embed @web.expose def view( self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True ): @@ -1390,51 +1375,4 @@ def get_item( self, trans, id ): return self.get_history( trans, id ) - - @web.json - def get_display_application_links( self, trans, hda_ids=None ): - """ - Returns external display application JSON data for all/given - HDAs within the current history. - """ - #TODO: fold into API and remove - try: - history = trans.get_history() - #TODO: allow id for more flexibility? (the following doesn't work if anonymous...) - #history = self.get_history( trans, id, check_ownership=True, check_accessible=True, deleted=None ) - if hda_ids: - unencoded_hda_ids = [ trans.security.decode_id( hda_id ) for hda_id in galaxy.util.listify( hda_ids ) ] - #TODO: this gets all - should narrow query by using hda_ids here - no way with this current method - hdas = self.get_history_datasets( trans, history, show_deleted=False, show_hidden=True, show_purged=False ) - - except Exception, exc: - log.error( 'Failed loading data for ids (%s): %s', hda_ids, str( exc ), exc_info=True ) - trans.response.status = 500 - return str( exc ) - - hda_display_links = [] - for hda in hdas: - # only get requested hdas - if hda_ids and hda.id not in unencoded_hda_ids: - continue - - hda_link_data = { 'id': trans.security.encode_id( hda.id ) } - # don't bail on entire list if one hda has an error; record and move on - try: - # 'old style': must be enabled in config (see universe_wsgi.ini) - if trans.app.config.enable_old_display_applications: - hda_link_data[ 'display_types' ] = self.get_old_display_applications( trans, hda ) - - # 'new style' - hda_link_data[ 'display_apps' ] = self.get_display_apps( trans, hda ) - - except Exception, exc: - log.error( 'Failed getting links, hda (%s): %s', hda_link_data[ 'id' ], str( exc ), exc_info=True ) - hda_link_data[ 'error' ] = str( exc ) - - hda_display_links.append( hda_link_data ) - - # send 'do not cache' headers to handle IE's caching of ajax get responses - trans.response.headers[ 'Cache-Control' ] = "max-age=0,no-cache,no-store" - trans.response.set_content_type( 'application/json' ) - return hda_display_links + #TODO: override of base ui controller? diff -r 3f8e4852623187152ffaea5fd529fac2001c8316 -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -34,26 +34,6 @@ // ........................................................................ urls urlRoot: galaxy_config.root + 'api/histories', - /** url for changing the name of the history */ - renameUrl : function(){ -//TODO: just use this.save() - var id = this.get( 'id' ); - if( !id ){ return undefined; } - return galaxy_config.root + 'history/rename_async?id=' + this.get( 'id' ); - }, - /** url for changing the annotation of the history */ - annotateUrl : function(){ - var id = this.get( 'id' ); - if( !id ){ return undefined; } - return galaxy_config.root + 'history/annotate_async?id=' + this.get( 'id' ); - }, - /** url for changing the tags of the history */ - tagUrl : function(){ - var id = this.get( 'id' ); - if( !id ){ return undefined; } - return galaxy_config.root + 'tag/get_tagging_elt_async?item_id=' + this.get( 'id' ) + '&item_class=History'; - }, - // ........................................................................ set up/tear down /** Set up the model * @param {Object} historyJSON model data for this History diff -r 3f8e4852623187152ffaea5fd529fac2001c8316 -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/base-mvc","utils/localization"],function(c,a,b){var e=Backbone.Model.extend(a.LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",renameUrl:function(){var g=this.get("id");if(!g){return undefined}return galaxy_config.root+"history/rename_async?id="+this.get("id")},annotateUrl:function(){var g=this.get("id");if(!g){return undefined}return galaxy_config.root+"history/annotate_async?id="+this.get("id")},tagUrl:function(){var g=this.get("id");if(!g){return undefined}return galaxy_config.root+"tag/get_tagging_elt_async?item_id="+this.get("id")+"&item_class=History"},initialize:function(h,i,g){g=g||{};this.logger=g.logger||null;this.log(this+".initialize:",h,i,g);this.hdas=new c.HDACollection(i||[],{historyId:this.get("id")});if(i&&_.isArray(i)){this.hdas.reset(i)}this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(h,k,g,j,i){this.errorHandler(h,k,g,j,i)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(h,g){if(this.hdas){this.hdas.historyId=g}},this)},errorHandler:function(h,k,g,j,i){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},hdaCount:function(){return _.reduce(_.values(this.get("state_details")),function(g,h){return g+h},0)},checkForUpdates:function(g){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(g)){g.call(this)}}return this},setUpdateTimeout:function(g){g=g||e.UPDATE_DELAY;var h=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){h.refresh()},g);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(h,g){h=h||[];g=g||{};var i=this;g.data=g.data||{};if(h.length){g.data.details=h.join(",")}var j=this.hdas.fetch(g);j.done(function(k){i.checkForUpdates(function(){this.fetch()})});return j},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});e.UPDATE_DELAY=4000;e.getHistoryData=function f(h,r){r=r||{};var l=r.hdaDetailIds||[];var n=jQuery.Deferred(),m=null;function i(s){return jQuery.ajax(galaxy_config.root+"api/histories/"+h)}function g(s){if(!s||!s.state_ids){return 0}return _.reduce(s.state_ids,function(t,v,u){return t+v.length},0)}function q(t){if(!g(t)){return[]}if(_.isFunction(l)){l=l(t)}var s=(l.length)?