5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/60ce4bb8e4ce/ Changeset: 60ce4bb8e4ce User: dannon Date: 2015-02-08 23:02:26+00:00 Summary: Allow specifying connection at launch of GalaxyQueueWorker. Affected #: 1 file diff -r ea23071cf22ea78b699264e04b59e3adf88ec619 -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -30,10 +30,13 @@ handler, will have one of these used for dispatching so called 'control' tasks. """ - def __init__(self, app, queue, task_mapping): + def __init__(self, app, queue, task_mapping, connection=None): super(GalaxyQueueWorker, self).__init__() log.info("Initalizing Galaxy Queue Worker on %s" % app.config.amqp_internal_connection) - self.connection = Connection(app.config.amqp_internal_connection) + if connection: + self.connection = connection + else: + self.connection = Connection(app.config.amqp_internal_connection) self.app = app # Eventually we may want different workers w/ their own queues and task # mappings. Right now, there's only the one. https://bitbucket.org/galaxy/galaxy-central/commits/01ac77bb90de/ Changeset: 01ac77bb90de User: dannon Date: 2015-02-09 16:36:45+00:00 Summary: Merge. Affected #: 32 files diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 CONTRIBUTING.md --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,12 +1,13 @@ # Contributing This document briefly describes how to contribute to the -galaxy-central core project - also checkout the video of our [2013 -Galaxy Community Conference -presentation](http://vimeo.com/channels/581875/73486255) on the -topic. For information on contributing more broadly to the Galaxy -ecosystem and a deeper discussion of some of these points - please see -the [Develop](https://wiki.galaxyproject.org/Develop/) section of the +galaxy-central core project - also checkout our 2013 Galaxy Community +Conference presentation] on the topic +([video](http://vimeo.com/channels/581875/73486255), +[presentation](https://wiki.galaxyproject.org/Documents/Presentations/GCC2013?action=AttachFile&do=view&target=BakerContribute.pdf)). For +information on contributing more broadly to the Galaxy ecosystem and a +deeper discussion of some of these points - please see the +[Develop](https://wiki.galaxyproject.org/Develop/) section of the [Galaxy Wiki](https://wiki.galaxyproject.org/). ## Before you Begin @@ -80,6 +81,13 @@ * A description of how to test the change. +## Ideas + +Galaxy's [Trello board](http://bit.ly/gxytrello) is filled with bugs and ideas +for enhancements, but we maintain a [card](https://trello.com/c/eFdPIdIB) with +links to smaller issues we believe would make the best entry points for new +developers. + ## A Quick Note about Tools For the most part, Galaxy tools should be published to the diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 client/galaxy/scripts/mvc/tools/tools-form-workflow.js --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -275,10 +275,16 @@ /** Request a new model for an already created tool form and updates the form inputs */ _updateModel: function() { + // link self + var self = this; + // create the request dictionary - var self = this; - var current_state = this.tree.finalize(); - + var current_state = { + tool_id : this.options.id, + tool_version : this.options.version, + inputs : this.tree.finalize() + } + // log tool state console.debug('tools-form-workflow::_refreshForm() - Refreshing states.'); console.debug(current_state); @@ -287,11 +293,11 @@ var process_id = this.deferred.register(); // build model url for request - var model_url = galaxy_config.root + 'workflow/editor_form_post?tool_id=' + this.options.id + '&__is_dynamic__=False'; + var model_url = galaxy_config.root + 'api/workflows/build_module'; // post job Utils.request({ - type : 'GET', + type : 'POST', url : model_url, data : current_state, success : function(data) { diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 client/galaxy/scripts/mvc/tools/tools-input.js --- a/client/galaxy/scripts/mvc/tools/tools-input.js +++ b/client/galaxy/scripts/mvc/tools/tools-input.js @@ -34,8 +34,7 @@ this.field.skip = false; var v = this.field.value && this.field.value(); this.field.skip = Boolean(options.optional && - ((this.default_value === undefined) || - ((this.field.validate && !this.field.validate()) || !v || + (((this.field.validate && !this.field.validate()) || !v || (v == this.default_value) || (Number(v) == Number(this.default_value)) || (JSON.stringify(v) == JSON.stringify(this.default_value))))); diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -294,17 +294,20 @@ // get id var id = input_def.id; + // add regular/default value if missing + if (input_def.value === undefined) { + input_def.value = null; + } + if (input_def.default_value === undefined) { + input_def.default_value = input_def.value; + } + // create input field var field = this._createField(input_def); // add to field list this.app.field_list[id] = field; - // fix default value if missing - if (input_def.default_value === undefined) { - input_def.default_value = input_def.value; - } - // create input field wrapper var input_element = new InputElement(this.app, { label : input_def.label, diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -10,13 +10,13 @@ initialize: function(app) { this.app = app; }, - + /** Convert dictionary representation into tool api specific flat dictionary format. */ finalize: function(patch) { // link this var self = this; - + // dictionary with api specific identifiers this.map_dict = {}; @@ -24,24 +24,24 @@ if (!this.app.section) { return {}; } - + // ensure that dictionary with patching functions exists patch = patch || {}; - + // dictionary formatted for job submission or tool form update var result_dict = {}; // prepare full dictionary var dict = {}; - + // fill dictionary from dom this._iterate(this.app.section.$el, dict); - + // add identifier and value to job definition function add(job_input_id, input_id, input_value) { // add entry to result dictionary result_dict[job_input_id] = input_value; - + // backup id mapping self.map_dict[job_input_id] = input_id; }; @@ -53,21 +53,21 @@ if (node.input) { // get node var input = node.input; - + // create identifier var job_input_id = identifier; if (identifier != '') { job_input_id += '|'; } job_input_id += input.name; - + // process input type switch (input.type) { // handle repeats case 'repeat': // section identifier var section_label = 'section-'; - + // collect repeat block identifiers var block_indices = []; var block_prefix = null; @@ -81,10 +81,10 @@ } } } - + // sort repeat blocks block_indices.sort(function(a,b) { return a - b; }); - + // add to response dictionary in created order var index = 0; for (var i in block_indices) { @@ -98,10 +98,10 @@ if (patch[input.test_param.type]) { value = patch[input.test_param.type](value); } - + // add conditional value add (job_input_id + '|' + input.test_param.name, input.id, value); - + // identify selected case var selectedCase = self.matchCase(input, value); if (selectedCase != -1) { @@ -116,22 +116,17 @@ // get field var field = self.app.field_list[input.id]; if (field && field.value) { + // validate field value + var value = field.value(); + if (field.validate && !field.validate()) { + value = null; + } + // get and patch field value - var value = field.value(); if (patch[input.type]) { value = patch[input.type](value); } - // validate field value - if (field.skip) { - continue; - } - - // validate field value - if (field.validate && !field.validate()) { - value = null; - } - // ignore certain values if (input.ignore === undefined || (value !