galaxy-commits August 2013

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commit/galaxy-central: fubar: Patch for missing options in FromDataTableOutputActionOption when these are used in an output filter
by commits-noreply＠bitbucket.org 10 Aug '13

10 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/009088d5e76f/ Changeset: 009088d5e76f User: fubar Date: 2013-08-10 03:28:28 Summary: Patch for missing options in FromDataTableOutputActionOption when these are used in an output filter Affected #: 1 file diff -r 31d2d58ebf102f87c21f170b16452d06fd510a14 -r 009088d5e76fb00794da78dc0ee3cdaa8524b7d8 lib/galaxy/tools/parameters/output.py --- a/lib/galaxy/tools/parameters/output.py +++ b/lib/galaxy/tools/parameters/output.py @@ -217,7 +217,10 @@ else: self.missing_tool_data_table_name = self.name def get_value( self, other_values ): - options = self.options + try: + options = self.options + except: + options = [] for filter in self.filters: options = filter.filter_options( options, other_values ) try: 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: jgoecks: Unify Trackster tool objects with generic tool objects. This unification enhances the generic tool framework and simplifies the trackster tool framework. Also, backbone-ify Trackster tool handling.
by commits-noreply＠bitbucket.org 09 Aug '13

09 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/31d2d58ebf10/ Changeset: 31d2d58ebf10 User: jgoecks Date: 2013-08-08 23:05:51 Summary: Unify Trackster tool objects with generic tool objects. This unification enhances the generic tool framework and simplifies the trackster tool framework. Also, backbone-ify Trackster tool handling. Affected #: 3 files diff -r 8c3b553871bbcce9170d235f5188b9803094ad3b -r 31d2d58ebf102f87c21f170b16452d06fd510a14 lib/galaxy/visualization/genome/visual_analytics.py --- a/lib/galaxy/visualization/genome/visual_analytics.py +++ b/lib/galaxy/visualization/genome/visual_analytics.py @@ -38,6 +38,8 @@ def get_tool_def( trans, hda ): """ Returns definition of an interactive tool for an HDA. """ + + #FIXME: use tools.to_dict rather than custom code here. job = get_dataset_job( hda ) # TODO: could use this assertion to provide more information. @@ -71,10 +73,10 @@ tool_params.append( param_dict ) elif type( input ) == SelectToolParameter and type( input.options ) != DynamicOptions: tool_params.append( { 'name' : name, 'label' : input.label, 'type' : 'select', \ - 'value' : tool_param_values.get( name, None ), \ + 'value' : tool_param_values.get( name, '' ), \ 'html' : urllib.quote( input.get_html() ) } ) # If tool has parameters that can be interactively modified, return tool. if len( tool_params ) != 0: - return { 'id': tool.id, 'name' : tool.name, 'params' : tool_params } + return { 'id': tool.id, 'name' : tool.name, 'inputs' : tool_params } return None \ No newline at end of file diff -r 8c3b553871bbcce9170d235f5188b9803094ad3b -r 31d2d58ebf102f87c21f170b16452d06fd510a14 static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -41,6 +41,7 @@ label: null, type: null, value: null, + html: null, num_samples: 5 }, @@ -70,7 +71,51 @@ } return samples; - } + }, + + set_value: function(value) { + this.set('value', value || ''); + } +}, +{ + /** + * Dictionary mapping parameter type strings to parameter classes. + */ + TYPE_DICT: { + 'number': IntegerToolParameter + }, + + /** + * Create new parameter from a dictionary. + */ + create: function(options) { + var param_class = ToolParameter.TYPE_DICT[options.type] || ToolParameter; + return new param_class(options); + } +}); + +/** + * A number tool parameter. + */ +var IntegerToolParameter = ToolParameter.extend({ + defaults: _.extend({}, ToolParameter.prototype.defaults, { + min: null, + max: null + }), + + initialize: function() { + ToolParameter.prototype.initialize.call(this); + if (this.attributes.min) { + this.attributes.min = parseInt(this.attributes.min, 10); + } + if (this.attributes.max) { + this.attributes.max = parseInt(this.attributes.max, 10); + } + }, + + set_value: function(value) { + this.set('value', parseInt(value, 10)) + } }); /** @@ -79,22 +124,22 @@ var Tool = BaseModel.extend({ // Default attributes. defaults: { + id: null, + name: null, description: null, target: null, inputs: [] }, - - relations: [ - { - type: Backbone.HasMany, - key: 'inputs', - relatedModel: ToolParameter, - reverseRelation: { - key: 'tool', - includeInJSON: false - } - } - ], + + initialize: function(options) { + // Unpack parameters manually so that different parameter types can be created. + this.attributes.inputs = new Backbone.Collection( _.map(options.inputs, function(param_dict) { + // FIXME: it is still useful to be able to save/restore tool state? + // Update parameter value from tool state dict. + //param_dict.value = tool_state_dict[ param_dict[name] ] || param_dict.value; + return ToolParameter.create(param_dict); + })); + }, urlRoot: galaxy_paths.get('tool_url'), @@ -209,6 +254,13 @@ }); /** + * Tool view. + */ +var ToolView = Backbone.View.extend({ + +}); + +/** * Wrap collection of tools for fast access/manipulation. */ var ToolCollection = Backbone.Collection.extend({ @@ -697,6 +749,8 @@ // Exports return { + ToolParameter: ToolParameter, + IntegerToolParameter: IntegerToolParameter, Tool: Tool, ToolSearch: ToolSearch, ToolPanel: ToolPanel, diff -r 8c3b553871bbcce9170d235f5188b9803094ad3b -r 31d2d58ebf102f87c21f170b16452d06fd510a14 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1,7 +1,7 @@ define( ["libs/underscore", "viz/visualization", "viz/trackster/util", - "viz/trackster/slotting", "viz/trackster/painters", "mvc/data", - "viz/trackster/filters" ], - function( _, visualization, util, slotting, painters, data, filters_mod ) { + "viz/trackster/slotting", "viz/trackster/painters", "viz/trackster/filters", + "mvc/data", "mvc/tools" ], + function(_, visualization, util, slotting, painters, filters_mod, data, tools_mod) { var extend = _.extend; @@ -1622,89 +1622,103 @@ /** * Encapsulation of a tool that users can apply to tracks/datasets. */ -var Tool = function(track, tool_dict, tool_state_dict) { - // - // Unpack tool information from dictionary. - // - this.track = track; - this.id = tool_dict.id; - this.name = tool_dict.name; - this.params = []; - var params_dict = tool_dict.params; - for (var i = 0; i < params_dict.length; i++) { - // FIXME: use dict for creating parameters. - var param_dict = params_dict[i], - name = param_dict.name, - label = param_dict.label, - html = unescape(param_dict.html), - value = param_dict.value, - type = param_dict.type; - if (type === "number") { - this.params.push( - new NumberParameter(name, label, html, - (name in tool_state_dict ? tool_state_dict[name] : value), - param_dict.min, param_dict.max) - ); +var TracksterTool = Backbone.RelationalModel.extend({ + defaults: { + track: null, + tool: null, + }, + + relations: [ + { + type: Backbone.HasOne, + key: 'tool', + relatedModel: tools_mod.Tool } - else if (type === "select") { - this.params.push( - new ToolParameter(name, label, html, - (name in tool_state_dict ? tool_state_dict[name] : value)) - ); - } - else { - console.log("WARNING: unrecognized tool parameter type:", name, type); - } - } - - // - // Create div elt for tool UI. - // - this.parent_div = $("<div/>").addClass("dynamic-tool").hide(); - // Disable dragging, clicking, double clicking on div so that actions on slider do not impact viz. - this.parent_div.bind("drag", function(e) { - e.stopPropagation(); - }).click(function(e) { - e.stopPropagation(); - }).bind("dblclick", function(e) { - e.stopPropagation(); - }); - var name_div = $("<div class='tool-name'>").appendTo(this.parent_div).text(this.name); - var tool_params = this.params; - var tool = this; - $.each(this.params, function(index, param) { - var param_div = $("<div>").addClass("param-row").appendTo(tool.parent_div); + ] + +}); + +/** + * View renders tool parameter HTML and updates parameter value as it is changed in the HTML. + */ + var ToolParameterView = Backbone.View.extend({ + + events: { + 'change input': 'update_value' + }, + + render: function() { + var param_div = this.$el.addClass("param-row"), + param = this.model; + // Param label. - var label_div = $("<div>").addClass("param-label").text(param.label).appendTo(param_div); + var label_div = $("<div>").addClass("param-label").text(param.get('label')).appendTo(param_div); // Param HTML. - var html_div = $("<div/>").addClass("param-input").html(param.html).appendTo(param_div); + var html_div = $("<div/>").addClass("param-input").html(param.get('html')).appendTo(param_div); // Set initial value. - html_div.find(":input").val(param.value); + html_div.find(":input").val(param.get('value')); // Add to clear floating layout. $("<div style='clear: both;'/>").appendTo(param_div); - }); - - // Highlight value for inputs for easy replacement. - this.parent_div.find("input").click(function() { $(this).select(); }); - - // Add buttons for running on dataset, region. - var run_tool_row = $("<div>").addClass("param-row").appendTo(this.parent_div); - var run_on_dataset_button = $("<input type='submit'>").attr("value", "Run on complete dataset").appendTo(run_tool_row); - var run_on_region_button = $("<input type='submit'>").attr("value", "Run on visible region").css("margin-left", "3em").appendTo(run_tool_row); - run_on_region_button.click( function() { - // Run tool to create new track. - tool.run_on_region(); - }); - run_on_dataset_button.click( function() { - tool.run_on_dataset(); - }); - - if ('visible' in tool_state_dict && tool_state_dict.visible) { - this.parent_div.show(); + }, + + update_value: function(update_event) { + this.model.set_value($(update_event.target).val()); } -}; -extend(Tool.prototype, { + }); + +/** + * View for TracksterTool. + */ +var TracksterToolView = Backbone.View.extend({ + + /** + * Render tool UI. + */ + render: function() { + var self = this; + tool = this.model.get('tool'), + parent_div = this.$el.addClass("dynamic-tool").hide(); + + // Prevent div events from propogating to other elements. + parent_div.bind("drag", function(e) { + e.stopPropagation(); + }).click(function(e) { + e.stopPropagation(); + }).bind("dblclick", function(e) { + e.stopPropagation(); + }).keydown(function(e) { e.stopPropagation(); }); + + // Add name, inputs. + var name_div = $("<div class='tool-name'>").appendTo(parent_div).text(tool.get('name')); + tool.get('inputs').each(function(param) { + var param_view = new ToolParameterView({ model: param }); + param_view.render(); + parent_div.append(param_view.$el); + }); + + // Highlight value for inputs for easy replacement. + parent_div.find("input").click(function() { $(this).select(); }); + + // Add buttons for running on dataset, region. + var run_tool_row = $("<div>").addClass("param-row").appendTo(parent_div); + var run_on_dataset_button = $("<input type='submit'>").attr("value", "Run on complete dataset").appendTo(run_tool_row); + var run_on_region_button = $("<input type='submit'>").attr("value", "Run on visible region").css("margin-left", "3em").appendTo(run_tool_row); + run_on_region_button.click( function() { + // Run tool to create new track. + self.run_on_region(); + }); + run_on_dataset_button.click( function() { + self.run_on_dataset(); + }); + + /* + if ('visible' in tool_state_dict && tool_state_dict.visible) { + this.parent_div.show(); + } + */ + }, + /** * Update tool parameters. */ @@ -1713,68 +1727,42 @@ this.params[i].update_value(); } }, + /** * Returns a dict with tool state information. */ state_dict: function() { // Save parameter values. - var tool_state = {}; - for (var i = 0; i < this.params.length; i++) { - tool_state[this.params[i].name] = this.params[i].value; - } + var tool_state = this.model.get('tool').get_param_values_dict(); // Save visibility. tool_state.visible = this.parent_div.is(":visible"); return tool_state; }, - /** - * Returns dictionary of parameter name-values. - */ - get_param_values_dict: function() { - var param_dict = {}; - this.parent_div.find(":input").each(function() { - var name = $(this).attr("name"), value = $(this).val(); - param_dict[name] = value; - }); - return param_dict; - }, - /** - * Returns array of parameter values. - */ - get_param_values: function() { - var param_values = []; - this.parent_div.find(":input").each(function() { - // Only include inputs with names; this excludes Run button. - var name = $(this).attr("name"), value = $(this).val(); - if (name) { - param_values[param_values.length] = value; - } - }); - return param_values; - }, + /** * Run tool on dataset. Output is placed in dataset's history and no changes to viz are made. */ run_on_dataset: function() { - var tool = this; - tool.run( - // URL params. - { - target_dataset_id: this.track.dataset.id, - action: 'rerun', - tool_id: tool.id - }, - null, - // Success callback. - function(track_data) { - show_modal(tool.name + " is Running", - tool.name + " is running on the complete dataset. Tool outputs are in dataset's history.", - { "Close" : hide_modal } ); - } - ); - + var tool = this.model.get('tool'); + this.run( + // URL params. + { + target_dataset_id: this.model.get('track').dataset.id, + action: 'rerun', + tool_id: tool.id + }, + null, + // Success callback. + function(track_data) { + show_modal(tool.get('name') + " is Running", + tool.get('name') + " is running on the complete dataset. Tool outputs are in dataset's history.", + { "Close" : hide_modal } ); + } + ); }, + /** * Run dataset on visible region. This creates a new track and sets the track's contents * to the tool's output. @@ -1783,21 +1771,23 @@ // // Create track for tool's output immediately to provide user feedback. // - var region = new visualization.GenomeRegion({ - chrom: this.track.view.chrom, - start: this.track.view.low, - end: this.track.view.high + var track = this.model.get('track'), + tool = this.model.get('tool'), + region = new visualization.GenomeRegion({ + chrom: track.view.chrom, + start: track.view.low, + end: track.view.high }), url_params = { - target_dataset_id: this.track.dataset.id, + target_dataset_id: track.dataset.id, action: 'rerun', - tool_id: this.id, + tool_id: tool.id, regions: [ region.toJSON() ] }, - current_track = this.track, + current_track = track, // Set name of track to include tool name, parameters, and region used. track_name = url_params.tool_id + current_track.tool_region_and_parameters_str(region), @@ -1838,25 +1828,25 @@ new_track.tiles_div.text("Starting job."); // Run tool. - this.update_params(); this.run(url_params, new_track, - // Success callback. - function(track_data) { - new_track.set_dataset(new data.Dataset(track_data)); - new_track.tiles_div.text("Running job."); - new_track.init(); - } - ); + // Success callback. + function(track_data) { + new_track.set_dataset(new data.Dataset(track_data)); + new_track.tiles_div.text("Running job."); + new_track.init(); + } + ); }, + /** * Run tool using a set of URL params and a success callback. */ run: function(url_params, new_track, success_callback) { // Run tool. - url_params.inputs = this.get_param_values_dict(); + url_params.inputs = this.model.get('tool').get_inputs_dict(); var ss_deferred = new util.ServerStateDeferred({ ajax_settings: { - url: config.root + "/api/tools", + url: config.root + "api/tools", data: JSON.stringify(url_params), dataType: "json", contentType: 'application/json', @@ -1889,36 +1879,7 @@ } }); } -}); - -/** - * Tool parameters. - */ -var ToolParameter = function(name, label, html, value) { - this.name = name; - this.label = label; - // Need to use jQuery for HTML so that value can be queried and updated dynamically. - this.html = $(html); - this.value = value; -}; - -extend(ToolParameter.prototype, { - update_value: function() { - this.value = $(this.html).val(); - } -}); - -var NumberParameter = function(name, label, html, value, min, max) { - ToolParameter.call(this, name, label, html, value); - this.min = min; - this.max = max; -}; - -extend(NumberParameter.prototype, ToolParameter.prototype, { - update_value: function() { - ToolParameter.prototype.update_value.call(this); - this.value = parseFloat(this.value); - } + }); /** @@ -2819,7 +2780,12 @@ // FIXME: prolly need function to set filters and update data_manager reference. this.data_manager.set('filters_manager', this.filters_manager); this.filters_available = false; - this.tool = ('tool' in obj_dict && obj_dict.tool ? new Tool(this, obj_dict.tool, obj_dict.tool_state) : null); + this.tool = (obj_dict.tool ? new TracksterTool({ + 'track': this, + 'tool': obj_dict.tool, + 'tool_state': obj_dict.tool_state + }) + : null); this.tile_cache = new visualization.Cache(TILE_CACHE_SIZE); this.left_offset = 0; @@ -2830,10 +2796,12 @@ this.set_filters_manager(this.filters_manager); // - // Create dynamic tool div. + // Create dynamic tool view. // - if (this.tool) { - this.dynamic_tool_div = this.tool.parent_div; + if (this.tool) { + var tool_view = new TracksterToolView({ model: this.tool }); + tool_view.render(); + this.dynamic_tool_div = tool_view.