({details:l.join(",")}):({});return jQuery.ajax(galaxy_config.root+"api/histories/"+t.id+"/contents",{data:s})}var p=r.historyFn||i,o=r.hdaFn||q;var k=p(h);k.done(function(s){m=s;n.notify({status:"history data retrieved",historyJSON:m})});k.fail(function(u,s,t){n.reject(u,"loading the history")});var j=k.then(o);j.then(function(s){n.notify({status:"dataset data retrieved",historyJSON:m,hdaJSON:s});n.resolve(m,s)});j.fail(function(u,s,t){n.reject(u,"loading the datasets",{history:m})});return n};var d=Backbone.Collection.extend(a.LoggableMixin).extend({model:e,urlRoot:galaxy_config.root+"api/histories"});return{History:e,HistoryCollection:d}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/base-mvc","utils/localization"],function(c,a,b){var e=Backbone.Model.extend(a.LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(h,i,g){g=g||{};this.logger=g.logger||null;this.log(this+".initialize:",h,i,g);this.hdas=new c.HDACollection(i||[],{historyId:this.get("id")});if(i&&_.isArray(i)){this.hdas.reset(i)}this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(h,k,g,j,i){this.errorHandler(h,k,g,j,i)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(h,g){if(this.hdas){this.hdas.historyId=g}},this)},errorHandler:function(h,k,g,j,i){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},hdaCount:function(){return _.reduce(_.values(this.get("state_details")),function(g,h){return g+h},0)},checkForUpdates:function(g){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(g)){g.call(this)}}return this},setUpdateTimeout:function(g){g=g||e.UPDATE_DELAY;var h=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){h.refresh()},g);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(h,g){h=h||[];g=g||{};var i=this;g.data=g.data||{};if(h.length){g.data.details=h.join(",")}var j=this.hdas.fetch(g);j.done(function(k){i.checkForUpdates(function(){this.fetch()})});return j},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});e.UPDATE_DELAY=4000;e.getHistoryData=function f(h,r){r=r||{};var l=r.hdaDetailIds||[];var n=jQuery.Deferred(),m=null;function i(s){return jQuery.ajax(galaxy_config.root+"api/histories/"+h)}function g(s){if(!s||!s.state_ids){return 0}return _.reduce(s.state_ids,function(t,v,u){return t+v.length},0)}function q(t){if(!g(t)){return[]}if(_.isFunction(l)){l=l(t)}var s=(l.length)?({details:l.join(",")}):({});return jQuery.ajax(galaxy_config.root+"api/histories/"+t.id+"/contents",{data:s})}var p=r.historyFn||i,o=r.hdaFn||q;var k=p(h);k.done(function(s){m=s;n.notify({status:"history data retrieved",historyJSON:m})});k.fail(function(u,s,t){n.reject(u,"loading the history")});var j=k.then(o);j.then(function(s){n.notify({status:"dataset data retrieved",historyJSON:m,hdaJSON:s});n.resolve(m,s)});j.fail(function(u,s,t){n.reject(u,"loading the datasets",{history:m})});return n};var d=Backbone.Collection.extend(a.LoggableMixin).extend({model:e,urlRoot:galaxy_config.root+"api/histories"});return{History:e,HistoryCollection:d}}); \ 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: devteam: Fix for generating metadata when a tool dependency definition sets multiple environment variables within a single <set_environment> tool dependency type.
by commits-noreply＠bitbucket.org 02 May '14

02 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3f8e48526231/ Changeset: 3f8e48526231 User: devteam Date: 2014-05-02 18:50:57 Summary: Fix for generating metadata when a tool dependency definition sets multiple environment variables within a single <set_environment> tool dependency type. Affected #: 1 file diff -r 888cd02028b37f93beba8b175fec8c85a912ac9f -r 3f8e4852623187152ffaea5fd529fac2001c8316 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -563,14 +563,11 @@ # <set_environment version="1.0"> # <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> # </set_environment> - requirements_dict = {} for env_elem in elem: # <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> env_name = env_elem.get( 'name', None ) if env_name: - requirements_dict[ 'name' ] = env_name - requirements_dict[ 'type' ] = 'set_environment' - if requirements_dict: + requirements_dict = dict( name=env_name, type='set_environment' ) if 'set_environment' in valid_tool_dependencies_dict: valid_tool_dependencies_dict[ 'set_environment' ].append( requirements_dict ) else: 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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