== null && input.ignore != value)) { // add value to submission @@ -149,20 +144,20 @@ } } } - + // start conversion convert('', dict); - + // return result return result_dict; }, - + /** Match job definition identifier to input element identifier */ match: function (job_input_id) { return this.map_dict && this.map_dict[job_input_id]; }, - + /** Match conditional values to selected cases */ matchCase: function(input, value) { @@ -174,27 +169,27 @@ value = input.test_param.falsevalue || 'false'; } } - + // find selected case for (var i in input.cases) { if (input.cases[i].value == value) { return i; } } - + // selected case not found return -1; }, - + /** Matches identifier from api model to input elements */ matchModel: function(model, callback) { // final result dictionary var result = {}; - + // link this var self = this; - + // search throughout response function search (id, head) { for (var i in head) { @@ -224,23 +219,23 @@ } } } - + // match all ids and return messages search('', model.inputs); // return matched results return result; }, - + /** Matches identifier from api response to input elements */ matchResponse: function(response) { // final result dictionary var result = {}; - + // link this var self = this; - + // search throughout response function search (id, head) { if (typeof head === 'string') { @@ -262,14 +257,14 @@ } } } - + // match all ids and return messages search('', response); - + // return matched results return result; }, - + /** Iterate through the tool form dom and map it to the dictionary. */ _iterate: function(parent, dict) { @@ -279,15 +274,15 @@ children.each(function() { // get child element var child = this; - + // get id var id = $(child).attr('id'); - + // create new branch if ($(child).hasClass('section-row')) { // create sub dictionary dict[id] = {}; - + // add input element if it exists var input = self.app.input_list[id]; if (input) { @@ -295,7 +290,7 @@ input : input } } - + // fill sub dictionary self._iterate(child, dict[id]); } else { diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 client/galaxy/scripts/utils/metrics-logger.js --- a/client/galaxy/scripts/utils/metrics-logger.js +++ b/client/galaxy/scripts/utils/metrics-logger.js @@ -34,7 +34,7 @@ var self = this; ///** get the current user's id from bootstrapped data or options */ - self.userId = window.bootstrapped? window.bootstrapped.user.id: null; + self.userId = ( window.bootstrapped && window.bootstrapped.user )? window.bootstrapped.user.id: null; self.userId = self.userId || options.userId || null; /** the (optional) console to emit logs to */ diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 config/plugins/visualizations/scatterplot/package.json --- a/config/plugins/visualizations/scatterplot/package.json +++ b/config/plugins/visualizations/scatterplot/package.json @@ -16,8 +16,8 @@ "devDependencies": { "grunt": "~0.4.1", "grunt-cli": "~0.1.9", - "grunt-contrib-handlebars": "~0.5.10", "grunt-contrib-concat": "~0.3.0", + "grunt-contrib-handlebars": "^0.9.3", "grunt-contrib-uglify": "~0.2.2", "grunt-contrib-watch": "~0.5.3" } diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 config/plugins/visualizations/scatterplot/static/scatterplot-edit.js --- a/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js +++ b/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js @@ -1,1 +1,1 @@ -function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line 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q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.xTicks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.yTicks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=6;q.x.label=o.append("text").attr("id","x-axis-label").attr("class","axis-label").text(b.xLabel).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("id","y-axis-label").attr("class","axis-label").text(b.yLabel).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",0);t.transition().duration(b.animDuration).attr("r",b.datapointSize),e(),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.classed("highlight",!0).style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")<b.height&&p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")).attr("y1",+d.attr("cy")+b.datapointSize).attr("x2",d.attr("cx")).attr("y2",b.height).classed("hoverline",!0);var e=this.getBoundingClientRect();$("body").append(g(e.top,e.right,a)),$(o.node()).trigger("mouseover-datapoint.scatterplot",[this,a,c])}),t.on("mouseout",function(){d3.select(this).classed("highlight",!1).style("fill","black").style("fill-opacity",.2),p.selectAll(".hoverline").remove(),$(".chart-info-box").remove()})}this.scatterplot=this.scatterplot||{},this.scatterplot.chartcontrol=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f,g="",h="function",i=this.escapeExpression;return g+='<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<div data-config-key="datapointSize" class="form-input 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y axis.\n</p>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.editor=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f="";return f+='<div class="scatterplot-editor tabbable tabs-left">\n \n <ul class="nav nav-tabs">\n \n <li class="active">\n <a title="Use this tab to change which data are used"\n href="#data-control" data-toggle="tab">Data Controls</a>\n </li>\n <li>\n <a title="Use this tab to change how the chart is drawn"\n href="#chart-control" data-toggle="tab" >Chart Controls</a>\n </li>\n \n <li class="disabled">\n <a title="This tab will display the chart"\n href="#chart-display" data-toggle="tab">Chart</a>\n </li>\n \n <li class="file-controls">\n<!-- <button class="copy-btn btn btn-default"\n title="Save this as a new visualization">Save to new</button>-->\n <button class="save-btn btn btn-default">Save</button>\n </li>\n </ul>\n\n \n <div class="tab-content">\n \n <div 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this.model.id&&_.isFinite(a.xColumn)&&_.isFinite(a.yColumn)&&this.renderChart(),this},_getColumnIndecesByType:function(){var a={numeric:[],text:[],all:[]};return _.each(this.dataset.metadata_column_types||[],function(b,c){"int"===b||"float"===b?a.numeric.push(c):("str"===b||"list"===b)&&a.text.push(c),a.all.push(c)}),a.numeric.length<2&&(a.numeric=[]),a},_render_dataControl:function(a){a=a||this.$el;var b=this,c=this.model.get("config"),d=this._getColumnIndecesByType(),e=a.find(".tab-pane#data-control");return e.html(ScatterplotConfigEditor.templates.dataControl({peek:this.dataset.peek})),e.find(".peek").peekColumnSelector({controls:[{label:"X Column",id:"xColumn",selected:c.xColumn,disabled:d.text},{label:"Y Column",id:"yColumn",selected:c.yColumn,disabled:d.text},{label:"ID Column",id:"idColumn",selected:c.idColumn}]}).on("peek-column-selector.change",function(a,c){b.model.set("config",c)}).on("peek-column-selector.rename",function(){}),e.find("[title]").tooltip(),e},_render_chartControls:function(a){function b(){var a=$(this),b=a.slider("value");c.model.set("config",_.object([[a.parent().data("config-key"),b]])),a.siblings(".slider-output").text(b)}a=a||this.$el;var c=this,d=this.model.get("config"),e=a.find("#chart-control");e.html(ScatterplotConfigEditor.templates.chartControl(d));var f={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};e.find(".numeric-slider-input").each(function(){var a=$(this),c=a.attr("data-config-key"),e=_.extend(f[c],{value:d[c],change:b,slide:b});a.find(".slider").slider(e),a.children(".slider-output").text(d[c])});var g=this.dataset.metadata_column_names||[],h=d.xLabel||g[d.xColumn]||"X",i=d.yLabel||g[d.yColumn]||"Y";return e.find('input[name="X-axis-label"]').val(h).on("change",function(){c.model.set("config",{xLabel:$(this).val()})}),e.find('input[name="Y-axis-label"]').val(i).on("change",function(){c.model.set("config",{yLabel:$(this).val()})}),e.find("[title]").tooltip(),e},_render_chartDisplay:function(a){a=a||this.