$el; this.header_div.after(this.dynamic_tool_div); } } @@ -3427,8 +3395,9 @@ */ tool_region_and_parameters_str: function(region) { var track = this, - region_str = (region !== undefined ? region.toString() : "all"); - return " - region=[" + region_str + "], parameters=[" + track.tool.get_param_values().join(", ") + "]"; + region_str = (region !== undefined ? region.toString() : "all"), + param_str = _.values( track.tool.get('tool').get_inputs_dict()).join(', '); + return " - region=[" + region_str + "], parameters=[" + param_str + "]"; }, /** 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: carlfeberhard: pull request #168 from Kyle Ellrott: add graphview visualization as visualization plugin
by commits-noreply＠bitbucket.org 09 Aug '13

09 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8c3b553871bb/ Changeset: 8c3b553871bb User: carlfeberhard Date: 2013-08-08 22:48:56 Summary: pull request #168 from Kyle Ellrott: add graphview visualization as visualization plugin Affected #: 5 files diff -r 6d3d5e571a43dc2defa94c0baef8c96461818a53 -r 8c3b553871bbcce9170d235f5188b9803094ad3b config/plugins/visualizations/graphview/config/graphview.xml --- /dev/null +++ b/config/plugins/visualizations/graphview/config/graphview.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "../../visualization.dtd"> +<visualization name="Graphview"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="has_dataprovider" test_attr="datatype">node-edge</test> + <to_param param_attr="id">dataset_id</to_param> + </data_source> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">graph.Rdf</test> + <to_param param_attr="id">dataset_id</to_param> + </data_source> + </data_sources> + <params> + <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> + </params> + <template>graphview/templates/graphview.mako</template> +</visualization> diff -r 6d3d5e571a43dc2defa94c0baef8c96461818a53 -r 8c3b553871bbcce9170d235f5188b9803094ad3b config/plugins/visualizations/graphview/static/graphview.css --- /dev/null +++ b/config/plugins/visualizations/graphview/static/graphview.css @@ -0,0 +1,70 @@ +svg { + border: 1px solid lightgrey; + background-color: #FFF; + cursor: default; + -webkit-user-select: none; + -moz-user-select: none; + -ms-user-select: none; + -o-user-select: none; + user-select: none; +} + +svg:not(.active):not(.ctrl) { + cursor: crosshair; +} + +path.link { + fill: none; + stroke: #000; + stroke-width: 4px; + cursor: default; +} + +svg:not(.active):not(.ctrl) path.link { + cursor: pointer; +} + +path.link.selected { + stroke-dasharray: 10,2; +} + +path.link.dragline { + pointer-events: none; +} + +path.link.hidden { + stroke-width: 0; +} + +circle.node { + stroke-width: 1.0px; + cursor: pointer; +} + +circle.node.reflexive { + stroke: #000 !important; + stroke-width: 2.5px; +} + +text { + font: 12px sans-serif; + pointer-events: none; +} + +text.id { + text-anchor: middle; + font-weight: bold; +} + +div.tooltip { + position: absolute; + text-align: center; + width: 60px; + height: 28px; + padding: 2px; + font: 12px sans-serif; + background: lightsteelblue; + border: 0px; + border-radius: 8px; + pointer-events: none; +} diff -r 6d3d5e571a43dc2defa94c0baef8c96461818a53 -r 8c3b553871bbcce9170d235f5188b9803094ad3b config/plugins/visualizations/graphview/static/graphview.js --- /dev/null +++ b/config/plugins/visualizations/graphview/static/graphview.js @@ -0,0 +1,175 @@ +function get_firstChild(n) { + y=n.firstChild; + while (y && y.nodeType!=1) { + y=y.nextSibling; + } + return y; +} + +function get_nextSibling(n) { + y=n.nextSibling; + while (y) { + if (y.nodeType==1) { + return y; + } + y=y.nextSibling; + } + return y; +} + +function parse_xgmml_attr(elm) { + out = {}; + var c = get_firstChild(elm); + while (c) { + if (c.nodeName == "att") { + if (c.attributes['type'].value == "string") { + out[c.attributes['name'].value] = c.attributes['value'].value; + } + } + c = get_nextSibling(c); + } + return out +} + +function parse_xgmml(root, add_node, add_edge) { + graph=root.getElementsByTagName("graph")[0]; + elm = get_firstChild(graph); + while (elm) { + if (elm.nodeName == "node") { + var attr = parse_xgmml_attr(elm); + add_node( elm.attributes['id'].value, elm.attributes['label'].value, attr ); + } + if (elm.nodeName == "edge") { + var attr = parse_xgmml_attr(elm); + add_edge( elm.attributes['source'].value, elm.attributes['target'].value, attr ); + } + + elm = get_nextSibling(elm); + } +} + +function parse_sif(data, add_node, add_edge) { + var lines = data.split("\n") + for (var i in lines) { + var tmp = lines[i].split("\t"); + if (tmp.length == 3) { + add_edge(tmp[0], tmp[2], {type:tmp[1]}); + } + } + +} + +jQuery.fn.graphViewer = function(config) { + + var svg, colors; + var nodes = [], + links = []; + + var height = config.height; + var width = config.width; + + + colors = d3.scale.category10(); + + this.each(function() { + svg = d3.select(this) + .append('svg') + .attr('width', width) + .attr('height', height); + } + ); + + var tooltip_div = d3.select("#tooltip").attr("class", "tooltip").style("opacity", 0);; + + this.add_node = function(node_id, node_label, attr) { + nodes.push( {id: node_id, label:node_label, attr:attr} ); + } + + this.add_edge = function(src_id, dst_id, attr) { + var src, target; + for (var i in nodes) { + if (nodes[i].id == src_id) { + src = nodes[i]; + } + if (nodes[i].id == dst_id) { + target = nodes[i]; + } + } + if (typeof src==="undefined") { + i = nodes.length + nodes.push( {id:src_id, label:src_id, attr:{}} ) + src = nodes[i] + } + if (typeof target==="undefined") { + i = nodes.length + nodes.push( {id:dst_id, label:dst_id, attr:{}} ) + target = nodes[i] + } + if (src && target) { + links.push( {source: src, target: target, left: false, right: true } ); + } + } + + this.render = function() { + var path = svg.append('svg:g').selectAll('path'), + circle = svg.append('svg:g').selectAll('g'); + + + circle = circle.data(nodes, function(d) { return d.id; }); + var g = circle.enter().append('svg:g'); + + circle.on('mouseover', function(d) { + tooltip_div.transition() + .duration(200) + .style("opacity", .9); + tooltip_div.html( "<div>" + d.label + "</div><div>" + d.attr.type + "</div>" ).style("left", (d3.event.pageX + 40) + "px") + .style("top", (d3.event.pageY - 35) + "px"); + }) + .on("mouseout", function(d) { + tooltip_div.transition() + .duration(500) + .style("opacity", 0); + }); + + path = path.data(links); + + + function tick() { + path.attr('d', function(d) { + return 'M' + d.source.x + ',' + d.source.y + 'L' + d.target.x + ',' + d.target.y; + }); + circle.attr('transform', function(d) { + return 'translate(' + d.x + ',' + d.y + ')'; + }); + } + + + g.append('svg:circle') + .attr('class', 'node') + .attr('r', 8) + .style('stroke', 'black') + .attr('fill', function(d) { + return colors(d['attr']['type']) + }); + + path.enter().append('svg:path') + .attr('class', 'link') + + + // init D3 force layout + var force = d3.layout.force() + .nodes(nodes) + .links(links) + .size([width, height]) + .linkDistance(25) + .charge(-50) + .on('tick', tick) + circle.call(force.drag) + force.start() + + } + + return this + +} + This diff is so big that we needed to truncate the remainder. 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: jgoecks: Update jquery.mousewheel plugin from version 3.0.4 to 3.1.3, introducing a necessary (for now) hack. This makes the plugin compatable with the most recent version of jquery.
by commits-noreply＠bitbucket.org 09 Aug '13

09 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6d3d5e571a43/ Changeset: 6d3d5e571a43 User: jgoecks Date: 2013-08-08 22:41:18 Summary: Update jquery.mousewheel plugin from version 3.0.4 to 3.1.3, introducing a necessary (for now) hack. This makes the plugin compatable with the most recent version of jquery. Affected #: 1 file diff -r 61ddd0d07950fafc18fed95354459e7715e6b1d7 -r 6d3d5e571a43dc2defa94c0baef8c96461818a53 static/scripts/libs/jquery/jquery.mousewheel.js --- a/static/scripts/libs/jquery/jquery.mousewheel.js +++ b/static/scripts/libs/jquery/jquery.mousewheel.js @@ -1,78 +1,125 @@ -/* Copyright (c) 2010 Brandon Aaron (http://brandonaaron.net) +/*! Copyright (c) 2013 Brandon Aaron (http://brandonaaron.net) * Licensed under the MIT License (LICENSE.txt). * * Thanks to: http://adomas.org/javascript-mouse-wheel/ for some pointers. * Thanks to: Mathias Bank(http://www.mathias-bank.de) for a scope bug fix. * Thanks to: Seamus Leahy for adding deltaX and deltaY * - * Version: 3.0.4 - * + * Version: 3.1.3 + * * Requires: 1.2.2+ */ -(function($) { +(function (factory) { + // GALAXY HACK + // (JG): Galaxy's mixing of a global jQuery and require modules doesn't work with + // the logic below. Instead, do the right thing for this configuration without any checks. + factory(jQuery); + // END HACK -var types = ['DOMMouseScroll', 'mousewheel']; + /* + if ( typeof define === 'function' && define.amd ) { + // AMD. Register as an anonymous module. + define(['jquery'], factory); + } else if (typeof exports === 'object') { + // Node/CommonJS style for Browserify + module.exports = factory; + } else { + // Browser globals + factory(jQuery); + } + */ +}(function ($) { -$.event.special.mousewheel = { - setup: function() { - if ( this.addEventListener ) { - for ( var i=types.length; i; ) { - this.addEventListener( types[--i], handler, false ); - } - } else { - this.onmousewheel = handler; - } - }, - - teardown: function() { - if ( this.removeEventListener ) { - for ( var i=types.length; i; ) { - this.removeEventListener( types[--i], handler, false ); - } - } else { - this.onmousewheel = null; + var toFix = ['wheel', 'mousewheel', 'DOMMouseScroll', 'MozMousePixelScroll']; + var toBind = 'onwheel' in document || document.documentMode >= 9 ? ['wheel'] : ['mousewheel', 'DomMouseScroll', 'MozMousePixelScroll']; + var lowestDelta, lowestDeltaXY; + + if ( $.event.fixHooks ) { + for ( var i = toFix.length; i; ) { + $.event.fixHooks[ toFix[--i] ] = $.event.mouseHooks; } } -}; -$.fn.extend({ - mousewheel: function(fn) { - return fn ? this.bind("mousewheel", fn) : this.trigger("mousewheel"); - }, - - unmousewheel: function(fn) { - return this.unbind("mousewheel", fn); + $.event.special.mousewheel = { + setup: function() { + if ( this.addEventListener ) { + for ( var i = toBind.length; i; ) { + this.addEventListener( toBind[--i], handler, false ); + } + } else { + this.onmousewheel = handler; + } + }, + + teardown: function() { + if ( this.removeEventListener ) { + for ( var i = toBind.length; i; ) { + this.removeEventListener( toBind[--i], handler, false ); + } + } else { + this.onmousewheel = null; + } + } + }; + + $.fn.extend({ + mousewheel: function(fn) { + return fn ? this.bind("mousewheel", fn) : this.trigger("mousewheel"); + }, + + unmousewheel: function(fn) { + return this.unbind("mousewheel", fn); + } + }); + + + function handler(event) { + var orgEvent = event || window.event, + args = [].slice.call(arguments, 1), + delta = 0, + deltaX = 0, + deltaY = 0, + absDelta = 0, + absDeltaXY = 0, + fn; + event = $.event.fix(orgEvent); + event.type = "mousewheel"; + + // Old school scrollwheel delta + if ( orgEvent.wheelDelta ) { delta = orgEvent.wheelDelta; } + if ( orgEvent.detail ) { delta = orgEvent.detail * -1; } + + // New school wheel delta (wheel event) + if ( orgEvent.deltaY ) { + deltaY = orgEvent.deltaY * -1; + delta = deltaY; + } + if ( orgEvent.deltaX ) { + deltaX = orgEvent.deltaX; + delta = deltaX * -1; + } + + // Webkit + if ( orgEvent.wheelDeltaY !== undefined ) { deltaY = orgEvent.wheelDeltaY; } + if ( orgEvent.wheelDeltaX !== undefined ) { deltaX = orgEvent.wheelDeltaX * -1; } + + // Look for lowest delta to normalize the delta values + absDelta = Math.abs(delta); + if ( !lowestDelta || absDelta < lowestDelta ) { lowestDelta = absDelta; } + absDeltaXY = Math.max(Math.abs(deltaY), Math.abs(deltaX)); + if ( !lowestDeltaXY || absDeltaXY < lowestDeltaXY ) { lowestDeltaXY = absDeltaXY; } + + // Get a whole value for the deltas + fn = delta > 0 ? 'floor' : 'ceil'; + delta = Math[fn](delta / lowestDelta); + deltaX = Math[fn](deltaX / lowestDeltaXY); + deltaY = Math[fn](deltaY / lowestDeltaXY); + + // Add event and delta to the front of the arguments + args.unshift(event, delta, deltaX, deltaY); + + return ($.event.dispatch || $.event.handle).apply(this, args); } -}); - -function handler(event) { - var orgEvent = event || window.event, args = [].slice.call( arguments, 1 ), delta = 0, returnValue = true, deltaX = 0, deltaY = 0; - event = $.event.fix(orgEvent); - event.type = "mousewheel"; - - // Old school scrollwheel delta - if ( event.wheelDelta ) { delta = event.wheelDelta/120; } - if ( event.detail ) { delta = -event.detail/3; } - - // New school multidimensional scroll (touchpads) deltas - deltaY = delta; - - // Gecko - if ( orgEvent.axis !== undefined && orgEvent.axis === orgEvent.HORIZONTAL_AXIS ) { - deltaY = 0; - deltaX = -1*delta; - } - - // Webkit - if ( orgEvent.wheelDeltaY !== undefined ) { deltaY = orgEvent.wheelDeltaY/120; } - if ( orgEvent.wheelDeltaX !== undefined ) { deltaX = -1*orgEvent.wheelDeltaX/120; } - - // Add event and delta to the front of the arguments - args.unshift(event, delta, deltaX, deltaY); - - return $.event.handle.apply(this, args); -} - -})(jQuery); +})); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 09 Aug '13