$el;var b=a.find(".tab-pane#chart-display");return this.display.setElement(b),this.display.render(),b.find("[title]").tooltip(),b},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart","click .save-btn":"saveVisualization"},saveVisualization:function(){var a=this;this.model.save().fail(function(b,c,d){console.error(b,c,d),a.trigger("save:error",view),alert("Error loading data:\n"+b.responseText)}).then(function(){a.display.render()})},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.display.fetchData()},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotDisplay=Backbone.View.extend({initialize:function(a){this.data=null,this.dataset=a.dataset,this.lineCount=this.dataset.metadata_data_lines||null},fetchData:function(){this.showLoadingIndicator();var a=this,b=this.model.get("config"),c=jQuery.getJSON("/api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:b.pagination.perPage,offset:b.pagination.currPage*b.pagination.perPage});return c.done(function(b){a.data=b.data,a.trigger("data:fetched",a),a.renderData()}),c.fail(function(b,c,d){console.error(b,c,d),a.trigger("data:error",a),alert("Error loading data:\n"+b.responseText)}),c},showLoadingIndicator:function(){this.$el.find(".scatterplot-data-info").html(['<div class="loading-indicator">','<span class="fa fa-spinner fa-spin"></span>','<span class="loading-indicator-message">loading...</span>',"</div>"].join(""))},template:function(){var a=['<div class="controls clear">','<div class="right">','<p class="scatterplot-data-info"></p>','<button class="stats-toggle-btn">Stats</button>','<button class="rerender-btn">Redraw</button>',"</div>",'<div class="left">','<div class="page-control"></div>',"</div>","</div>","<svg/>",'<div class="stats-display"></div>'].join("");return a},render:function(){return this.$el.addClass("scatterplot-display").html(this.template()),this.data&&this.renderData(),this},renderData:function(){this.renderLeftControls(),this.renderRightControls(),this.renderPlot(this.data),this.getStats()},renderLeftControls:function(){var a=this,b=this.model.get("config");return this.$el.find(".controls .left .page-control").pagination({startingPage:b.pagination.currPage,perPage:b.pagination.perPage,totalDataSize:this.lineCount,currDataSize:this.data.length}).off().on("pagination.page-change",function(c,d){b.pagination.currPage=d,a.model.set("config",{pagination:b.pagination}),a.resetZoom(),a.fetchData()}),this},renderRightControls:function(){var a=this;this.setLineInfo(this.data),this.$el.find(".stats-toggle-btn").off().click(function(){a.toggleStats()}),this.$el.find(".rerender-btn").off().click(function(){a.resetZoom(),a.renderPlot(this.data)})},renderPlot:function(){var a=this,b=this.$el.find("svg");this.toggleStats(!1),b.off().empty().show().on("zoom.scatterplot",function(b,c){a.model.set("config",c)}),scatterplot(b.get(0),this.model.get("config"),this.data)},setLineInfo:function(a,b){if(a){var c=this.model.get("config"),d=this.lineCount||"an unknown total",e=c.pagination.currPage*c.pagination.perPage,f=e+a.length;this.$el.find(".controls p.scatterplot-data-info").text([e+1,"to",f,"of",d].join(" "))}else this.$el.find(".controls p.scatterplot-data-info").html(b||"");return this},resetZoom:function(a,b){return a=void 0!==a?a:1,b=void 0!==b?b:[0,0],this.model.set("config",{scale:a,translate:b}),this},getStats:function(){if(this.data){var a=this,b=this.model.get("config"),c=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js");c.postMessage({data:this.data,keys:[b.xColumn,b.yColumn]}),c.onerror=function(){c.terminate()},c.onmessage=function(b){a.renderStats(b.data)}}},renderStats:function(a){var b=this.model.get("config"),c=this.$el.find(".stats-display"),d=b.xLabel,e=b.yLabel,f=$("<table/>").addClass("table").append(["<thead><th></th><th>",d,"</th><th>",e,"</th></thead>"].join("")).append(_.map(a,function(a,b){return $(["<tr><td>",b,"</td><td>",a[0],"</td><td>",a[1],"</td></tr>"].join(""))}));c.empty().append(f)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},xTicks:10,xLabel:"X",yTicks:10,yLabel:"Y",datapointSize:4,animDuration:500,scale:1,translate:[0,0]}}}); \ No newline at end of file +function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(){var a=d3.select(this).attr("cx"),c=d3.select(this).attr("cy");return 0>a||a>b.width?!0:0>c||c>b.height?!0:!1}).style("display","none")}function f(){$(".chart-info-box").remove(),q.redraw(),e(),s=d(),$(o.node()).trigger("zoom.scatterplot",{scale:n.scale(),translate:n.translate()})}function g(a,c,d){return c+=8,$(['<div class="chart-info-box" style="position: absolute">',void 0!==b.idColumn?"<div>"+d[b.idColumn]+"</div>":"","<div>",j(d),"</div>","<div>",k(d),"</div>","</div>"].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a){return a[b.xColumn]},k=function(a){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,30]).scale(b.scale||1).translate(b.translate||[0,0]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.xTicks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.yTicks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=6;q.x.label=o.append("text").attr("id","x-axis-label").attr("class","axis-label").text(b.xLabel).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("id","y-axis-label").attr("class","axis-label").text(b.yLabel).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",0);t.transition().duration(b.animDuration).attr("r",b.datapointSize),e(),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.classed("highlight",!0).style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")<b.height&&p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")).attr("y1",+d.attr("cy")+b.datapointSize).attr("x2",d.attr("cx")).attr("y2",b.height).classed("hoverline",!0);var e=this.getBoundingClientRect();$("body").append(g(e.top,e.right,a)),$(o.node()).trigger("mouseover-datapoint.scatterplot",[this,a,c])}),t.on("mouseout",function(){d3.select(this).classed("highlight",!1).style("fill","black").style("fill-opacity",.2),p.selectAll(".hoverline").remove(),$(".chart-info-box").remove()})}this.scatterplot=this.scatterplot||{},this.scatterplot.chartcontrol=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(a,b,c,d){var e,f="function",g=b.helperMissing,h=this.escapeExpression;return'<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<div data-config-key="datapointSize" class="form-input numeric-slider-input">\n <label for="datapointSize">Size of data point: </label>\n <div class="slider-output">'+h((e=null!=(e=b.datapointSize||(null!=a?a.datapointSize:a))?e:g,typeof e===f?e.call(a,{name:"datapointSize",hash:{},data:d}):e))+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Size of the graphic representation of each data point\n </p>\n</div>\n\n<div data-config-key="width" class="form-input numeric-slider-input">\n <label for="width">Chart width: </label>\n <div class="slider-output">'+h((e=null!=(e=b.width||(null!=a?a.width:a))?e:g,typeof e===f?e.call(a,{name:"width",hash:{},data:d}):e))+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="height" class="form-input numeric-slider-input">\n <label for="height">Chart height: </label>\n <div class="slider-output">'+h((e=null!=(e=b.height||(null!=a?a.height:a))?e:g,typeof e===f?e.call(a,{name:"height",hash:{},data:d}):e))+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="X-axis-label"class="text-input form-input">\n <label for="X-axis-label">Re-label the X axis: </label>\n <input type="text" name="X-axis-label" id="X-axis-label" value="'+h((e=null!=(e=b.xLabel||(null!=a?a.xLabel:a))?e:g,typeof e===f?e.call(a,{name:"xLabel",hash:{},data:d}):e))+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<div data-config-key="Y-axis-label" class="text-input form-input">\n <label for="Y-axis-label">Re-label the Y axis: </label>\n <input type="text" name="Y-axis-label" id="Y-axis-label" value="'+h((e=null!=(e=b.yLabel||(null!