09 Aug '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e7e82003f235/ Changeset: e7e82003f235 Branch: next-stable User: natefoo Date: 2013-08-08 21:40:00 Summary: Define the ActionInputError exception that was being caught in the quotas API controller. Thanks Jim Johnson. Affected #: 3 files diff -r 8d8429484ac3ffef21fedd1077acf050c8aed459 -r e7e82003f235c4cca84939e04aa432d128093866 lib/galaxy/actions/admin.py --- a/lib/galaxy/actions/admin.py +++ b/lib/galaxy/actions/admin.py @@ -4,7 +4,7 @@ import logging from galaxy import util -from galaxy.exceptions import MessageException +from galaxy.exceptions import ActionInputError log = logging.getLogger( __name__ ) @@ -21,21 +21,21 @@ except AssertionError: create_amount = False if not params.name or not params.description: - raise MessageException( "Enter a valid name and a description.", type='error' ) + raise ActionInputError( "Enter a valid name and a description." ) elif self.sa_session.query( self.app.model.Quota ).filter( self.app.model.Quota.table.c.name==params.name ).first(): - raise MessageException( "Quota names must be unique and a quota with that name already exists, so choose another name.", type='error' ) + raise ActionInputError( "Quota names must be unique and a quota with that name already exists, so choose another name." ) elif not params.get( 'amount', None ): - raise MessageException( "Enter a valid quota amount.", type='error' ) + raise ActionInputError( "Enter a valid quota amount." ) elif create_amount is False: - raise MessageException( "Unable to parse the provided amount.", type='error' ) + raise ActionInputError( "Unable to parse the provided amount." ) elif params.operation not in self.app.model.Quota.valid_operations: - raise MessageException( "Enter a valid operation.", type='error' ) + raise ActionInputError( "Enter a valid operation." ) elif params.default != 'no' and params.default not in self.app.model.DefaultQuotaAssociation.types.__dict__.values(): - raise MessageException( "Enter a valid default type.", type='error' ) + raise ActionInputError( "Enter a valid default type." ) elif params.default != 'no' and params.operation != '=': - raise MessageException( "Operation for a default quota must be '='.", type='error' ) + raise ActionInputError( "Operation for a default quota must be '='." ) elif create_amount is None and params.operation != '=': - raise MessageException( "Operation for an unlimited quota must be '='.", type='error' ) + raise ActionInputError( "Operation for an unlimited quota must be '='." ) else: # Create the quota quota = self.app.model.Quota( name=params.name, description=params.description, amount=create_amount, operation=params.operation ) @@ -59,9 +59,9 @@ def _rename_quota( self, quota, params ): if not params.name: - raise MessageException( 'Enter a valid name', type='error' ) + raise ActionInputError( 'Enter a valid name' ) elif params.name != quota.name and self.sa_session.query( self.app.model.Quota ).filter( self.app.model.Quota.table.c.name==params.name ).first(): - raise MessageException( 'A quota with that name already exists', type='error' ) + raise ActionInputError( 'A quota with that name already exists' ) else: old_name = quota.name quota.name = params.name @@ -73,7 +73,7 @@ def _manage_users_and_groups_for_quota( self, quota, params ): if quota.default: - raise MessageException( 'Default quotas cannot be associated with specific users and groups', type='error' ) + raise ActionInputError( 'Default quotas cannot be associated with specific users and groups' ) else: in_users = [ self.sa_session.query( self.app.model.User ).get( x ) for x in util.listify( params.in_users ) ] in_groups = [ self.sa_session.query( self.app.model.Group ).get( x ) for x in util.listify( params.in_groups ) ] @@ -91,11 +91,11 @@ except AssertionError: new_amount = False if not params.amount: - raise MessageException( 'Enter a valid amount', type='error' ) + raise ActionInputError( 'Enter a valid amount' ) elif new_amount is False: - raise MessageException( 'Unable to parse the provided amount', type='error' ) + raise ActionInputError( 'Unable to parse the provided amount' ) elif params.operation not in self.app.model.Quota.valid_operations: - raise MessageException( 'Enter a valid operation', type='error' ) + raise ActionInputError( 'Enter a valid operation' ) else: quota.amount = new_amount quota.operation = params.operation @@ -106,7 +106,7 @@ def _set_quota_default( self, quota, params ): if params.default != 'no' and params.default not in self.app.model.DefaultQuotaAssociation.types.__dict__.values(): - raise MessageException( 'Enter a valid default type.', type='error' ) + raise ActionInputError( 'Enter a valid default type.' ) else: if params.default != 'no': self.app.quota_agent.set_default_quota( params.default, quota ) @@ -123,7 +123,7 @@ def _unset_quota_default( self, quota, params ): if not quota.default: - raise MessageException( "Quota '%s' is not a default." % quota.name, type='error' ) + raise ActionInputError( "Quota '%s' is not a default." % quota.name ) else: message = "Quota '%s' is no longer the default for %s users." % ( quota.name, quota.default[0].type ) for dqa in quota.default: @@ -138,9 +138,9 @@ if q.default: names.append( q.name ) if len( names ) == 1: - raise MessageException( "Quota '%s' is a default, please unset it as a default before deleting it" % ( names[0] ), type='error' ) + raise ActionInputError( "Quota '%s' is a default, please unset it as a default before deleting it" % ( names[0] ) ) elif len( names ) > 1: - raise MessageException( "Quotas are defaults, please unset them as defaults before deleting them: " + ', '.join( names ), type='error' ) + raise ActionInputError( "Quotas are defaults, please unset them as defaults before deleting them: " + ', '.join( names ) ) message = "Deleted %d quotas: " % len( quotas ) for q in quotas: q.deleted = True @@ -157,9 +157,9 @@ if not q.deleted: names.append( q.name ) if len( names ) == 1: - raise MessageException( "Quota '%s' has not been deleted, so it cannot be undeleted." % ( names[0] ), type='error' ) + raise ActionInputError( "Quota '%s' has not been deleted, so it cannot be undeleted." % ( names[0] ) ) elif len( names ) > 1: - raise MessageException( "Quotas have not been deleted so they cannot be undeleted: " + ', '.join( names ), type='error' ) + raise ActionInputError( "Quotas have not been deleted so they cannot be undeleted: " + ', '.join( names ) ) message = "Undeleted %d quotas: " % len( quotas ) for q in quotas: q.deleted = False @@ -182,9 +182,9 @@ if not q.deleted: names.append( q.name ) if len( names ) == 1: - raise MessageException( "Quota '%s' has not been deleted, so it cannot be purged." % ( names[0] ), type='error' ) + raise ActionInputError( "Quota '%s' has not been deleted, so it cannot be purged." % ( names[0] ) ) elif len( names ) > 1: - raise MessageException( "Quotas have not been deleted so they cannot be undeleted: " + ', '.join( names ), type='error' ) + raise ActionInputError( "Quotas have not been deleted so they cannot be undeleted: " + ', '.join( names ) ) message = "Purged %d quotas: " % len( quotas ) for q in quotas: # Delete UserQuotaAssociations diff -r 8d8429484ac3ffef21fedd1077acf050c8aed459 -r e7e82003f235c4cca84939e04aa432d128093866 lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -21,6 +21,10 @@ class ItemOwnershipException( MessageException ): pass +class ActionInputError( MessageException ): + def __init__( self, err_msg, type="error" ): + super( ActionInputError, self ).__init__( err_msg, type ) + class ObjectNotFound( Exception ): """ Accessed object was not found """ pass diff -r 8d8429484ac3ffef21fedd1077acf050c8aed459 -r e7e82003f235c4cca84939e04aa432d128093866 lib/galaxy/webapps/galaxy/api/quotas.py --- a/lib/galaxy/webapps/galaxy/api/quotas.py +++ b/lib/galaxy/webapps/galaxy/api/quotas.py @@ -11,7 +11,7 @@ from galaxy.actions.admin import AdminActions from paste.httpexceptions import HTTPBadRequest -from galaxy.exceptions import * +from galaxy.exceptions import ActionInputError log = logging.getLogger( __name__ ) https://bitbucket.org/galaxy/galaxy-central/commits/61ddd0d07950/ Changeset: 61ddd0d07950 User: natefoo Date: 2013-08-08 21:50:05 Summary: Merge next-stable. Affected #: 3 files diff -r 3778811f053a5f71c68408a9e8beb627f6ccdede -r 61ddd0d07950fafc18fed95354459e7715e6b1d7 lib/galaxy/actions/admin.py --- a/lib/galaxy/actions/admin.py +++ b/lib/galaxy/actions/admin.py @@ -4,7 +4,7 @@ import logging from galaxy import util -from galaxy.exceptions import MessageException +from galaxy.exceptions import ActionInputError log = logging.getLogger( __name__ ) @@ -21,21 +21,21 @@ except AssertionError: create_amount = False if not params.name or not params.description: - raise MessageException( "Enter a valid name and a description.", type='error' ) + raise ActionInputError( "Enter a valid name and a description." ) elif self.sa_session.query( self.app.model.Quota ).filter( self.app.model.Quota.table.c.name==params.name ).first(): - raise MessageException( "Quota names must be unique and a quota with that name already exists, so choose another name.", type='error' ) + raise ActionInputError( "Quota names must be unique and a quota with that name already exists, so choose another name." ) elif not params.get( 'amount', None ): - raise MessageException( "Enter a valid quota amount.", type='error' ) + raise ActionInputError( "Enter a valid quota amount." ) elif create_amount is False: - raise MessageException( "Unable to parse the provided amount.", type='error' ) + raise ActionInputError( "Unable to parse the provided amount." ) elif params.operation not in self.app.model.Quota.valid_operations: - raise MessageException( "Enter a valid operation.", type='error' ) + raise ActionInputError( "Enter a valid operation." ) elif params.default != 'no' and params.default not in self.app.model.DefaultQuotaAssociation.types.__dict__.values(): - raise MessageException( "Enter a valid default type.", type='error' ) + raise ActionInputError( "Enter a valid default type." ) elif params.default != 'no' and params.operation != '=': - raise MessageException( "Operation for a default quota must be '='.", type='error' ) + raise ActionInputError( "Operation for a default quota must be '='." ) elif create_amount is None and params.operation != '=': - raise MessageException( "Operation for an unlimited quota must be '='.", type='error' ) + raise ActionInputError( "Operation for an unlimited quota must be '='." ) else: # Create the quota quota = self.app.model.Quota( name=params.name, description=params.description, amount=create_amount, operation=params.operation ) @@ -59,9 +59,9 @@ def _rename_quota( self, quota, params ): if not params.name: - raise MessageException( 'Enter a valid name', type='error' ) + raise ActionInputError( 'Enter a valid name' ) elif params.name != quota.name and self.sa_session.query( self.app.model.Quota ).filter( self.app.model.Quota.table.c.name==params.name ).first(): - raise MessageException( 'A quota with that name already exists', type='error' ) + raise ActionInputError( 'A quota with that name already exists' ) else: old_name = quota.name quota.name = params.name @@ -73,7 +73,7 @@ def _manage_users_and_groups_for_quota( self, quota, params ): if quota.default: - raise MessageException( 'Default quotas cannot be associated with specific users and groups', type='error' ) + raise ActionInputError( 'Default quotas cannot be associated with specific users and groups' ) else: in_users = [ self.sa_session.query( self.app.model.User ).get( x ) for x in util.listify( params.in_users ) ] in_groups = [ self.sa_session.query( self.app.model.Group ).get( x ) for x in util.listify( params.in_groups ) ] @@ -91,11 +91,11 @@ except AssertionError: new_amount = False if not params.amount: - raise MessageException( 'Enter a valid amount', type='error' ) + raise ActionInputError( 'Enter a valid amount' ) elif new_amount is False: - raise MessageException( 'Unable to parse the provided amount', type='error' ) + raise ActionInputError( 'Unable to parse the provided amount' ) elif params.operation not in self.app.model.Quota.valid_operations: - raise MessageException( 'Enter a valid operation', type='error' ) + raise ActionInputError( 'Enter a valid operation' ) else: quota.amount = new_amount quota.operation = params.operation @@ -106,7 +106,7 @@ def _set_quota_default( self, quota, params ): if params.default != 'no' and params.default not in self.app.model.DefaultQuotaAssociation.types.__dict__.values(): - raise MessageException( 'Enter a valid default type.', type='error' ) + raise ActionInputError( 'Enter a valid default type.' ) else: if params.default != 'no': self.app.quota_agent.set_default_quota( params.default, quota ) @@ -123,7 +123,7 @@ def _unset_quota_default( self, quota, params ): if not quota.default: - raise MessageException( "Quota '%s' is not a default." % quota.name, type='error' ) + raise ActionInputError( "Quota '%s' is not a default." % quota.name ) else: message = "Quota '%s' is no longer the default for %s users." % ( quota.name, quota.default[0].type ) for dqa in quota.default: @@ -138,9 +138,9 @@ if q.default: names.append( q.name ) if len( names ) == 1: - raise MessageException( "Quota '%s' is a default, please unset it as a default before deleting it" % ( names[0] ), type='error' ) + raise ActionInputError( "Quota '%s' is a default, please unset it as a default before deleting it" % ( names[0] ) ) elif len( names ) > 1: - raise MessageException( "Quotas are defaults, please unset them as defaults before deleting them: " + ', '.join( names ), type='error' ) + raise ActionInputError( "Quotas are defaults, please unset them as defaults before deleting them: " + ', '.join( names ) ) message = "Deleted %d quotas: " % len( quotas ) for q in quotas: q.deleted = True @@ -157,9 +157,9 @@ if not q.deleted: names.append( q.name ) if len( names ) == 1: - raise MessageException( "Quota '%s' has not been deleted, so it cannot be undeleted." % ( names[0] ), type='error' ) + raise ActionInputError( "Quota '%s' has not been deleted, so it cannot be undeleted." % ( names[0] ) ) elif len( names ) > 1: - raise MessageException( "Quotas have not been deleted so they cannot be undeleted: " + ', '.join( names ), type='error' ) + raise ActionInputError( "Quotas have not been deleted so they cannot be undeleted: " + ', '.join( names ) ) message = "Undeleted %d quotas: " % len( quotas ) for q in quotas: q.deleted = False @@ -182,9 +182,9 @@ if not q.deleted: names.append( q.name ) if len( names ) == 1: - raise MessageException( "Quota '%s' has not been deleted, so it cannot be purged." % ( names[0] ), type='error' ) + raise ActionInputError( "Quota '%s' has not been deleted, so it cannot be purged." % ( names[0] ) ) elif len( names ) > 1: - raise MessageException( "Quotas have not been deleted so they cannot be undeleted: " + ', '.join( names ), type='error' ) + raise ActionInputError( "Quotas have not been deleted so they cannot be undeleted: " + ', '.join( names ) ) message = "Purged %d quotas: " % len( quotas ) for q in quotas: # Delete UserQuotaAssociations diff -r 3778811f053a5f71c68408a9e8beb627f6ccdede -r 61ddd0d07950fafc18fed95354459e7715e6b1d7 lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -21,6 +21,10 @@ class ItemOwnershipException( MessageException ): pass +class ActionInputError( MessageException ): + def __init__( self, err_msg, type="error" ): + super( ActionInputError, self ).__init__( err_msg, type ) + class ObjectNotFound( Exception ): """ Accessed object was not found """ pass diff -r 3778811f053a5f71c68408a9e8beb627f6ccdede -r 61ddd0d07950fafc18fed95354459e7715e6b1d7 lib/galaxy/webapps/galaxy/api/quotas.py --- a/lib/galaxy/webapps/galaxy/api/quotas.py +++ b/lib/galaxy/webapps/galaxy/api/quotas.py @@ -11,7 +11,7 @@ from galaxy.actions.admin import AdminActions from paste.httpexceptions import HTTPBadRequest -from galaxy.exceptions import * +from galaxy.exceptions import ActionInputError log = logging.getLogger( __name__ ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Graph datatype: add data providers for SIF & XGMML; simple graph data structure to util
by commits-noreply＠bitbucket.org 09 Aug '13

09 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3778811f053a/ Changeset: 3778811f053a User: carlfeberhard Date: 2013-08-08 21:04:53 Summary: Graph datatype: add data providers for SIF & XGMML; simple graph data structure to util Affected #: 2 files diff -r 2e0abb7f9b04540e616458a90a87191ed98a3ba4 -r 3778811f053a5f71c68408a9e8beb627f6ccdede lib/galaxy/datatypes/graph.py --- a/lib/galaxy/datatypes/graph.py +++ b/lib/galaxy/datatypes/graph.py @@ -2,12 +2,18 @@ Graph content classes. """ -import data, tabular, xml +import data +import tabular +import xml + +import dataproviders +from galaxy.util import simplegraph import logging log = logging.getLogger( __name__ ) +(a)dataproviders.decorators.has_dataproviders class Xgmml( xml.GenericXml ): """ XGMML graph format @@ -48,7 +54,13 @@ #For one file only, use base class method (move/copy) data.Text.merge( split_files, output_file ) + @dataproviders.decorators.dataprovider_factory( 'node-edge', dataproviders.hierarchy.XMLDataProvider.settings ) + def node_edge_dataprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return XGMMLGraphDataProvider( dataset_source, **settings ) + +(a)dataproviders.decorators.has_dataproviders class Sif( tabular.Tabular ): """ SIF graph format @@ -75,7 +87,6 @@ """ Determines whether the file is SIF """ - print '---------------------------------------- sniffing Siffing' line = '' with open( filename ) as infile: correct = True @@ -92,6 +103,11 @@ def merge( split_files, output_file ): data.Text.merge( split_files, output_file ) + @dataproviders.decorators.dataprovider_factory( 'node-edge', dataproviders.column.ColumnarDataProvider.settings ) + def node_edge_dataprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return SIFGraphDataProvider( dataset_source, **settings ) + #TODO: we might want to look at rdflib or a similar, larger lib/egg class Rdf( xml.GenericXml ): @@ -108,3 +124,75 @@ else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' + + #TODO: won't be as simple + #(a)dataproviders.decorators.dataprovider_factory( 'node-edge', dataproviders.column.ColumnarDataProvider.settings ) + #def node_edge_dataprovider( self, dataset, **settings ): + # dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + # return None + + +# ----------------------------------------------------------------------------- graph specific data providers +class XGMMLGraphDataProvider( dataproviders.hierarchy.XMLDataProvider ): + """ + Provide two lists: nodes, edges:: + + 'nodes': contains objects of the form: + { 'id' : <some string id>, 'data': <any extra data> } + 'edges': contains objects of the form: + { 'source' : <an index into nodes>, 'target': <an index into nodes>, 'data': <any extra data> } + """ + def __iter__( self ): + # use simple graph to store nodes and links, later providing them as a dict + # essentially this is a form of aggregation + graph = simplegraph.SimpleGraph() + + parent_gen = super( XGMMLGraphDataProvider, self ).__iter__() + for graph_elem in parent_gen: + if 'children' not in graph_elem: + continue + for elem in graph_elem[ 'children' ]: + # use endswith to work around Elementtree namespaces + if elem[ 'tag' ].endswith( 'node' ): + node_id = elem[ 'attrib' ][ 'id' ] + # pass the entire, parsed xml element as the data + graph.add_node( node_id, **elem ) + + elif elem[ 'tag' ].endswith( 'edge' ): + source_id = elem[ 'attrib' ][ 'source' ] + target_id = elem[ 'attrib' ][ 'target' ] + graph.add_edge( source_id, target_id, **elem ) + + yield graph.as_dict() + + +class SIFGraphDataProvider( dataproviders.column.ColumnarDataProvider ): + """ + Provide two lists: nodes, edges:: + + 'nodes': contains objects of the form: + { 'id' : <some string id>, 'data': <any extra data> } + 'edges': contains objects of the form: + { 'source' : <an index into nodes>, 'target': <an index into nodes>, 'data': <any extra data> } + """ + def __iter__( self ): + # use simple graph to store nodes and links, later providing them as a dict + # essentially this is a form of aggregation + graph = simplegraph.SimpleGraph() + # SIF is tabular with the source, link-type, and all targets in the columns + parent_gen = super( SIFGraphDataProvider, self ).__iter__() + for columns in parent_gen: + if columns: + source_id = columns[0] + # there's no extra data for nodes (or links) in the examples I've seen + graph.add_node( source_id ) + + # targets are the (variadic) remaining columns + if len( columns ) >= 3: + relation = columns[1] + targets = columns[2:] + for target_id in targets: + graph.add_node( target_id ) + graph.add_edge( source_id, target_id, type=relation ) + + yield graph.as_dict() diff -r 2e0abb7f9b04540e616458a90a87191ed98a3ba4 -r 3778811f053a5f71c68408a9e8beb627f6ccdede lib/galaxy/util/simplegraph.py --- /dev/null +++ b/lib/galaxy/util/simplegraph.py @@ -0,0 +1,127 @@ +""" +Fencepost-simple graph structure implementation. +""" +# Currently (2013.7.12) only used in easing the parsing of graph datatype data. + +from galaxy.util.odict import odict + + +class SimpleGraphNode( object ): + """ + Node representation. + """ + def __init__( self, index, **data ): + """ + :param index: index of this node in some parent list + :type index: int + :param data: any extra data that needs to be saved + :type data: (variadic dictionary) + """ + # a bit application specific (could be 'id') + self.index = index + self.data = data + + +class SimpleGraphEdge( object ): + """ + Edge representation. + """ + def __init__( self, source_index, target_index, **data ): + """ + :param source_index: index of the edge's source node in some parent list + :type source_index: int + :param target_index: index of the edge's target node in some parent list + :type target_index: int + :param data: any extra data that needs to be saved + :type data: (variadic dictionary) + """ + self.source_index = source_index + self.target_index = target_index + self.data = data + + +class SimpleGraph( object ): + """ + Each node is unique (by id) and stores it's own index in the node list/odict. + Each edge is represented as two indeces into the node list/odict. + Both nodes and edges allow storing extra information if needed. + + Allows: + multiple edges between two nodes + self referential edges (an edge from a node to itself) + + These graphs are not specifically directed but since source and targets on the + edges are listed - it could easily be used that way. + """ + def __init__( self, nodes=None, edges=None ): + # use an odict so that edge indeces actually match the final node list indeces + self.nodes = nodes or odict() + self.edges = edges or [] + + def add_node( self, node_id, **data ): + """ + Adds a new node only if it doesn't already exist. + :param node_id: some unique identifier + :type node_id: (hashable) + :param data: any extra data that needs to be saved + :type data: (variadic dictionary) + :returns: the new node + """ + if node_id in self.nodes: + return self.nodes[ node_id ] + node_index = len( self.nodes ) + new_node = SimpleGraphNode( node_index, **data ) + self.nodes[ node_id ] = new_node + return new_node + + def add_edge( self, source_id, target_id, **data ): + """ + Adds a new node only if it doesn't already exist. + :param source_id: the id of the source node + :type source_id: (hashable) + :param target_id: the id of the target node + :type target_id: (hashable) + :param data: any extra data that needs to be saved for the edge + :type data: (variadic dictionary) + :returns: the new node + + ..note: that, although this will create new nodes if necessary, there's + no way to pass `data` to them - so if you need to assoc. more data with + the nodes, use `add_node` first. + """ + # adds target_id to source_id's edge list + # adding source_id and/or target_id to nodes if not there already + if source_id not in self.nodes: + self.add_node( source_id ) + if target_id not in self.nodes: + self.add_node( target_id ) + new_edge = SimpleGraphEdge( self.nodes[ source_id ].index, self.nodes[ target_id ].index, **data ) + self.edges.append( new_edge ) + return new_edge + + def gen_node_dicts( self ): + """ + Returns a generator that yields node dictionaries in the form: + { 'id': <the nodes unique id>, 'data': <any additional node data> } + """ + for node_id, node in self.nodes.items(): + yield { 'id': node_id, 'data': node.data } + + def gen_edge_dicts( self ): + """ + Returns a generator that yields node dictionaries in the form: + { + 'source': <the index of the source node in the graph's node list>, + 'target': <the index of the target node in the graph's node list>, + 'data' : <any additional edge data> + } + """ + for edge in self.edges: + yield { 'source': edge.source_index, 'target': edge.target_index, 'data': edge.data } + + def as_dict( self ): + """ + Returns a dictionary of the form + { 'nodes': <a list of node dictionaries>, 'edges': <a list of node dictionaries> } + """ + return { 'nodes': list( self.gen_node_dicts() ), 'edges': list( self.gen_edge_dicts() ) } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Update jquery.autocomplete.js to 2.4.4
by commits-noreply＠bitbucket.org 09 Aug '13

09 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2e0abb7f9b04/ Changeset: 2e0abb7f9b04 User: guerler Date: 2013-08-08 20:22:42 Summary: Update jquery.autocomplete.js to 2.4.4 Affected #: 2 files diff -r bf6bf3b5edfdc409f235cb91edcc9d91246df816 -r 2e0abb7f9b04540e616458a90a87191ed98a3ba4 static/scripts/galaxy.autocom_tagging.js --- a/static/scripts/galaxy.autocom_tagging.js +++ b/static/scripts/galaxy.autocom_tagging.js @@ -100,12 +100,6 @@ var new_value = this.value; - // Do nothing if return key was used to autocomplete. - if (return_key_pressed_for_autocomplete === true) { - return_key_pressed_for_autocomplete = false; - return false; - } - // Suppress space after a ":" if ( new_value.indexOf(": ", new_value.length - 2) !== -1) { this.value = new_value.substring(0, new_value.length-1); @@ -166,7 +160,7 @@ // Flush autocomplete cache because it's not out of date. // TODO: in the future, we could remove the particular item // that was chosen from the cache rather than flush it. - zz.flushCache(); + zz.data('autocompleter').cacheFlush(); } }); diff -r bf6bf3b5edfdc409f235cb91edcc9d91246df816 -r 2e0abb7f9b04540e616458a90a87191ed98a3ba4 static/scripts/libs/jquery/jquery.autocomplete.js --- a/static/scripts/libs/jquery/jquery.autocomplete.js +++ b/static/scripts/libs/jquery/jquery.autocomplete.js @@ -1,832 +1,1152 @@ -/* - * Autocomplete - jQuery plugin 1.0.2 - * - * Copyright (c) 2007 Dylan Verheul, Dan G. Switzer, Anjesh Tuladhar, Jörn Zaefferer - * - * Dual licensed under the MIT and GPL licenses: - * http://www.opensource.org/licenses/mit-license.php - * http://www.gnu.org/licenses/gpl.html - * - * Revision: $Id: jquery.autocomplete.js 5747 2008-06-25 18:30:55Z joern.zaefferer $ - * +/** + * @fileOverview jquery-autocomplete, the jQuery Autocompleter + * @author <a href="mailto:dylan@dyve.net">Dylan Verheul</a> + * @version 2.4.4 + * @requires jQuery 1.6+ + * @license MIT | GPL | Apache 2.0, see LICENSE.txt + * @see https://github.com/dyve/jquery-autocomplete */ +(function($) { + "use strict"; -String.prototype.endsWith = function(str) {return (this.match(str+"$")==str)} - -// JG HACK: each autocomplete object should have its own return_key flag. -var return_key_pressed_for_autocomplete = false; - -;(function($) { - -$.fn.extend({ - autocomplete: function(urlOrData, options) { - var isUrl = typeof urlOrData == "string"; - options = $.extend({}, $.Autocompleter.defaults, { - url: isUrl ? urlOrData : null, - data: isUrl ? null : urlOrData, - delay: isUrl ? $.Autocompleter.defaults.delay : 10, - max: options && !options.scroll ? 10 : 150 - }, options); - - // if highlight is set to false, replace it with a do-nothing function - options.highlight = options.highlight || function(value) { return value; }; - - // if the formatMatch option is not specified, then use formatItem for backwards compatibility - options.formatMatch = options.formatMatch || options.formatItem; - + /** + * jQuery autocomplete plugin + * @param {object|string} options + * @returns (object} jQuery object + */ + $.fn.autocomplete = function(options) { + var url; + if (arguments.length > 1) { + url = options; + options = arguments[1]; + options.url = url; + } else if (typeof options === 'string') { + url = options; + options = { url: url }; + } + var opts = $.extend({}, $.fn.autocomplete.defaults, options); return this.each(function() { - new $.Autocompleter(this, options); + var $this = $(this); + $this.data('autocompleter', new $.Autocompleter( + $this, + $.meta ? $.extend({}, opts, $this.data()) : opts + )); }); - }, - result: function(handler) { - return this.bind("result", handler); - }, - search: function(handler) { - return this.trigger("search", [handler]); - }, - flushCache: function() { - return this.trigger("flushCache"); - }, - setOptions: function(options){ - return this.trigger("setOptions", [options]); - }, - unautocomplete: function() { - return this.trigger("unautocomplete"); - }, - // JG: add method to show all data in cache. - showAllInCache: function() { - return this.trigger("showAllInCache"); - } -}); - -$.Autocompleter = function(input, options) { - - var KEY = { - UP: 38, - DOWN: 40, - DEL: 46, - TAB: 9, - RETURN: 13, - ESC: 27, - COMMA: 188, - PAGEUP: 33, - PAGEDOWN: 34, - BACKSPACE: 8, - COLON: 16 }; - // Create $ object for input element - var $input = $(input).attr("autocomplete", "off").addClass(options.inputClass); + /** + * Store default options + * @type {object} + */ + $.fn.autocomplete.defaults = { + inputClass: 'acInput', + loadingClass: 'acLoading', + resultsClass: 'acResults', + selectClass: 'acSelect', + queryParamName: 'q', + extraParams: {}, + remoteDataType: false, + lineSeparator: '\n', + cellSeparator: '|', + minChars: 2, + maxItemsToShow: 10, + delay: 400, + useCache: true, + maxCacheLength: 10, + matchSubset: true, + matchCase: false, + matchInside: true, + mustMatch: false, + selectFirst: false, + selectOnly: false, + showResult: null, + preventDefaultReturn: 1, + preventDefaultTab: 0, + autoFill: false, + filterResults: true, + filter: true, + sortResults: true, + sortFunction: null, + onItemSelect: null, + onNoMatch: null, + onFinish: null, + matchStringConverter: null, + beforeUseConverter: null, + autoWidth: 'min-width', + useDelimiter: false, + delimiterChar: ',', + delimiterKeyCode: 188, + processData: null, + onError: null, + enabled: true + }; - var timeout; - var previousValue = ""; - var cache = $.Autocompleter.Cache(options); - var hasFocus = 0; - var lastKeyPressCode; - var config = { - mouseDownOnSelect: false + /** + * Sanitize result + * @param {Object} result + * @returns {Object} object with members value (String) and data (Object) + * @private + */ + var sanitizeResult = function(result) { + var value, data; + var type = typeof result; + if (type === 'string') { + value = result; + data = {}; + } else if ($.isArray(result)) { + value = result[0]; + data = result.slice(1); + } else if (type === 'object') { + value = result.value; + data = result.data; + } + value = String(value); + if (typeof data !