=a?a.yLabel:a))?e:g,typeof e===f?e.call(a,{name:"yLabel",hash:{},data:d}):e))+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'},useData:!0}),this.scatterplot.datacontrol=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(a,b,c,d){var e,f,g="function",h=b.helperMissing,i='<p class="help-text">\n Use the following control to change which columns are used by the chart. Click any cell\n from the last three rows of the table to select the column for the appropriate data.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<ul class="help-text" style="margin-left: 8px">\n <li><b>X Column</b>: which column values will be used for the x axis of the chart.</li>\n <li><b>Y Column</b>: which column values will be used for the y axis of the chart.</li>\n <li><b>ID Column</b>: an additional column value displayed when the user hovers over a data point.\n It may be useful to select unique or categorical identifiers here (such as gene ids).\n </li>\n</ul>\n\n<div class="column-selection">\n <pre class="peek">';return f=null!=(f=b.peek||(null!=a?a.peek:a))?f:h,e=typeof f===g?f.call(a,{name:"peek",hash:{},data:d}):f,null!=e&&(i+=e),i+'</pre>\n</div>\n\n<p class="help-text help-text-small">\n <b>Note</b>: If it can be determined from the dataset\'s filetype that a column is not numeric,\n that column choice may be disabled for either the x or y axis.\n</p>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'},useData:!0}),this.scatterplot.editor=Handlebars.template({compiler:[6,">= 2.0.0-beta.1"],main:function(){return'<div class="scatterplot-editor tabbable tabs-left">\n <ul class="nav nav-tabs">\n <li class="active">\n <a title="Use this tab to change which data are used"\n href="#data-control" data-toggle="tab">Data Controls</a>\n </li>\n <li>\n <a title="Use this tab to change how the chart is drawn"\n href="#chart-control" data-toggle="tab" >Chart Controls</a>\n </li>\n <li class="disabled">\n <a title="This tab will display the chart"\n href="#chart-display" data-toggle="tab">Chart</a>\n </li>\n <li class="file-controls">\n<!-- <button class="copy-btn btn btn-default"\n title="Save this as a new visualization">Save to new</button>-->\n <button class="save-btn btn btn-default">Save</button>\n </li>\n </ul>\n\n <div class="tab-content">\n <div id="data-control" class="scatterplot-config-control tab-pane active">\n </div>\n \n <div id="chart-control" class="scatterplot-config-control tab-pane">\n </div>\n\n <div id="chart-display" class="scatterplot-display tab-pane"></div>\n\n </div>\n</div>\n'},useData:!0});var ScatterplotConfigEditor=Backbone.View.extend({className:"scatterplot-control-form",initialize:function(a){if(this.model||(this.model=new Visualization({type:"scatterplot"})),!a||!a.dataset)throw new Error("ScatterplotConfigEditor requires a dataset");this.dataset=a.dataset,this.display=new ScatterplotDisplay({dataset:a.dataset,model:this.model})},render:function(){this.$el.empty().append(ScatterplotConfigEditor.templates.mainLayout({})),this.model.id&&(this.$el.find(".copy-btn").show(),this.$el.find(".save-btn").text("Update saved")),this.$el.find("[title]").tooltip(),this._render_dataControl(),this._render_chartControls(),this._render_chartDisplay();var a=this.model.get("config");return this.model.id&&_.isFinite(a.xColumn)&&_.isFinite(a.yColumn)&&this.renderChart(),this},_getColumnIndecesByType:function(){var a={numeric:[],text:[],all:[]};return _.each(this.dataset.metadata_column_types||[],function(b,c){"int"===b||"float"===b?a.numeric.push(c):("str"===b||"list"===b)&&a.text.push(c),a.all.push(c)}),a.numeric.length<2&&(a.numeric=[]),a},_render_dataControl:function(a){a=a||this.$el;var b=this,c=this.model.get("config"),d=this._getColumnIndecesByType(),e=a.find(".tab-pane#data-control");return e.html(ScatterplotConfigEditor.templates.dataControl({peek:this.dataset.peek})),e.find(".peek").peekColumnSelector({controls:[{label:"X Column",id:"xColumn",selected:c.xColumn,disabled:d.text},{label:"Y Column",id:"yColumn",selected:c.yColumn,disabled:d.text},{label:"ID Column",id:"idColumn",selected:c.idColumn}]}).on("peek-column-selector.change",function(a,c){b.model.set("config",c)}).on("peek-column-selector.rename",function(){}),e.find("[title]").tooltip(),e},_render_chartControls:function(a){function b(){var a=$(this),b=a.slider("value");c.model.set("config",_.object([[a.parent().data("config-key"),b]])),a.siblings(".slider-output").text(b)}a=a||this.$el;var c=this,d=this.model.get("config"),e=a.find("#chart-control");e.html(ScatterplotConfigEditor.templates.chartControl(d));var f={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};e.find(".numeric-slider-input").each(function(){var a=$(this),c=a.attr("data-config-key"),e=_.extend(f[c],{value:d[c],change:b,slide:b});a.find(".slider").slider(e),a.children(".slider-output").text(d[c])});var g=this.dataset.metadata_column_names||[],h=d.xLabel||g[d.xColumn]||"X",i=d.yLabel||g[d.yColumn]||"Y";return e.find('input[name="X-axis-label"]').val(h).on("change",function(){c.model.set("config",{xLabel:$(this).val()})}),e.find('input[name="Y-axis-label"]').val(i).on("change",function(){c.model.set("config",{yLabel:$(this).val()})}),e.find("[title]").tooltip(),e},_render_chartDisplay:function(a){a=a||this.$el;var b=a.find(".tab-pane#chart-display");return this.display.setElement(b),this.display.render(),b.find("[title]").tooltip(),b},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart","click .save-btn":"saveVisualization"},saveVisualization:function(){var a=this;this.model.save().fail(function(b,c,d){console.error(b,c,d),a.trigger("save:error",view),alert("Error loading data:\n"+b.responseText)}).then(function(){a.display.render()})},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.display.fetchData()},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotDisplay=Backbone.View.extend({initialize:function(a){this.data=null,this.dataset=a.dataset,this.lineCount=this.dataset.metadata_data_lines||null},fetchData:function(){this.showLoadingIndicator();var a=this,b=this.model.get("config"),c=jQuery.getJSON("/api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:b.pagination.perPage,offset:b.pagination.currPage*b.pagination.perPage});return c.done(function(b){a.data=b.data,a.trigger("data:fetched",a),a.renderData()}),c.fail(function(b,c,d){console.error(b,c,d),a.trigger("data:error",a),alert("Error loading data:\n"+b.responseText)}),c},showLoadingIndicator:function(){this.$el.find(".scatterplot-data-info").html(['<div class="loading-indicator">','<span class="fa fa-spinner fa-spin"></span>','<span class="loading-indicator-message">loading...</span>',"</div>"].join(""))},template:function(){var a=['<div class="controls clear">','<div class="right">','<p class="scatterplot-data-info"></p>','<button class="stats-toggle-btn">Stats</button>','<button class="rerender-btn">Redraw</button>',"</div>",'<div class="left">','<div class="page-control"></div>',"</div>","</div>","<svg/>",'<div class="stats-display"></div>'].join("");return a},render:function(){return this.$el.addClass("scatterplot-display").html(this.template()),this.data&&this.renderData(),this},renderData:function(){this.renderLeftControls(),this.renderRightControls(),this.renderPlot(this.data),this.getStats()},renderLeftControls:function(){var a=this,b=this.model.get("config");return this.$el.find(".controls .left .page-control").pagination({startingPage:b.pagination.currPage,perPage:b.pagination.perPage,totalDataSize:this.lineCount,currDataSize:this.data.length}).off().on("pagination.page-change",function(c,d){b.pagination.currPage=d,a.model.set("config",{pagination:b.pagination}),a.resetZoom(),a.fetchData()}),this},renderRightControls:function(){var a=this;this.setLineInfo(this.data),this.$el.find(".stats-toggle-btn").off().click(function(){a.toggleStats()}),this.