== 'object') { + data = {}; + } + return { + value: value, + data: data + }; }; - var select = $.Autocompleter.Select(options, input, selectCurrent, config); - - var blockSubmit; - - // prevent form submit in opera when selecting with return key - $.browser.opera && $(input.form).bind("submit.autocomplete", function() { - if (blockSubmit) { - blockSubmit = false; - return false; + + /** + * Sanitize integer + * @param {mixed} value + * @param {Object} options + * @returns {Number} integer + * @private + */ + var sanitizeInteger = function(value, stdValue, options) { + var num = parseInt(value, 10); + options = options || {}; + if (isNaN(num) || (options.min && num < options.min)) { + num = stdValue; } - }); - - // Firefox only triggers holding down a key with keypress - $input.bind(($.browser.mozilla ? "keypress" : "keydown") + ".autocomplete", function(event) { - // track last key pressed - lastKeyPressCode = event.keyCode; - switch(event.keyCode) { - - case KEY.UP: - event.preventDefault(); - if ( select.visible() ) { - select.prev(); - } else { - onChange(0, true); - } + return num; + }; + + /** + * Create partial url for a name/value pair + */ + var makeUrlParam = function(name, value) { + return [name, encodeURIComponent(value)].join('='); + }; + + /** + * Build an url + * @param {string} url Base url + * @param {object} [params] Dictionary of parameters + */ + var makeUrl = function(url, params) { + var urlAppend = []; + $.each(params, function(index, value) { + urlAppend.push(makeUrlParam(index, value)); + }); + if (urlAppend.length) { + url += url.indexOf('?') === -1 ? '?' : '&'; + url += urlAppend.join('&'); + } + return url; + }; + + /** + * Default sort filter + * @param {object} a + * @param {object} b + * @param {boolean} matchCase + * @returns {number} + */ + var sortValueAlpha = function(a, b, matchCase) { + a = String(a.value); + b = String(b.value); + if (!matchCase) { + a = a.toLowerCase(); + b = b.toLowerCase(); + } + if (a > b) { + return 1; + } + if (a < b) { + return -1; + } + return 0; + }; + + /** + * Parse data received in text format + * @param {string} text Plain text input + * @param {string} lineSeparator String that separates lines + * @param {string} cellSeparator String that separates cells + * @returns {array} Array of autocomplete data objects + */ + var plainTextParser = function(text, lineSeparator, cellSeparator) { + var results = []; + var i, j, data, line, value, lines; + // Be nice, fix linebreaks before splitting on lineSeparator + lines = String(text).replace('\r\n', '\n').split(lineSeparator); + for (i = 0; i < lines.length; i++) { + line = lines[i].split(cellSeparator); + data = []; + for (j = 0; j < line.length; j++) { + data.push(decodeURIComponent(line[j])); + } + value = data.shift(); + results.push({ value: value, data: data }); + } + return results; + }; + + /** + * Autocompleter class + * @param {object} $elem jQuery object with one input tag + * @param {object} options Settings + * @constructor + */ + $.Autocompleter = function($elem, options) { + + /** + * Assert parameters + */ + if (!$elem || !($elem instanceof $) || $elem.length !== 1 || ($elem.get(0).tagName.toUpperCase() !== 'INPUT' && $elem.get(0).tagName.toUpperCase() !== 'TEXTAREA')) { + throw new Error('Invalid parameter for jquery.Autocompleter, jQuery object with one element with INPUT or TEXTAREA tag expected.'); + } + + /** + * @constant Link to this instance + * @type object + * @private + */ + var self = this; + + /** + * @property {object} Options for this instance + * @public + */ + this.options = options; + + /** + * @property object Cached data for this instance + * @private + */ + this.cacheData_ = {}; + + /** + * @property {number} Number of cached data items + * @private + */ + this.cacheLength_ = 0; + + /** + * @property {string} Class name to mark selected item + * @private + */ + this.selectClass_ = 'jquery-autocomplete-selected-item'; + + /** + * @property {number} Handler to activation timeout + * @private + */ + this.keyTimeout_ = null; + + /** + * @property {number} Handler to finish timeout + * @private + */ + this.finishTimeout_ = null; + + /** + * @property {number} Last key pressed in the input field (store for behavior) + * @private + */ + this.lastKeyPressed_ = null; + + /** + * @property {string} Last value processed by the autocompleter + * @private + */ + this.lastProcessedValue_ = null; + + /** + * @property {string} Last value selected by the user + * @private + */ + this.lastSelectedValue_ = null; + + /** + * @property {boolean} Is this autocompleter active (showing results)? + * @see showResults + * @private + */ + this.active_ = false; + + /** + * @property {boolean} Is this autocompleter allowed to finish on blur? + * @private + */ + this.finishOnBlur_ = true; + + /** + * Sanitize options + */ + this.options.minChars = sanitizeInteger(this.options.minChars, $.fn.autocomplete.defaults.minChars, { min: 0 }); + this.options.maxItemsToShow = sanitizeInteger(this.options.maxItemsToShow, $.fn.autocomplete.defaults.maxItemsToShow, { min: 0 }); + this.options.maxCacheLength = sanitizeInteger(this.options.maxCacheLength, $.fn.autocomplete.defaults.maxCacheLength, { min: 1 }); + this.options.delay = sanitizeInteger(this.options.delay, $.fn.autocomplete.defaults.delay, { min: 0 }); + if (this.options.preventDefaultReturn != 2) { + this.options.preventDefaultReturn = this.options.preventDefaultReturn ? 1 : 0; + } + if (this.options.preventDefaultTab != 2) { + this.options.preventDefaultTab = this.options.preventDefaultTab ? 1 : 0; + } + + /** + * Init DOM elements repository + */ + this.dom = {}; + + /** + * Store the input element we're attached to in the repository + */ + this.dom.$elem = $elem; + + /** + * Switch off the native autocomplete and add the input class + */ + this.dom.$elem.attr('autocomplete', 'off').addClass(this.options.inputClass); + + /** + * Create DOM element to hold results, and force absolute position + */ + this.dom.$results = $('<div></div>').hide().addClass(this.options.resultsClass).css({ + position: 'absolute' + }); + $('body').append(this.dom.$results); + + /** + * Attach keyboard monitoring to $elem + */ + $elem.keydown(function(e) { + self.lastKeyPressed_ = e.keyCode; + switch(self.lastKeyPressed_) { + + case self.options.delimiterKeyCode: // comma = 188 + if (self.options.useDelimiter && self.active_) { + self.selectCurrent(); + } + break; + + // ignore navigational & special keys + case 35: // end + case 36: // home + case 16: // shift + case 17: // ctrl + case 18: // alt + case 37: // left + case 39: // right + break; + + case 38: // up + e.preventDefault(); + if (self.active_) { + self.focusPrev(); + } else { + self.activate(); + } + return false; + + case 40: // down + e.preventDefault(); + if (self.active_) { + self.focusNext(); + } else { + self.activate(); + } + return false; + + case 9: // tab + if (self.active_) { + self.selectCurrent(); + if (self.options.preventDefaultTab) { + e.preventDefault(); + return false; + } + } + if (self.options.preventDefaultTab === 2) { + e.preventDefault(); + return false; + } break; - - case KEY.DOWN: - event.preventDefault(); - if ( select.visible() ) { - select.next(); - } else { - onChange(0, true); - } + + case 13: // return + if (self.active_) { + self.selectCurrent(); + if (self.options.preventDefaultReturn) { + e.preventDefault(); + return false; + } + } + if (self.options.preventDefaultReturn === 2) { + e.preventDefault(); + return false; + } break; - - case KEY.PAGEUP: - event.preventDefault(); - if ( select.visible() ) { - select.pageUp(); - } else { - onChange(0, true); - } + + case 27: // escape + if (self.active_) { + e.preventDefault(); + self.deactivate(true); + return false; + } break; - - case KEY.PAGEDOWN: - event.preventDefault(); - if ( select.visible() ) { - select.pageDown(); - } else { - onChange(0, true); - } - break; - - // matches also semicolon - case options.multiple && $.trim(options.multipleSeparator) == "," && KEY.COMMA: - case KEY.TAB: - case KEY.RETURN: - if (event.keyCode == KEY.RETURN) - return_key_pressed_for_autocomplete = false; - if( selectCurrent() ) { - // stop default to prevent a form submit, Opera needs special handling - event.preventDefault(); - blockSubmit = true; - - // JG: set flag to indicate that a selection just occurred using the return key. FYI: - // event.stopPropagation() does not work. - if (event.keyCode == KEY.RETURN) - return_key_pressed_for_autocomplete = true; - - return false; - } - - case KEY.ESC: - select.hide(); - break; - case KEY.COLON: - break; - - default: - clearTimeout(timeout); - timeout = setTimeout(onChange, options.delay); - break; - } - }).focus(function(){ - // track whether the field has focus, we shouldn't process any - // results if the field no longer has focus - hasFocus++; - }).blur(function() { - hasFocus = 0; - if (!config.mouseDownOnSelect) { - // JG: if blur and user is not selecting with mouse, hide - // object. - select.hide(); - } - return this; - }).click(function() { - // show select when clicking in a focused field - if ( hasFocus++ > 1 && !select.visible() ) { - onChange(0, true); - } - return this; - }).bind("search", function() { - // TODO why not just specifying both arguments? - var fn = (arguments.length > 1) ? arguments[1] : null; - function findValueCallback(q, data) { - var result; - if( data && data.length ) { - for (var i=0; i < data.length; i++) { - if( data[i].result.toLowerCase() == q.toLowerCase() ) { - result = data[i]; - break; - } - } + + default: + self.activate(); + } - if( typeof fn == "function" ) fn(result); - else $input.trigger("result", result && [result.data, result.value]); - } - $.each(trimWords($input.val()), function(i, value) { - request(value, findValueCallback, findValueCallback); }); - return this; - }).bind("flushCache", function() { - cache.flush(); - }).bind("setOptions", function() { - $.extend(options, arguments[1]); - // if we've updated the data, repopulate - if ( "data" in arguments[1] ) - cache.populate(); - }).bind("unautocomplete", function() { - select.unbind(); - $input.unbind(); - $(input.form).unbind(".autocomplete"); - }) - // JG: Show all data in cache. - .bind("showAllInCache", function() { - receiveData('', cache.load('')); - }); - - function selectCurrent() { - var selected = select.selected(); - if( !selected ) - return false; - - var v = selected.result; - previousValue = v; - - if ( options.multiple ) { - var words = trimWords($input.val()); - if ( words.length > 1 ) { - v = words.slice(0, words.length - 1).join( options.multipleSeparator ) + options.multipleSeparator + v; + /** + * Attach paste event listener because paste may occur much later then keydown or even without a keydown at all + */ + $elem.on('paste', function() { + self.activate(); + }); + + /** + * Finish on blur event + * Use a timeout because instant blur gives race conditions + */ + var onBlurFunction = function() { + self.deactivate(true); + } + $elem.blur(function() { + if (self.finishOnBlur_) { + self.finishTimeout_ = setTimeout(onBlurFunction, 200); } - v += options.multipleSeparator; + }); + /** + * Catch a race condition on form submit + */ + $elem.parents('form').on('submit', onBlurFunction); + + }; + + /** + * Position output DOM elements + * @private + */ + $.Autocompleter.prototype.position = function() { + var offset = this.dom.$elem.offset(); + var height = this.dom.$results.outerHeight(); + var totalHeight = $(window).outerHeight(); + var inputBottom = offset.top + this.dom.$elem.outerHeight(); + var bottomIfDown = inputBottom + height; + // Set autocomplete results at the bottom of input + var position = {top: inputBottom, left: offset.left}; + if (bottomIfDown > totalHeight) { + // Try to set autocomplete results at the top of input + var topIfUp = offset.top - height; + if (topIfUp >= 0) { + position.top = topIfUp; + } } - - $input.val(v); - hideResultsNow(); - $input.trigger("result", [selected.data, selected.value]); - return true; - } - - function onChange(crap, skipPrevCheck) { - if( lastKeyPressCode == KEY.DEL ) { - select.hide(); - return; + this.dom.$results.css(position); + }; + + /** + * Read from cache + * @private + */ + $.Autocompleter.prototype.cacheRead = function(filter) { + var filterLength, searchLength, search, maxPos, pos; + if (this.options.useCache) { + filter = String(filter); + filterLength = filter.length; + if (this.options.matchSubset) { + searchLength = 1; + } else { + searchLength = filterLength; + } + while (searchLength <= filterLength) { + if (this.options.matchInside) { + maxPos = filterLength - searchLength; + } else { + maxPos = 0; + } + pos = 0; + while (pos <= maxPos) { + search = filter.substr(0, searchLength); + if (this.cacheData_[search] !== undefined) { + return this.cacheData_[search]; + } + pos++; + } + searchLength++; + } } + return false; + }; - var currentValue = $input.val(); - - if ( !skipPrevCheck && currentValue == previousValue ) - return; - - previousValue = currentValue; - - currentValue = lastWord(currentValue); - if ( currentValue.length >= options.minChars) { - $input.addClass(options.loadingClass); - if (!options.matchCase) - currentValue = currentValue.toLowerCase(); - request(currentValue, receiveData, hideResultsNow); - } else { - stopLoading(); - select.hide(); + /** + * Write to cache + * @private + */ + $.Autocompleter.prototype.cacheWrite = function(filter, data) { + if (this.options.useCache) { + if (this.cacheLength_ >= this.options.maxCacheLength) { + this.cacheFlush(); + } + filter = String(filter); + if (this.cacheData_[filter] !== undefined) { + this.cacheLength_++; + } + this.cacheData_[filter] = data; + return this.cacheData_[filter]; } + return false; }; - - function trimWords(value) { - if ( !value ) { - return [""]; + + /** + * Flush cache + * @public + */ + $.Autocompleter.prototype.cacheFlush = function() { + this.cacheData_ = {}; + this.cacheLength_ = 0; + }; + + /** + * Call hook + * Note that all called hooks are passed the autocompleter object + * @param {string} hook + * @param data + * @returns Result of called hook, false if hook is undefined + */ + $.Autocompleter.prototype.callHook = function(hook, data) { + var f = this.options[hook]; + if (f && $.isFunction(f)) { + return f(data, this); } - var words = value.split( options.multipleSeparator ); - var result = []; - $.each(words, function(i, value) { - if ( $.trim(value) ) - result[i] = $.trim(value); - }); - return result; - } - - function lastWord(value) { - if ( !options.multiple ) - return value; - var words = trimWords(value); - return words[words.length - 1]; - } - - // fills in the input box w/the first match (assumed to be the best match) - // q: the term entered - // sValue: the first matching result - function autoFill(q, sValue){ - // autofill in the complete box w/the first match as long as the user hasn't entered in more data - // if the last user key pressed was backspace, don't autofill - if( options.autoFill && (lastWord($input.val()).toLowerCase() == q.toLowerCase()) && lastKeyPressCode != KEY.BACKSPACE ) { - // fill in the value (keep the case the user has typed) - $input.val($input.val() + sValue.substring(lastWord(previousValue).length)); - // select the portion of the value not typed by the user (so the next character will erase) - $.Autocompleter.Selection(input, previousValue.length, previousValue.length + sValue.length); + return false; + }; + + /** + * Set timeout to activate autocompleter + */ + $.Autocompleter.prototype.activate = function() { + if (!this.options.enabled) return; + var self = this; + if (this.keyTimeout_) { + clearTimeout(this.keyTimeout_); + } + this.keyTimeout_ = setTimeout(function() { + self.activateNow(); + }, this.options.delay); + }; + + /** + * Activate autocompleter immediately + */ + $.Autocompleter.prototype.activateNow = function() { + var value = this.beforeUseConverter(this.dom.$elem.val()); + if (value !== this.lastProcessedValue_ && value !== this.lastSelectedValue_) { + this.fetchData(value); } }; - function hideResults() { - clearTimeout(timeout); - timeout = setTimeout(hideResultsNow, 200); - }; - - function hideResultsNow() { - var wasVisible = select.visible(); - select.hide(); - clearTimeout(timeout); - stopLoading(); - if (options.mustMatch) { - // call search and run callback - $input.search( - function (result){ - // if no value found, clear the input box - if( !result ) { - if (options.multiple) { - var words = trimWords($input.val()).slice(0, -1); - $input.val( words.join(options.multipleSeparator) + (words.length ? options.multipleSeparator : "") ); - } - else - $input.val( "" ); - } - } - ); - } - if (wasVisible) - // position cursor at end of input field - $.Autocompleter.Selection(input, input.value.length, input.value.length); - }; - - function receiveData(q, data) { - if ( data && data.length && hasFocus ) { - stopLoading(); - select.display(data, q); - autoFill(q, data[0].value); - select.show(); + /** + * Get autocomplete data for a given value + * @param {string} value Value to base autocompletion on + * @private + */ + $.Autocompleter.prototype.fetchData = function(value) { + var self = this; + var processResults = function(results, filter) { + if (self.options.processData) { + results = self.options.processData(results); + } + self.showResults(self.filterResults(results, filter), filter); + }; + this.lastProcessedValue_ = value; + if (value.length < this.options.minChars) { + processResults([], value); + } else if (this.options.data) { + processResults(this.options.data, value); } else { - hideResultsNow(); + this.fetchRemoteData(value, function(remoteData) { + processResults(remoteData, value); + }); } }; - function request(term, success, failure) { - if (!options.matchCase) - term = term.toLowerCase(); - var data = cache.load(term); - - // JG: hack: if term ends with ':', kill data to force an ajax request. - if (term.endsWith(":")) - data = null; - - // recieve the cached data - if (data && data.length) { - success(term, data); - // if an AJAX url has been supplied, try loading the data now - } else if( (typeof options.url == "string") && (options.url.length > 0) ){ - var extraParams = { - timestamp: +new Date() + /** + * Get remote autocomplete data for a given value + * @param {string} filter The filter to base remote data on + * @param {function} callback The function to call after data retrieval + * @private + */ + $.Autocompleter.prototype.fetchRemoteData = function(filter, callback) { + var data = this.cacheRead(filter); + if (data) { + callback(data); + } else { + var self = this; + var dataType = self.options.remoteDataType === 'json' ? 'json' : 'text'; + var ajaxCallback = function(data) { + var parsed = false; + if (data !== false) { + parsed = self.parseRemoteData(data); + self.cacheWrite(filter, parsed); + } + self.dom.$elem.removeClass(self.options.loadingClass); + callback(parsed); }; - $.each(options.extraParams, function(key, param) { - extraParams[key] = typeof param == "function" ? param() : param; + this.dom.$elem.addClass(this.options.loadingClass); + $.ajax({ + url: this.makeUrl(filter), + success: ajaxCallback, + error: function(jqXHR, textStatus, errorThrown) { + if($.isFunction(self.options.onError)) { + self.options.onError(jqXHR, textStatus, errorThrown); + } else { + ajaxCallback(false); + } + }, + dataType: dataType }); - - $.ajax({ - // try to leverage ajaxQueue plugin to abort previous requests - mode: "abort", - // limit abortion to this input - port: "autocomplete" + input.name, - dataType: options.dataType, - url: options.url, - data: $.extend({ - q: lastWord(term), - limit: options.max - }, extraParams), - success: function(data) { - var parsed = options.parse && options.parse(data) || parse(data); - cache.add(term, parsed); - success(term, parsed); - } - }); - } else { - // if we have a failure, we need to empty the list -- this prevents the the [TAB] key from selecting the last successful match - select.emptyList(); - failure(term); } }; - - function parse(data) { - var parsed = []; - var rows = data.split("\n"); - for (var i=0; i < rows.length; i++) { - var row = $.trim(rows[i]); - if (row) { - row = row.split("|"); - parsed[parsed.length] = { - data: row, - value: row[0], - result: options.formatResult && options.formatResult(row, row[0]) || row[0] - }; + + /** + * Create or update an extra parameter for the remote request + * @param {string} name Parameter name + * @param {string} value Parameter value + * @public + */ + $.Autocompleter.prototype.setExtraParam = function(name, value) { + var index = $.trim(String(name)); + if (index) { + if (!this.options.extraParams) { + this.options.extraParams = {}; + } + if (this.options.extraParams[index] !== value) { + this.options.extraParams[index] = value; + this.cacheFlush(); } } - return parsed; + + return this; }; - function stopLoading() { - $input.removeClass(options.loadingClass); + /** + * Build the url for a remote request + * If options.queryParamName === false, append query to url instead of using a GET parameter + * @param {string} param The value parameter to pass to the backend + * @returns {string} The finished url with parameters + */ + $.Autocompleter.prototype.makeUrl = function(param) { + var self = this; + var url = this.options.url; + var params = $.extend({}, this.options.extraParams); + + if (this.options.queryParamName === false) { + url += encodeURIComponent(param); + } else { + params[this.options.queryParamName] = param; + } + + return makeUrl(url, params); }; -}; + /** + * Parse data received from server + * @param remoteData Data received from remote server + * @returns {array} Parsed data + */ + $.Autocompleter.prototype.parseRemoteData = function(remoteData) { + var remoteDataType; + var data = remoteData; + if (this.options.remoteDataType === 'json') { + remoteDataType = typeof(remoteData); + switch (remoteDataType) { + case 'object': + data = remoteData; + break; + case 'string': + data = $.parseJSON(remoteData); + break; + default: + throw new Error("Unexpected remote data type: " + remoteDataType); + } + return data; + } + return plainTextParser(data, this.options.lineSeparator, this.options.cellSeparator); + }; -$.Autocompleter.defaults = { - inputClass: "ac_input", - resultsClass: "ac_results", - loadingClass: "ac_loading", - minChars: 1, - delay: 400, - matchCase: false, - matchSubset: true, - matchContains: false, - cacheLength: 10, - max: 100, - mustMatch: false, - extraParams: {}, - selectFirst: true, - formatItem: function(row) { return row[0]; }, - formatMatch: null, - autoFill: false, - width: 0, - multiple: false, - multipleSeparator: ", ", - highlight: function(value, term) { - // JG: short-circuit highlighting if term is empty string. - if (term == "") - return value; - return value.replace(new RegExp("(?![^&;]+;)(?!<[^<>]*)(" + term.replace(/([\^\$\[\]\{\}\*\.\+\?\|\\])/gi, "\\$1") + ")(?![^<>]*>)(?![^&;]+;)", "gi"), "<strong>$1</strong>"); - }, - scroll: true, - scrollHeight: 180 -}; + /** + * Default filter for results + * @param {Object} result + * @param {String} filter + * @returns {boolean} Include this result + * @private + */ + $.Autocompleter.prototype.defaultFilter = function(result, filter) { + if (!result.value) { + return false; + } + if (this.options.filterResults) { + var pattern = this.matchStringConverter(filter); + var testValue = this.matchStringConverter(result.value); + if (!this.options.matchCase) { + pattern = pattern.toLowerCase(); + testValue = testValue.toLowerCase(); + } + var patternIndex = testValue.indexOf(pattern); + if (this.options.matchInside) { + return patternIndex > -1; + } else { + return patternIndex === 0; + } + } + return true; + }; -$.Autocompleter.Cache = function(options) { + /** + * Filter result + * @param {Object} result + * @param {String} filter + * @returns {boolean} Include this result + * @private + */ + $.Autocompleter.prototype.filterResult = function(result, filter) { + // No filter + if (this.options.filter === false) { + return true; + } + // Custom filter + if ($.isFunction(this.options.filter)) { + return this.options.filter(result, filter); + } + // Default filter + return this.defaultFilter(result, filter); + }; - var data = {}; - var length = 0; + /** + * Filter results + * @param results + * @param filter + */ + $.Autocompleter.prototype.filterResults = function(results, filter) { + var filtered = []; + var i, result; - function matchSubset(s, sub) { - if (!options.matchCase) - s = s.toLowerCase(); - var i = s.indexOf(sub); - if (i == -1) return false; - return i == 0 || options.matchContains; + for (i = 0; i < results.length; i++) { + result = sanitizeResult(results[i]); + if (this.filterResult(result, filter)) { + filtered.push(result); + } + } + if (this.options.sortResults) { + filtered = this.sortResults(filtered, filter); + } + if (this.options.maxItemsToShow > 0 && this.options.maxItemsToShow < filtered.length) { + filtered.length = this.options.maxItemsToShow; + } + return filtered; }; - - function add(q, value) { - if (length > options.cacheLength){ - flush(); + + /** + * Sort results + * @param results + * @param filter + */ + $.Autocompleter.prototype.sortResults = function(results, filter) { + var self = this; + var sortFunction = this.options.sortFunction; + if (!$.isFunction(sortFunction)) { + sortFunction = function(a, b, f) { + return sortValueAlpha(a, b, self.options.matchCase); + }; } - if (!data[q]){ - length++; + results.sort(function(a, b) { + return sortFunction(a, b, filter, self.options); + }); + return results; + }; + + /** + * Convert string before matching + * @param s + * @param a + * @param b + */ + $.Autocompleter.prototype.matchStringConverter = function(s, a, b) { + var converter = this.options.matchStringConverter; + if ($.isFunction(converter)) { + s = converter(s, a, b); } - data[q] = value; - } - - function populate(){ - if( !options.data ) return false; - // track the matches - var stMatchSets = {}, - nullData = 0; + return s; + }; - // no url was specified, we need to adjust the cache length to make sure it fits the local data store - if( !options.url ) options.cacheLength = 1; - - // track all options for minChars = 0 - stMatchSets[""] = []; - - // loop through the array and create a lookup structure - for ( var i = 0, ol = options.data.length; i < ol; i++ ) { - var rawValue = options.data[i]; - // if rawValue is a string, make an array otherwise just reference the array - rawValue = (typeof rawValue == "string") ? [rawValue] : rawValue; - - var value = options.formatMatch(rawValue, i+1, options.data.length); - if ( value === false ) - continue; - - if( !stMatchSets[value] ) { - stMatchSets[value] = []; + /** + * Convert string before use + * @param {String} s + */ + $.Autocompleter.prototype.beforeUseConverter = function(s) { + s = this.getValue(s); + var converter = this.options.beforeUseConverter; + if ($.isFunction(converter)) { + s = converter(s); + } + return s; + }; + + /** + * Enable finish on blur event + */ + $.Autocompleter.prototype.enableFinishOnBlur = function() { + this.finishOnBlur_ = true; + }; + + /** + * Disable finish on blur event + */ + $.Autocompleter.prototype.disableFinishOnBlur = function() { + this.finishOnBlur_ = false; + }; + + /** + * Create a results item (LI element) from a result + * @param result + */ + $.Autocompleter.prototype.createItemFromResult = function(result) { + var self = this; + var $li = $('<li/>'); + $li.html(this.showResult(result.value, result.data)); + $li.data({value: result.value, data: result.data}) + .click(function() { + self.selectItem($li); + }) + .mousedown(self.disableFinishOnBlur) + .mouseup(self.enableFinishOnBlur) + ; + return $li; + }; + + /** + * Get all items from the results list + * @param result + */ + $.Autocompleter.prototype.getItems = function() { + return $('>ul>li', this.dom.$results); + }; + + /** + * Show all results + * @param results + * @param filter + */ + $.Autocompleter.prototype.showResults = function(results, filter) { + var numResults = results.length; + var self = this; + var $ul = $('<ul></ul>'); + var i, result, $li, autoWidth, first = false, $first = false; + + if (numResults) { + for (i = 0; i < numResults; i++) { + result = results[i]; + $li = this.createItemFromResult(result); + $ul.append($li); + if (first === false) { + first = String(result.value); + $first = $li; + $li.addClass(this.options.firstItemClass); + } + if (i === numResults - 1) { + $li.addClass(this.options.lastItemClass); + } } - // if the match is a string - var row = { - value: value, - data: rawValue, - result: options.formatResult && options.formatResult(rawValue) || value - }; - - // push the current match into the set list - stMatchSets[value].push(row); + this.dom.$results.html($ul).show(); - // keep track of minChars zero items - if ( nullData++ < options.max ) { - stMatchSets[""].push(row); + // Always recalculate position since window size or + // input element location may have changed. + this.position(); + if (this.options.autoWidth) { + autoWidth = this.dom.$elem.outerWidth() - this.dom.$results.outerWidth() + this.dom.$results.width(); + this.dom.