$el.find(".rerender-btn").off().click(function(){a.resetZoom(),a.renderPlot(this.data)})},renderPlot:function(){var a=this,b=this.$el.find("svg");this.toggleStats(!1),b.off().empty().show().on("zoom.scatterplot",function(b,c){a.model.set("config",c)}),scatterplot(b.get(0),this.model.get("config"),this.data)},setLineInfo:function(a,b){if(a){var c=this.model.get("config"),d=this.lineCount||"an unknown total",e=c.pagination.currPage*c.pagination.perPage,f=e+a.length;this.$el.find(".controls p.scatterplot-data-info").text([e+1,"to",f,"of",d].join(" "))}else this.$el.find(".controls p.scatterplot-data-info").html(b||"");return this},resetZoom:function(a,b){return a=void 0!==a?a:1,b=void 0!==b?b:[0,0],this.model.set("config",{scale:a,translate:b}),this},getStats:function(){if(this.data){var a=this,b=this.model.get("config"),c=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js");c.postMessage({data:this.data,keys:[b.xColumn,b.yColumn]}),c.onerror=function(){c.terminate()},c.onmessage=function(b){a.renderStats(b.data)}}},renderStats:function(a){var b=this.model.get("config"),c=this.$el.find(".stats-display"),d=b.xLabel,e=b.yLabel,f=$("<table/>").addClass("table").append(["<thead><th></th><th>",d,"</th><th>",e,"</th></thead>"].join("")).append(_.map(a,function(a,b){return $(["<tr><td>",b,"</td><td>",a[0],"</td><td>",a[1],"</td></tr>"].join(""))}));c.empty().append(f)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},xTicks:10,xLabel:"X",yTicks:10,yLabel:"Y",datapointSize:4,animDuration:500,scale:1,translate:[0,0]}}}); \ No newline at end of file diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 lib/galaxy/datatypes/dataproviders/column.py --- a/lib/galaxy/datatypes/dataproviders/column.py +++ b/lib/galaxy/datatypes/dataproviders/column.py @@ -3,6 +3,9 @@ is further subdivided into multiple data (e.g. columns from a line). """ +import urllib +import re + import line _TODO = """ @@ -34,12 +37,13 @@ 'column_count' : 'int', 'column_types' : 'list:str', 'parse_columns' : 'bool', - 'deliminator' : 'str' + 'deliminator' : 'str', + 'filters' : 'list:str' } def __init__( self, source, indeces=None, column_count=None, column_types=None, parsers=None, parse_columns=True, - deliminator='\t', **kwargs ): + deliminator='\t', filters=None, **kwargs ): """ :param indeces: a list of indeces of columns to gather from each row Optional: will default to `None`. @@ -103,6 +107,104 @@ # overwrite with user desired parsers self.parsers.update( parsers or {} ) + filters = filters or [] + self.column_filters = [] + for filter_ in filters: + parsed = self.parse_filter( filter_ ) + #TODO: might be better to error on bad filter/None here + if callable( parsed ): + self.column_filters.append( parsed ) + + def parse_filter( self, filter_param_str ): + split = filter_param_str.split( '-', 3 ) + if not len( split ) == 3: + return None + column, op, val = split + + # better checking v. len and indeces + column = int( column ) + if column > len( self.column_types ): + return None + if self.column_types[ column ] in ( 'float', 'int' ): + return self.create_numeric_filter( column, op, val ) + if self.column_types[ column ] in ( 'str' ): + return self.create_string_filter( column, op, val ) + if self.column_types[ column ] in ( 'list' ): + return self.create_list_filter( column, op, val ) + return None + + def create_numeric_filter( self, column, op, val ): + """ + Return an anonymous filter function that will be passed the array + of parsed columns. Return None if no filter function can be + created for the given params. + + The function will compare the column at index `column` against `val` + using the given op where op is one of: + lt: less than, le: less than or equal to, + eq: equal to, ne: not equal to, + ge: greather than or equal to, gt: greater than + + `val` is cast as float here and will return None if there's a parsing error. + """ + try: + val = float( val ) + except ValueError: + return None + if 'lt' == op: + return lambda d: d[column] < val + elif 'le' == op: + return lambda d: d[column] <= val + elif 'eq' == op: + return lambda d: d[column] == val + elif 'ne' == op: + return lambda d: d[column] != val + elif 'ge' == op: + return lambda d: d[column] >= val + elif 'gt' == op: + return lambda d: d[column] > val + return None + + def create_string_filter( self, column, op, val ): + """ + Return an anonymous filter function that will be passed the array + of parsed columns. Return None if no filter function can be + created for the given params. + + The function will compare the column at index `column` against `val` + using the given op where op is one of: + eq: exactly matches, + has: the column contains the substring `val`, + re: the column matches the regular expression in `val` + """ + if 'eq' == op: + return lambda d: d[column] == val + elif 'has' == op: + return lambda d: val in d[column] + elif 're' == op: + val = urllib.unquote_plus( val ) + val = re.compile( val ) + return lambda d: val.match( d[column] ) is not None + return None + + def create_list_filter( self, column, op, val ): + """ + Return an anonymous filter function that will be passed the array + of parsed columns. Return None if no filter function can be + created for the given params. + + The function will compare the column at index `column` against `val` + using the given op where op is one of: + eq: the list `val` exactly matches the list in the column, + has: the list in the column contains the sublist `val`, + """ + if 'eq' == op: + val = self.parse_value( val, 'list' ) + return lambda d: d[column] == val + elif 'has' == op: + return lambda d: val in d[column] + return None + def get_default_parsers( self ): """ Return parser dictionary keyed for each columnar type @@ -140,6 +242,39 @@ #'gffstrand': # -, +, ?, or '.' for None, etc. } + def filter( self, line ): + line = super( ColumnarDataProvider, self ).filter( line ) + if line == None: + return line + columns = self.parse_columns_from_line( line ) + return self.filter_by_columns( columns ) + + def parse_columns_from_line( self, line ): + """ + Returns a list of the desired, parsed columns. + :param line: the line to parse + :type line: str + """ + #TODO: too much going on in this loop - the above should all be precomputed AMAP... + all_columns = line.split( self.deliminator ) + # if no indeces were passed to init, return all columns + selected_indeces = self.selected_column_indeces or list( xrange( len( all_columns ) ) ) + parsed_columns = [] + for parser_index, column_index in enumerate( selected_indeces ): + parsed_columns.append( self.parse_column_at_index( all_columns, parser_index, column_index ) ) + return parsed_columns + + def parse_column_at_index( self, columns, parser_index, index ): + """ + Get the column type for the parser from `self.column_types` or `None` + if the type is unavailable. + """ + try: + return self.parse_value( columns[ index ], self.get_column_type( parser_index ) ) + # if a selected index is not within columns, return None + except IndexError, index_err: + return None + def parse_value( self, val, type ): """ Attempt to parse and return the given value based on the given type. @@ -173,51 +308,11 @@ except IndexError, ind_err: return None - def parse_column_at_index( self, columns, parser_index, index ): - """ - Get the column type for the parser from `self.column_types` or `None` - if the type is unavailable. - """ - try: - return self.parse_value( columns[ index ], self.get_column_type( parser_index ) ) - # if a selected index is not within columns, return None - except IndexError, index_err: - return None - - def parse_columns_from_line( self, line ): - """ - Returns a list of the desired, parsed columns. - :param line: the line to parse - :type line: str - """ - #TODO: too much going on in this loop - the above should all be precomputed AMAP... - all_columns = line.split( self.deliminator ) - # if no indeces were passed to init, return all columns - selected_indeces = self.selected_column_indeces or list( xrange( len( all_columns ) ) ) - parsed_columns = [] - for parser_index, column_index in enumerate( selected_indeces ): - parsed_columns.append( self.parse_column_at_index( all_columns, parser_index, column_index ) ) - return parsed_columns - - def __iter__( self ): - parent_gen = super( ColumnarDataProvider, self ).__iter__() - for line in parent_gen: - columns = self.parse_columns_from_line( line ) - yield columns - - #TODO: implement column filters here and not below - flatten hierarchy - -class FilteredByColumnDataProvider( ColumnarDataProvider ): - """ - Data provider that provide a list of columns from the lines of its source - _only_ if they pass a given filter function. - - e.g. column #3 is type int and > N - """ - # TODO: how to do this and still have limit and offset work? - def __init__( self, source, **kwargs ): - raise NotImplementedError() - super( FilteredByColumnDataProvider, self ).__init__( source, **kwargs ) + def filter_by_columns( self, columns ): + for filter_fn in self.column_filters: + if not filter_fn( columns ): + return None + return columns class DictDataProvider( ColumnarDataProvider ): diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 lib/galaxy/jobs/runners/util/cli/job/slurm.py --- a/lib/galaxy/jobs/runners/util/cli/job/slurm.py +++ b/lib/galaxy/jobs/runners/util/cli/job/slurm.py @@ -7,7 +7,7 @@ except ImportError: # Not in Galaxy, map Galaxy job states to Pulsar ones. from galaxy.util import enum - job_states = enum(RUNNING='running', OK='complete', QUEUED='queued') + job_states = enum(RUNNING='running', OK='complete', QUEUED='queued', ERROR="failed") from ..job import BaseJobExec @@ -59,10 +59,10 @@ return 'scancel %s' % job_id def get_status(self, job_ids=None): - return 'squeue -a -o \\"%A %t\\"' + return "squeue -a -o '%A %t'" def get_single_status(self, job_id): - return 'squeue -a -o \\"%A %t\\" -j ' + job_id + return "squeue -a -o '%A %t' -j " + job_id def parse_status(self, status, job_ids): # Get status for each job, skipping header. @@ -80,6 +80,7 @@ # Job still on cluster and has state. id, state = status[1].split() return self._get_job_state(state) + # else line like "slurm_load_jobs error: Invalid job id specified" return job_states.OK def _get_job_state(self, state): diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 lib/galaxy/managers/users.py --- a/lib/galaxy/managers/users.py +++ b/lib/galaxy/managers/users.py @@ -199,6 +199,42 @@ #TODO: use quota manager return self.app.quota_agent.get_percent( user=user ) + def tags_used( self, trans, user, tag_models=None ): + """ + Return a list of distinct 'user_tname:user_value' strings that the + given user has used. + """ + #TODO: simplify and unify with tag manager + if self.is_anonymous( user ): + return [] + + # get all the taggable model TagAssociations + if not tag_models: + tag_models = [ v.tag_assoc_class for v in self.app.tag_handler.item_tag_assoc_info.values() ] + # create a union of subqueries for each for this user - getting only the tname and user_value + all_tags_query = None + for tag_model in tag_models: + subq = ( self.app.model.context.query( tag_model.user_tname, tag_model.user_value ) + .filter( tag_model.user == trans.user ) ) + all_tags_query = subq if all_tags_query is None else all_tags_query.union( subq ) + + # if nothing init'd the query, bail + if all_tags_query is None: + return [] + + # boil the tag tuples down into a sorted list of DISTINCT name:val strings + tags = all_tags_query.distinct().all() + tags = [( ( name + ':' + val ) if val else name ) for name, val in tags ] + return sorted( tags ) + + def has_requests( self, trans, user ): + """ + """ + if self.is_anonymous( user ): + return False + request_types = self.app.security_agent.get_accessible_request_types( trans, user ) + return ( user.requests or request_types ) + class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ): @@ -214,21 +250,22 @@ 'id', 'email', 'username' ]) self.add_view( 'detailed', [ - 'update_time', - 'create_time', - - 'deleted', - 'purged', - 'active', + #'update_time', + #'create_time', 'total_disk_usage', 'nice_total_disk_usage', 'quota_percent' - # 'preferences', - # # all tags - # 'tags', - # # all annotations - # 'annotations' + + #'deleted', + #'purged', + #'active', + + #'preferences', + # all tags + 'tags_used', + ## all annotations + #'annotations' ], include_keys_from='summary' ) def add_serializers( self ): @@ -240,7 +277,13 @@ 'create_time' : self.serialize_date, 'update_time' : self.serialize_date, 'is_admin' : lambda t, i, k: self.user_manager.is_admin( t, i ), - 'quota_percent' : lambda t, i, k: self.user_manager.quota( t, i ) + + 'total_disk_usage' : lambda t, i, k: float( i.total_disk_usage ), + 'quota_percent' : lambda t, i, k: self.user_manager.quota( t, i ), + + 'tags_used' : lambda t, i, k: self.user_manager.tags_used( t, i ), + #TODO: 'has_requests' is more apt + 'requests' : lambda t, i, k: self.user_manager.has_requests( t, i ) }) def serialize_current_anonymous_user( self, trans, user, keys ): diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2250,13 +2250,12 @@ return tool_dict - def to_json (self, trans, **kwd): + def to_json (self, trans, kwd={}, is_dynamic=True): """ Recursively creates a tool dictionary containing repeats, dynamic options and updated states. """ job_id = kwd.get('__job_id__', None) dataset_id = kwd.get('__dataset_id__', None) - is_dynamic = string_as_bool(kwd.get('__is_dynamic__', True)) # load job details if provided job = None diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1618,6 +1618,8 @@ return UnvalidatedValue( None ) initial_values = [] recurse_options( initial_values, self.get_options( trans=trans, other_values=context ) ) + if len( initial_values ) == 0: + initial_values = None return initial_values def value_to_display_text( self, value, app ): diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 lib/galaxy/web/__init__.py --- a/lib/galaxy/web/__init__.py +++ b/lib/galaxy/web/__init__.py @@ -19,6 +19,7 @@ from framework.decorators import _future_expose_api_raw from framework.decorators import _future_expose_api_raw_anonymous from framework.decorators import _future_expose_api_anonymous_and_sessionless +from framework.decorators import _future_expose_api_raw_anonymous_and_sessionless from framework.formbuilder import form from framework.formbuilder import FormBuilder diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 lib/galaxy/web/framework/decorators.py --- a/lib/galaxy/web/framework/decorators.py +++ b/lib/galaxy/web/framework/decorators.py @@ -344,3 +344,6 @@ def _future_expose_api_raw_anonymous( func ): return _future_expose_api( func, to_json=False, user_required=False ) + +def _future_expose_api_raw_anonymous_and_sessionless( func ): + return _future_expose_api( func, to_json=False, user_required=False, user_or_session_required=False ) diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 lib/galaxy/webapps/galaxy/api/job_files.py --- a/lib/galaxy/webapps/galaxy/api/job_files.py +++ b/lib/galaxy/webapps/galaxy/api/job_files.py @@ -8,8 +8,8 @@ from galaxy import util from galaxy import model from galaxy.web.base.controller import BaseAPIController -from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous -from galaxy.web import _future_expose_api_raw_anonymous as expose_api_raw_anonymous +from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless +from galaxy.web import _future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless import logging @@ -28,7 +28,7 @@ security model for tool execution. """ - @expose_api_raw_anonymous + @expose_api_raw_anonymous_and_sessionless def index( self, trans, job_id, **kwargs ): """ index( self, trans, job_id, **kwargs ) @@ -54,7 +54,7 @@ path = kwargs.get("path", None) return open(path, 'rb') - @expose_api_anonymous + @expose_api_anonymous_and_sessionless def create( self, trans, job_id, payload, **kwargs ): """ create( self, trans, job_id, payload, **kwargs ) diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -76,14 +76,10 @@ GET /api/tools/{tool_id}/build Returns a tool model including dynamic parameters and updated values, repeats block etc. """ - tool_id = urllib.unquote_plus( id ) tool_version = kwd.get( 'tool_version', None ) - tool = self.app.toolbox.get_tool( tool_id, tool_version ) - if not tool: - trans.response.status = 500 - return { 'error': 'Could not find tool with id \'%s\'' % tool_id } - return tool.to_json(trans, **kwd) - + tool = self._get_tool( id, tool_version=tool_version, user=trans.user ) + return tool.to_json(trans, kwd) + @_future_expose_api @web.require_admin def reload( self, trans, tool_id, **kwd ): diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -6,6 +6,8 @@ import uuid import logging +import copy +import urllib from sqlalchemy import desc, or_, and_ from galaxy import exceptions, util from galaxy.model.item_attrs import UsesAnnotations @@ -17,6 +19,7 @@ from galaxy.workflow.extract import extract_workflow from galaxy.workflow.run import invoke, queue_invoke from galaxy.workflow.run_request import build_workflow_run_config +from galaxy.workflow.modules import module_factory log = logging.getLogger(__name__) @@ -305,6 +308,52 @@ raise exceptions.RequestParameterInvalidException( message ) return self.workflow_contents_manager.workflow_to_dict( trans, stored_workflow, style="instance" ) + @expose_api + def build_module( self, trans, payload={}): + """ + POST /api/workflows/build_module + Builds module details including a tool model for the workflow editor. + """ + tool_id = payload.get( 'tool_id', None ) + tool_version = payload.get( 'tool_version', None ) + tool_inputs = payload.get( 'inputs', None ) + annotation = payload.get( 'annotation', '' ) + + # load tool + tool = self._get_tool( tool_id, tool_version=tool_version, user=trans.user ) + + # initialize module + trans.workflow_building_mode = True + module = module_factory.from_dict( trans, { + 'type' : 'tool', + 'tool_id' : tool.id, + 'tool_state' : None + } ) + + # create tool model and default tool state (if missing) + tool_model = module.tool.to_json(trans, tool_inputs, is_dynamic=False) + module.state.inputs = copy.deepcopy(tool_model['state_inputs']) + return { + 'tool_model' : tool_model, + 'tool_state' : module.get_state(), + 'data_inputs' : module.get_data_inputs(), + 'data_outputs' : module.get_data_outputs(), + 'tool_errors' : module.get_errors(), + 'form_html' : module.get_config_form(), + 'annotation' : annotation, + 'post_job_actions' : module.get_post_job_actions(tool_inputs) + } + + # + # -- Helper methods -- + # + def _get_tool( self, id, tool_version=None, user=None ): + id = urllib.unquote_plus( id ) + tool = self.app.toolbox.get_tool( id, tool_version ) + if not tool or not tool.allow_user_access( user ): + raise exceptions.ObjectNotFound("Could not find tool with id '%s'" % id) + return tool + def __api_import_new_workflow( self, trans, payload, **kwd ): data = payload['workflow'] diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -217,6 +217,7 @@ webapp.mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) webapp.mapper.resource( 'genome', 'genomes', path_prefix='/api' ) webapp.mapper.resource( 'visualization', 'visualizations', path_prefix='/api' ) + webapp.mapper.connect( '/api/workflows/build_module', action='build_module', controller="workflows" ) webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" ) diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -609,7 +609,6 @@ This is used for the form shown in the right pane when a node is selected. """ - tool_state = incoming.pop('tool_state', None) trans.workflow_building_mode = True module = module_factory.from_dict( trans, { @@ -617,22 +616,7 @@ 'tool_id': tool_id, 'tool_state': tool_state } ) - - # create tool model and default tool state (if missing) - if type == 'tool' and not tool_state: - tool_model = module.tool.to_json(trans, **incoming) - module.state.inputs = copy.deepcopy(tool_model['state_inputs']) - return { - 'tool_model': tool_model, - 'tool_state': module.get_state(), - 'data_inputs': module.get_data_inputs(), - 'data_outputs': module.get_data_outputs(), - 'tool_errors': module.get_errors(), - 'form_html': module.get_config_form(), - 'annotation': annotation, - 'post_job_actions': module.get_post_job_actions(incoming) - } - + # update module state module.update_state( incoming ) @@ -669,7 +653,8 @@ module = module_factory.new( trans, type, **kwargs ) tool_model = None if type == 'tool': - tool_model = module.tool.to_json(trans) + tool_model = module.tool.to_json(trans, is_dynamic=False) + module.state.inputs = copy.deepcopy(tool_model['state_inputs']) return { 'type': module.type, 'name': module.get_name(), diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 static/scripts/mvc/tools/tools-form-workflow.js --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/static/scripts/mvc/tools/tools-form-workflow.js @@ -275,10 +275,16 @@ /** Request a new model for an already created tool form and updates the form inputs */ _updateModel: function() { + // link self + var self = this; + // create the request dictionary - var self = this; - var current_state = this.tree.finalize(); - + var current_state = { + tool_id : this.options.id, + tool_version : this.options.version, + inputs : this.tree.finalize() + } + // log tool state console.debug('tools-form-workflow::_refreshForm() - Refreshing states.'); console.debug(current_state); @@ -287,11 +293,11 @@ var process_id = this.deferred.register(); // build model url for request - var model_url = galaxy_config.root + 'workflow/editor_form_post?tool_id=' + this.options.id + '&__is_dynamic__=False'; + var model_url = galaxy_config.root + 'api/workflows/build_module'; // post job Utils.request({ - type : 'GET', + type : 'POST', url : model_url, data : current_state, success : function(data) { diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 static/scripts/mvc/tools/tools-input.js --- a/static/scripts/mvc/tools/tools-input.js +++ b/static/scripts/mvc/tools/tools-input.js @@ -34,8 +34,7 @@ this.field.skip = false; var v = this.field.value && this.field.value(); this.field.skip = Boolean(options.optional && - ((this.default_value === undefined) || - ((this.field.validate && !this.field.validate()) || !v || + (((this.field.validate && !this.field.validate()) || !v || (v == this.default_value) || (Number(v) == Number(this.default_value)) || (JSON.stringify(v) == JSON.stringify(this.default_value))))); diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -294,17 +294,20 @@ // get id var id = input_def.id; + // add regular/default value if missing + if (input_def.value === undefined) { + input_def.value = null; + } + if (input_def.default_value === undefined) { + input_def.default_value = input_def.value; + } + // create input field var field = this._createField(input_def); // add to field list this.app.field_list[id] = field; - // fix default value if missing - if (input_def.default_value === undefined) { - input_def.default_value = input_def.value; - } - // create input field wrapper var input_element = new InputElement(this.app, { label : input_def.label, diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -10,13 +10,13 @@ initialize: function(app) { this.app = app; }, - + /** Convert dictionary representation into tool api specific flat dictionary format. */ finalize: function(patch) { // link this var self = this; - + // dictionary with api specific identifiers this.map_dict = {}; @@ -24,24 +24,24 @@ if (!this.app.section) { return {}; } - + // ensure that dictionary with patching functions exists patch = patch || {}; - + // dictionary formatted for job submission or tool form update var result_dict = {}; // prepare full dictionary var dict = {}; - + // fill dictionary from dom this._iterate(this.app.section.