$results.css(this.options.autoWidth, autoWidth); } - }; - - // add the data items to the cache - $.each(stMatchSets, function(i, value) { - // increase the cache size - options.cacheLength++; - // add to the cache - add(i, value); - }); - } - - // populate any existing data - setTimeout(populate, 25); - - function flush(){ - data = {}; - length = 0; - } - - return { - flush: flush, - add: add, - populate: populate, - load: function(q) { - if (!options.cacheLength || !length) - return null; - - /* - * if dealing w/local data and matchContains than we must make sure - * to loop through all the data collections looking for matches - */ - if( !options.url && options.matchContains ) { - // track all matches - var csub = []; - // loop through all the data grids for matches - for( var k in data ) { - // don't search through the stMatchSets[""] (minChars: 0) cache - // this prevents duplicates - if( k.length > 0 ){ - var c = data[k]; - $.each(c, function(i, x) { - // if we've got a match, add it to the array - if (matchSubset(x.value, q)) { - csub.push(x); - } - }); - } - } - return csub; - } else - // if the exact item exists, use it - if (data[q]) { - return data[q]; - } else - if (options.matchSubset) { - for (var i = q.length - 1; i >= options.minChars; i--) { - var c = data[q.substr(0, i)]; - if (c) { - var csub = []; - $.each(c, function(i, x) { - if ( (x.data.indexOf("#Header") == 0) || - (matchSubset(x.value, q)) ) { - csub[csub.length] = x; - } - }); - return csub; - } - } - + this.getItems().hover( + function() { self.focusItem(this); }, + function() { /* void */ } + ); + if (this.autoFill(first, filter) || this.options.selectFirst || (this.options.selectOnly && numResults === 1)) { + this.focusItem($first); } - return null; + this.active_ = true; + } else { + this.hideResults(); + this.active_ = false; } }; -}; -$.Autocompleter.Select = function (options, input, select, config) { - var CLASSES = { - ACTIVE: "ac_over" + $.Autocompleter.prototype.showResult = function(value, data) { + if ($.isFunction(this.options.showResult)) { + return this.options.showResult(value, data); + } else { + return $('<p></p>').text(value).html(); + } }; - - var listItems, - active = -1, - data, - term = "", - needsInit = true, - element, - list; - - // Create results - function init() { - if (!needsInit) - return; - - element = $("<div/>") - .hide() - .addClass(options.resultsClass) - .css("position", "absolute") - .bind("mouseleave", function() { - element.hide(); - }) - .appendTo(document.body); - list = $("<ul/>").appendTo(element).mouseover( function(event) { - if(target(event).nodeName && target(event).nodeName.toUpperCase() == 'LI') { - active = $("li", list).removeClass(CLASSES.ACTIVE).index(target(event)); - // JG: Only add active class if target is not a header. - if (!headerAtPosition(active)) - $(target(event)).addClass(CLASSES.ACTIVE); + $.Autocompleter.prototype.autoFill = function(value, filter) { + var lcValue, lcFilter, valueLength, filterLength; + if (this.options.autoFill && this.lastKeyPressed_ !== 8) { + lcValue = String(value).toLowerCase(); + lcFilter = String(filter).toLowerCase(); + valueLength = value.length; + filterLength = filter.length; + if (lcValue.substr(0, filterLength) === lcFilter) { + var d = this.getDelimiterOffsets(); + var pad = d.start ? ' ' : ''; // if there is a preceding delimiter + this.setValue( pad + value ); + var start = filterLength + d.start + pad.length; + var end = valueLength + d.start + pad.length; + this.selectRange(start, end); + return true; } - }).click(function(event) { - // JG: Ignore click on header. - active = $("li", list).index(target(event)); - if (headerAtPosition(active)) - return; + } + return false; + }; - // Handle click on autocomplete options. - $(target(event)).addClass(CLASSES.ACTIVE); - select(); - // TODO provide option to avoid setting focus again after selection? useful for cleanup-on-focus - input.focus(); - return false; - }).mousedown(function() { - config.mouseDownOnSelect = true; - }).mouseup(function() { - config.mouseDownOnSelect = false; - }); + $.Autocompleter.prototype.focusNext = function() { + this.focusMove(+1); + }; - if( options.width > 0 ) - element.css("width", options.width); + $.Autocompleter.prototype.focusPrev = function() { + this.focusMove(-1); + }; - needsInit = false; - } - - function target(event) { - var element = event.target; - while(element && element.tagName != "LI") - element = element.parentNode; - // more fun with IE, sometimes event.target is empty, just ignore it then - if(!element) - return []; - return element; - } + $.Autocompleter.prototype.focusMove = function(modifier) { + var $items = this.getItems(); + modifier = sanitizeInteger(modifier, 0); + if (modifier) { + for (var i = 0; i < $items.length; i++) { + if ($($items[i]).hasClass(this.selectClass_)) { + this.focusItem(i + modifier); + return; + } + } + } + this.focusItem(0); + }; - // JG: Returns true iff there is a header element at the given position. - function headerAtPosition(position) { - dataAtPosition = data[position].data; - return (dataAtPosition[0].indexOf("#Header") == 0); - } - - function moveSelect(step) { - listItems.slice(active, active + 1).removeClass(CLASSES.ACTIVE); - // JG: while active item is a header, continue stepping. - var isHeader = false; - do { - movePosition(step); - isHeader = headerAtPosition(active); - } - while (isHeader); - var activeItem = listItems.slice(active, active + 1).addClass(CLASSES.ACTIVE); - - if(options.scroll) { - var offset = 0; - listItems.slice(0, active).each(function() { - offset += this.offsetHeight; - }); - if((offset + activeItem[0].offsetHeight - list.scrollTop()) > list[0].clientHeight) { - list.scrollTop(offset + activeItem[0].offsetHeight - list.innerHeight()); - } else if(offset < list.scrollTop()) { - list.scrollTop(offset); + $.Autocompleter.prototype.focusItem = function(item) { + var $item, $items = this.getItems(); + if ($items.length) { + $items.removeClass(this.selectClass_).removeClass(this.options.selectClass); + if (typeof item === 'number') { + if (item < 0) { + item = 0; + } else if (item >= $items.length) { + item = $items.length - 1; + } + $item = $($items[item]); + } else { + $item = $(item); + } + if ($item) { + $item.addClass(this.selectClass_).addClass(this.options.selectClass); } } }; - - function movePosition(step) { - active += step; - if (active < 0) { - active = listItems.size() - 1; - } else if (active >= listItems.size()) { - active = 0; - } - } - - function limitNumberOfItems(available) { - return options.max && options.max < available - ? options.max - : available; - } - - function fillList() { - list.empty(); - var max = limitNumberOfItems(data.length); - for (var i=0; i < max; i++) { - if (!data[i]) - continue; - - var formatted = options.formatItem(data[i].data, i+1, max, data[i].value, term); - if ( formatted === false ) - continue; - // JG: Build list item by formatting the item and choosing a CSS class. - if (headerAtPosition(i)) { - // Found header element; only add header if there are subsequent elements. - if (i != max-1) - var li = $("<li/>").html(data[i].data[1]).addClass("ac_header").appendTo(list)[0]; - } else { - // Found completion element. - var li = $("<li/>").html(options.highlight(formatted, term)).addClass(i%2 == 0 ? "ac_even" : "ac_odd").appendTo(list)[0]; - } - - $.data(li, "ac_data", data[i]); - } - listItems = list.find("li"); - if ( options.selectFirst ) { - listItems.slice(0, 1).addClass(CLASSES.ACTIVE); - active = 0; - } - // apply bgiframe if available - if ( $.fn.bgiframe ) - list.bgiframe(); - } - - return { - display: function(d, q) { - init(); - data = d; - term = q; - fillList(); - }, - next: function() { - moveSelect(1); - }, - prev: function() { - moveSelect(-1); - }, - pageUp: function() { - if (active != 0 && active - 8 < 0) { - moveSelect( -active ); - } else { - moveSelect(-8); - } - }, - pageDown: function() { - if (active != listItems.size() - 1 && active + 8 > listItems.size()) { - moveSelect( listItems.size() - 1 - active ); - } else { - moveSelect(8); - } - }, - hide: function() { - element && element.hide(); - listItems && listItems.removeClass(CLASSES.ACTIVE); - active = -1; - }, - visible : function() { - return element && element.is(":visible"); - }, - current: function() { - return this.visible() && (listItems.filter("." + CLASSES.ACTIVE)[0] || options.selectFirst && listItems[0]); - }, - show: function() { - var offset = $(input).offset(); - element.css({ - width: typeof options.width == "string" || options.width > 0 ? options.width : $(input).width(), - top: offset.top + input.offsetHeight, - left: offset.left - }).show(); - if(options.scroll) { - list.scrollTop(0); - list.css({ - maxHeight: options.scrollHeight, - overflow: 'auto' - }); - - if($.browser.msie && typeof document.body.style.maxHeight === "undefined") { - var listHeight = 0; - listItems.each(function() { - listHeight += this.offsetHeight; - }); - var scrollbarsVisible = listHeight > options.scrollHeight; - list.css('height', scrollbarsVisible ? options.scrollHeight : listHeight ); - if (!scrollbarsVisible) { - // IE doesn't recalculate width when scrollbar disappears - listItems.width( list.width() - parseInt(listItems.css("padding-left")) - parseInt(listItems.css("padding-right")) ); - } - } - - } - }, - selected: function() { - var selected = listItems && listItems.filter("." + CLASSES.ACTIVE).removeClass(CLASSES.ACTIVE); - return selected && selected.length && $.data(selected[0], "ac_data"); - }, - emptyList: function (){ - list && list.empty(); - }, - unbind: function() { - element && element.remove(); + $.Autocompleter.prototype.selectCurrent = function() { + var $item = $('li.' + this.selectClass_, this.dom.$results); + if ($item.length === 1) { + this.selectItem($item); + } else { + this.deactivate(false); } }; -}; -$.Autocompleter.Selection = function(field, start, end) { - if( field.createTextRange ){ - var selRange = field.createTextRange(); - selRange.collapse(true); - selRange.moveStart("character", start); - selRange.moveEnd("character", end); - selRange.select(); - } else if( field.setSelectionRange ){ - field.setSelectionRange(start, end); - } else { - if( field.selectionStart ){ - field.selectionStart = start; - field.selectionEnd = end; + $.Autocompleter.prototype.selectItem = function($li) { + var value = $li.data('value'); + var data = $li.data('data'); + var displayValue = this.displayValue(value, data); + var processedDisplayValue = this.beforeUseConverter(displayValue); + this.lastProcessedValue_ = processedDisplayValue; + this.lastSelectedValue_ = processedDisplayValue; + var d = this.getDelimiterOffsets(); + var delimiter = this.options.delimiterChar; + var elem = this.dom.$elem; + var extraCaretPos = 0; + if ( this.options.useDelimiter ) { + // if there is a preceding delimiter, add a space after the delimiter + if ( elem.val().substring(d.start-1, d.start) == delimiter && delimiter != ' ' ) { + displayValue = ' ' + displayValue; + } + // if there is not already a delimiter trailing this value, add it + if ( elem.val().substring(d.end, d.end+1) != delimiter && this.lastKeyPressed_ != this.options.delimiterKeyCode ) { + displayValue = displayValue + delimiter; + } else { + // move the cursor after the existing trailing delimiter + extraCaretPos = 1; + } } - } - field.focus(); -}; + this.setValue(displayValue); + this.setCaret(d.start + displayValue.length + extraCaretPos); + this.callHook('onItemSelect', { value: value, data: data }); + this.deactivate(true); + elem.focus(); + }; -})(jQuery); + $.Autocompleter.prototype.displayValue = function(value, data) { + if ($.isFunction(this.options.displayValue)) { + return this.options.displayValue(value, data); + } + return value; + }; + + $.Autocompleter.prototype.hideResults = function() { + this.dom.$results.hide(); + }; + + $.Autocompleter.prototype.deactivate = function(finish) { + if (this.finishTimeout_) { + clearTimeout(this.finishTimeout_); + } + if (this.keyTimeout_) { + clearTimeout(this.keyTimeout_); + } + if (finish) { + if (this.lastProcessedValue_ !== this.lastSelectedValue_) { + if (this.options.mustMatch) { + this.setValue(''); + } + this.callHook('onNoMatch'); + } + if (this.active_) { + this.callHook('onFinish'); + } + this.lastKeyPressed_ = null; + this.lastProcessedValue_ = null; + this.lastSelectedValue_ = null; + this.active_ = false; + } + this.hideResults(); + }; + + $.Autocompleter.prototype.selectRange = function(start, end) { + var input = this.dom.$elem.get(0); + if (input.setSelectionRange) { + input.focus(); + input.setSelectionRange(start, end); + } else if (input.createTextRange) { + var range = input.createTextRange(); + range.collapse(true); + range.moveEnd('character', end); + range.moveStart('character', start); + range.select(); + } + }; + + /** + * Move caret to position + * @param {Number} pos + */ + $.Autocompleter.prototype.setCaret = function(pos) { + this.selectRange(pos, pos); + }; + + /** + * Get caret position + */ + $.Autocompleter.prototype.getCaret = function() { + var $elem = this.dom.$elem; + var elem = $elem[0]; + var val, selection, range, start, end, stored_range; + if (elem.createTextRange) { // IE + selection = document.selection; + if (elem.tagName.toLowerCase() != 'textarea') { + val = $elem.val(); + range = selection.createRange().duplicate(); + range.moveEnd('character', val.length); + if (range.text === '') { + start = val.length; + } else { + start = val.lastIndexOf(range.text); + } + range = selection.createRange().duplicate(); + range.moveStart('character', -val.length); + end = range.text.length; + } else { + range = selection.createRange(); + stored_range = range.duplicate(); + stored_range.moveToElementText(elem); + stored_range.setEndPoint('EndToEnd', range); + start = stored_range.text.length - range.text.length; + end = start + range.text.length; + } + } else { + start = $elem[0].selectionStart; + end = $elem[0].selectionEnd; + } + return { + start: start, + end: end + }; + }; + + /** + * Set the value that is currently being autocompleted + * @param {String} value + */ + $.Autocompleter.prototype.setValue = function(value) { + if ( this.options.useDelimiter ) { + // set the substring between the current delimiters + var val = this.dom.$elem.val(); + var d = this.getDelimiterOffsets(); + var preVal = val.substring(0, d.start); + var postVal = val.substring(d.end); + value = preVal + value + postVal; + } + this.dom.$elem.val(value); + }; + + /** + * Get the value currently being autocompleted + * @param {String} value + */ + $.Autocompleter.prototype.getValue = function(value) { + if ( this.options.useDelimiter ) { + var d = this.getDelimiterOffsets(); + return value.substring(d.start, d.end).trim(); + } else { + return value; + } + }; + + /** + * Get the offsets of the value currently being autocompleted + */ + $.Autocompleter.prototype.getDelimiterOffsets = function() { + var val = this.dom.$elem.val(); + if ( this.options.useDelimiter ) { + var preCaretVal = val.substring(0, this.getCaret().start); + var start = preCaretVal.lastIndexOf(this.options.delimiterChar) + 1; + var postCaretVal = val.substring(this.getCaret().start); + var end = postCaretVal.indexOf(this.options.delimiterChar); + if ( end == -1 ) end = val.length; + end += this.getCaret().start; + } else { + start = 0; + end = val.length; + } + return { + start: start, + end: end + }; + }; + +})(jQuery); \ 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: carlfeberhard: DataProviders: add hierarchy module and xml provider, add provider to datatype
by commits-noreply＠bitbucket.org 09 Aug '13

09 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bf6bf3b5edfd/ Changeset: bf6bf3b5edfd User: carlfeberhard Date: 2013-08-08 18:59:34 Summary: DataProviders: add hierarchy module and xml provider, add provider to datatype Affected #: 5 files diff -r f46505803e8f0efd26be16f9e18353fbdc969205 -r bf6bf3b5edfdc409f235cb91edcc9d91246df816 lib/galaxy/datatypes/dataproviders/__init__.py --- a/lib/galaxy/datatypes/dataproviders/__init__.py +++ b/lib/galaxy/datatypes/dataproviders/__init__.py @@ -23,6 +23,7 @@ import base import chunk import line +import hierarchy import column import external import dataset diff -r f46505803e8f0efd26be16f9e18353fbdc969205 -r bf6bf3b5edfdc409f235cb91edcc9d91246df816 lib/galaxy/datatypes/dataproviders/decorators.py --- a/lib/galaxy/datatypes/dataproviders/decorators.py +++ b/lib/galaxy/datatypes/dataproviders/decorators.py @@ -134,6 +134,7 @@ Parse the values in `query_kwargs` from strings to the proper types listed in the same key in `settings`. """ + #TODO: this was a relatively late addition: review and re-think def list_from_query_string( s ): # assume csv return s.split( ',' ) @@ -155,10 +156,11 @@ #TODO: this would be the place to sanitize any strings query_value = query_kwargs[ key ] needed_type = settings[ key ] - try: - query_kwargs[ key ] = parsers[ needed_type ]( query_value ) - except ( KeyError, ValueError ): - del query_kwargs[ key ] + if needed_type != 'str': + try: + query_kwargs[ key ] = parsers[ needed_type ]( query_value ) + except ( KeyError, ValueError ): + del query_kwargs[ key ] #TODO:?? do we want to remove query_kwarg entries NOT in settings? return query_kwargs diff -r f46505803e8f0efd26be16f9e18353fbdc969205 -r bf6bf3b5edfdc409f235cb91edcc9d91246df816 lib/galaxy/datatypes/dataproviders/hierarchy.py --- /dev/null +++ b/lib/galaxy/datatypes/dataproviders/hierarchy.py @@ -0,0 +1,142 @@ +""" +Dataproviders that iterate over lines from their sources. +""" + +import line +import xml.etree.ElementTree as elementtree + +_TODO = """ +""" + +import logging +log = logging.getLogger( __name__ ) + + +# ----------------------------------------------------------------------------- hierarchal/tree data providers +class HierarchalDataProvider( line.BlockDataProvider ): + """ + Class that uses formats where a datum may have a parent or children + data. + + e.g. XML, HTML, GFF3, Phylogenetic + """ + def __init__( self, source, **kwargs ): + #TODO: (and defer to better (than I can write) parsers for each subtype) + super( HierarchalDataProvider, self ).__init__( source, **kwargs ) + + +# ----------------------------------------------------------------------------- xml +class XMLDataProvider( HierarchalDataProvider ): + """ + Data provider that converts selected XML elements to dictionaries. + """ + # using elementtree's iterparse method to keep mem down + #TODO: this, however (AFAIK), prevents the use of xpath + settings = { + 'selector' : 'str', #urlencoded + 'max_depth' : 'int', + } + ITERPARSE_ALL_EVENTS = ( 'start', 'end', 'start-ns', 'end-ns' ) + #TODO: move appropo into super + + def __init__( self, source, selector=None, max_depth=None, **kwargs ): + """ + :param selector: some partial string in the desired tags to return + :param max_depth: the number of generations of descendents to return + """ + self.selector = selector + self.max_depth = max_depth + self.namespaces = {} + + super( XMLDataProvider, self ).__init__( source, **kwargs ) + + def matches_selector( self, element, selector=None ): + """ + Returns true if the ``element`` matches the ``selector``. + + :param element: an XML ``ElementTree.Element`` + :param selector: some partial string in the desired tags to return + + Change point for more sophisticated selectors. + """ + # search for partial match of selector to the element tag + #TODO: add more flexibility here w/o re-implementing xpath + #TODO: fails with '#' - browser thinks it's anchor - use urlencode + #TODO: need removal/replacement of etree namespacing here - then move to string match + return bool( ( selector == None ) + or ( isinstance( element, elementtree.Element ) and selector in element.tag ) ) + + def element_as_dict( self, element ): + """ + Converts an XML element (its text, tag, and attributes) to dictionary form. + + :param element: an XML ``ElementTree.Element`` + """ + #TODO: Key collision is unlikely here, but still should be better handled + return { + 'tag' : element.tag, + 'text' : element.text.strip() if element.text else None, + # needs shallow copy to protect v. element.clear() + 'attrib' : dict( element.attrib ) + } + + def get_children( self, element, max_depth=None ): + """ + Yield all children of element (and their children - recursively) + in dictionary form. + :param element: an XML ``ElementTree.Element`` + :param max_depth: the number of generations of descendents to return + """ + if not isinstance( max_depth, int ) or max_depth >= 1: + for child in element.getchildren(): + child_data = self.element_as_dict( child ) + + next_depth = max_depth - 1 if isinstance( max_depth, int ) else None + grand_children = list( self.get_children( child, next_depth ) ) + if grand_children: + child_data[ 'children' ] = grand_children + + yield child_data + + def __iter__( self ): + context = elementtree.iterparse( self.source, events=self.ITERPARSE_ALL_EVENTS ) + context = iter( context ) + + selected_element = None + for event, element in context: + #print 'iterparse, event:', event + #print 'iterparse, element:', element, ( element.tag if hasattr( element, 'tag' ) else '' ) + + if event == 'start-ns': + ns, uri = element + self.namespaces[ ns ] = uri + + elif event == 'start': + if( ( selected_element == None ) + and ( self.matches_selector( element, self.selector ) ) ): + # start tag of selected element - wait for 'end' to emit/yield + selected_element = element + + elif event == 'end': + if( ( selected_element != None ) + and ( element == selected_element ) ): + self.num_valid_data_read += 1 + + # offset + if self.num_valid_data_read > self.offset: + # convert to dict and yield + selected_element_dict = self.element_as_dict( selected_element ) + children = list( self.get_children( selected_element, self.max_depth ) ) + if children: + selected_element_dict[ 'children' ] = children + yield selected_element_dict + + # limit + self.num_data_returned += 1 + if self.limit is not None and self.num_data_returned >= self.limit: + break + + selected_element.clear() + selected_element = None + + self.num_data_read += 1 diff -r f46505803e8f0efd26be16f9e18353fbdc969205 -r bf6bf3b5edfdc409f235cb91edcc9d91246df816 lib/galaxy/datatypes/dataproviders/line.py --- a/lib/galaxy/datatypes/dataproviders/line.py +++ b/lib/galaxy/datatypes/dataproviders/line.py @@ -132,7 +132,7 @@ e.g. Fasta, GenBank, MAF, hg log Note: mem intensive (gathers list of lines before output) """ - def __init__( self, source, new_block_delim_fn, block_filter_fn=None, **kwargs ): + def __init__( self, source, new_block_delim_fn=None, block_filter_fn=None, **kwargs ): """ :param new_block_delim_fn: T/F function to determine whether a given line is the start of a new block. @@ -214,7 +214,7 @@ """ if self.new_block_delim_fn: return self.new_block_delim_fn( line ) - return False + return True # NOTE: # some formats have one block attr per line @@ -251,17 +251,3 @@ if self.block_filter_fn: return self.block_filter_fn( block ) return block - - -# ----------------------------------------------------------------------------- hierarchal/tree data providers -class HierarchalDataProvider( BlockDataProvider ): - """ - Class that uses formats where a datum may have a parent or children - data. - - e.g. XML, HTML, GFF3, Phylogenetic - """ - def __init__( self, source, **kwargs ): - #TODO: (and defer to better (than I can write) parsers for each subtype) - raise NotImplementedError( 'Abstract class' ) - super( HierarchalDataProvider, self ).__init__( source, **kwargs ) diff -r f46505803e8f0efd26be16f9e18353fbdc969205 -r bf6bf3b5edfdc409f235cb91edcc9d91246df816 lib/galaxy/datatypes/xml.py --- a/lib/galaxy/datatypes/xml.py +++ b/lib/galaxy/datatypes/xml.py @@ -4,9 +4,11 @@ import data import logging from galaxy.datatypes.sniff import * +import dataproviders log = logging.getLogger(__name__) +(a)dataproviders.decorators.has_dataproviders class GenericXml( data.Text ): """Base format class for any XML file.""" file_ext = "xml" @@ -47,6 +49,12 @@ data.Text.merge(split_files, output_file) merge = staticmethod(merge) + @dataproviders.decorators.dataprovider_factory( 'xml', dataproviders.hierarchy.XMLDataProvider.settings ) + def xml_dataprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.hierarchy.XMLDataProvider( dataset_source, **settings ) + + class MEMEXml( GenericXml ): """MEME XML Output data""" file_ext = "memexml" @@ -62,6 +70,7 @@ def sniff( self, filename ): return False + class CisML( GenericXml ): """CisML XML data""" #see: http://www.ncbi.nlm.nih.gov/pubmed/15001475 file_ext = "cisml" @@ -77,6 +86,7 @@ def sniff( self, filename ): return False + class Phyloxml( GenericXml ): """Format for defining phyloxml data http://www.phyloxml.org/""" file_ext = "phyloxml" @@ -105,4 +115,4 @@ Returns a list of visualizations for datatype. """ - return [ 'phyloviz' ] \ No newline at end of file + return [ 'phyloviz' ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 08 Aug '13

08 Aug '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8d8429484ac3/ Changeset: 8d8429484ac3 Branch: next-stable User: carlfeberhard Date: 2013-08-08 16:40:27 Summary: History view: fix broken scrollbar Affected #: 1 file diff -r 8ee4176d44bad2c1029356e869d601752ae54cd0 -r 8d8429484ac3ffef21fedd1077acf050c8aed459 templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -27,6 +27,7 @@ <style type="text/css"> + /* these don't appear to be used? */ .page-body { padding: 10px; @@ -44,20 +45,38 @@ border-top: 4px solid #DDDDDD; } + + body { + padding: 0px; + margin: 0px; + } + div.unified-panel-body { - position: relative; + position: absolute; top: 0px; - width: auto; + width: 100%; + } + + #history-name-area { + margin: 12px 0px 0px 16px; + font-size: 120%; + } + #top-links { + margin: 4px 0px 8px 16px; } .historyItemContainer { - padding-right: 3px; - border-right-style: solid; - border-right-color: #66AA66; + /*padding-right: 3px;*/ } .historyItemBody { display: none; } + div.historyItemWrapper { + margin: 0px 4px 0px 4px ; + border-left: 1px solid #999999; + border-right: 1px solid #999999; + } + /* TODO: unify with other history css and into .less */ </style><noscript> @@ -92,14 +111,13 @@ href_to_user_histories = h.url_for( controller='/history', action='list_published' )##should this instead be be None or empty string? %> - %if context.get( 'use_panels' ): - <div class="unified-panel-header" unselectable="on"> - </div> - %endif - <div class="unified-panel-body"> - <div class="wrapping" style="overflow: auto; height: 100%;"> + <div style="overflow: auto; height: 100%;"> ## Render view of history. + <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> + <div id="history-name">${history.get_display_name()}</div> + </div> + <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> %if not history.purged: <a href="${h.url_for(controller='history', action='imp', id=trans.security.encode_id(history.id) )}">import and start using history</a> | @@ -113,10 +131,6 @@ <a href="#" class="toggle">collapse all</a></div> - <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> - <div id="history-name">${history.get_display_name()}</div> - </div> - %if history.deleted: <div class="warningmessagesmall"> ${_('You are currently viewing a deleted history!')} https://bitbucket.org/galaxy/galaxy-central/commits/f46505803e8f/ Changeset: f46505803e8f User: carlfeberhard Date: 2013-08-08 16:41:18 Summary: merge next-stable Affected #: 2 files diff -r 3f8f52fa01f807b624ce05ef2186284b947c2e34 -r f46505803e8f0efd26be16f9e18353fbdc969205 templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -27,6 +27,7 @@ <style type="text/css"> + /* these don't appear to be used? */ .page-body { padding: 10px; @@ -44,20 +45,38 @@ border-top: 4px solid #DDDDDD; } + + body { + padding: 0px; + margin: 0px; + } + div.unified-panel-body { - position: relative; + position: absolute; top: 0px; - width: auto; + width: 100%; + } + + #history-name-area { + margin: 12px 0px 0px 16px; + font-size: 120%; + } + #top-links { + margin: 4px 0px 8px 16px; } .historyItemContainer { - padding-right: 3px; - border-right-style: solid; - border-right-color: #66AA66; + /*padding-right: 3px;*/ } .historyItemBody { display: none; } + div.historyItemWrapper { + margin: 0px 4px 0px 4px ; + border-left: 1px solid #999999; + border-right: 1px solid #999999; + } + /* TODO: unify with other history css and into .less */ </style><noscript> @@ -92,14 +111,13 @@ href_to_user_histories = h.url_for( controller='/history', action='list_published' )##should this instead be be None or empty string? %> - %if context.get( 'use_panels' ): - <div class="unified-panel-header" unselectable="on"> - </div> - %endif - <div class="unified-panel-body"> - <div class="wrapping" style="overflow: auto; height: 100%;"> + <div style="overflow: auto; height: 100%;"> ## Render view of history. + <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> + <div id="history-name">${history.get_display_name()}</div> + </div> + <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> %if not history.purged: <a href="${h.url_for(controller='history', action='imp', id=trans.security.encode_id(history.id) )}">import and start using history</a> | @@ -113,10 +131,6 @@ <a href="#" class="toggle">collapse all</a></div> - <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> - <div id="history-name">${history.get_display_name()}</div> - </div> - %if history.deleted: <div class="warningmessagesmall"> ${_('You are currently viewing a deleted history!')} 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: Fix precision formatting in Circster
by commits-noreply＠bitbucket.org 08 Aug '13

08 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3f8f52fa01f8/ Changeset: 3f8f52fa01f8 User: guerler Date: 2013-08-08 10:10:36 Summary: Fix precision formatting in Circster Affected #: 1 file diff -r ba8330a9fdefe0431ee1869e3a60c55caebc937c -r 3f8f52fa01f807b624ce05ef2186284b947c2e34 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -85,10 +85,14 @@ */ formatNum: function(num, sigDigits) { // Use default of 2 sig. digits. - if (sigDigits === undefined) { + if (sigDigits === undefined) sigDigits = 2; - } - + + // Verify input number + if (num === null) + return null; + + // Calculate return value var rval = null; if (num < 1) { rval = num.toPrecision(sigDigits); 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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galaxy-commits August 2013