$el, dict); - + // add identifier and value to job definition function add(job_input_id, input_id, input_value) { // add entry to result dictionary result_dict[job_input_id] = input_value; - + // backup id mapping self.map_dict[job_input_id] = input_id; }; @@ -53,21 +53,21 @@ if (node.input) { // get node var input = node.input; - + // create identifier var job_input_id = identifier; if (identifier != '') { job_input_id += '|'; } job_input_id += input.name; - + // process input type switch (input.type) { // handle repeats case 'repeat': // section identifier var section_label = 'section-'; - + // collect repeat block identifiers var block_indices = []; var block_prefix = null; @@ -81,10 +81,10 @@ } } } - + // sort repeat blocks block_indices.sort(function(a,b) { return a - b; }); - + // add to response dictionary in created order var index = 0; for (var i in block_indices) { @@ -98,10 +98,10 @@ if (patch[input.test_param.type]) { value = patch[input.test_param.type](value); } - + // add conditional value add (job_input_id + '|' + input.test_param.name, input.id, value); - + // identify selected case var selectedCase = self.matchCase(input, value); if (selectedCase != -1) { @@ -116,22 +116,17 @@ // get field var field = self.app.field_list[input.id]; if (field && field.value) { + // validate field value + var value = field.value(); + if (field.validate && !field.validate()) { + value = null; + } + // get and patch field value - var value = field.value(); if (patch[input.type]) { value = patch[input.type](value); } - // validate field value - if (field.skip) { - continue; - } - - // validate field value - if (field.validate && !field.validate()) { - value = null; - } - // ignore certain values if (input.ignore === undefined || (value !== null && input.ignore != value)) { // add value to submission @@ -149,20 +144,20 @@ } } } - + // start conversion convert('', dict); - + // return result return result_dict; }, - + /** Match job definition identifier to input element identifier */ match: function (job_input_id) { return this.map_dict && this.map_dict[job_input_id]; }, - + /** Match conditional values to selected cases */ matchCase: function(input, value) { @@ -174,27 +169,27 @@ value = input.test_param.falsevalue || 'false'; } } - + // find selected case for (var i in input.cases) { if (input.cases[i].value == value) { return i; } } - + // selected case not found return -1; }, - + /** Matches identifier from api model to input elements */ matchModel: function(model, callback) { // final result dictionary var result = {}; - + // link this var self = this; - + // search throughout response function search (id, head) { for (var i in head) { @@ -224,23 +219,23 @@ } } } - + // match all ids and return messages search('', model.inputs); // return matched results return result; }, - + /** Matches identifier from api response to input elements */ matchResponse: function(response) { // final result dictionary var result = {}; - + // link this var self = this; - + // search throughout response function search (id, head) { if (typeof head === 'string') { @@ -262,14 +257,14 @@ } } } - + // match all ids and return messages search('', response); - + // return matched results return result; }, - + /** Iterate through the tool form dom and map it to the dictionary. */ _iterate: function(parent, dict) { @@ -279,15 +274,15 @@ children.each(function() { // get child element var child = this; - + // get id var id = $(child).attr('id'); - + // create new branch if ($(child).hasClass('section-row')) { // create sub dictionary dict[id] = {}; - + // add input element if it exists var input = self.app.input_list[id]; if (input) { @@ -295,7 +290,7 @@ input : input } } - + // fill sub dictionary self._iterate(child, dict[id]); } else { diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 static/scripts/packed/mvc/tools/tools-form-workflow.js --- a/static/scripts/packed/mvc/tools/tools-form-workflow.js +++ b/static/scripts/packed/mvc/tools/tools-form-workflow.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.is_dynamic=false;this.options.narrow=true;this.options.initial_errors=true;this.options.cls_portlet="ui-portlet-narrow";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id+"&__is_dynamic__=False";b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.is_dynamic=false;this.options.narrow=true;this.options.initial_errors=true;this.options.cls_portlet="ui-portlet-narrow";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e={tool_id:this.options.id,tool_version:this.options.version,inputs:this.tree.finalize()};console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"api/workflows/build_module";b.request({type:"POST",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 static/scripts/packed/mvc/tools/tools-input.js --- a/static/scripts/packed/mvc/tools/tools-input.js +++ b/static/scripts/packed/mvc/tools/tools-input.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.text_enable=d.options.text_enable||"Enable";this.text_disable=d.options.text_disable||"Disable";this.field=c.field;this.default_value=c.default_value;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&((this.default_value===undefined)||((this.field.validate&&!this.field.validate())||!b||(b==this.default_value)||(Number(b)==Number(this.default_value))||(JSON.stringify(b)==JSON.stringify(this.default_value)))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.show();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html(this.text_disable)}else{this.reset();this.$field.hide();this.$title_optional.html(this.text_enable);this.field.value&&this.field.value(this.default_value)}this.app.trigger("refresh")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span> [<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file +define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.text_enable=d.options.text_enable||"Enable";this.text_disable=d.options.text_disable||"Disable";this.field=c.field;this.default_value=c.default_value;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&(((this.field.validate&&!this.field.validate())||!b||(b==this.default_value)||(Number(b)==Number(this.default_value))||(JSON.stringify(b)==JSON.stringify(this.default_value)))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.show();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html(this.text_disable)}else{this.reset();this.$field.hide();this.$title_optional.html(this.text_enable);this.field.value&&this.field.value(this.default_value)}this.app.trigger("refresh")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span> [<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls="ui-table-plain";i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs});o.$el.addClass("ui-table-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;var l=new c.View({title:p.title,title_new:p.title,min:p.min,max:p.max,onnew:function(){n(p.inputs);s.app.trigger("refresh")}});function n(i){var t=p.id+"-section-"+(q++);var u=new g(s.app,{inputs:i});l.add({id:t,$el:u.$el,ondel:function(){l.del(t);s.app.trigger("refresh")}})}var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o)}var k=new f(this.app,{label:p.title,help:p.help,field:l});this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);l.append($("<div/>").addClass("ui-table-form-info").html(i.help));var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;var j=this._createField(i);this.app.field_list[l]=j;if(i.default_value===undefined){i.default_value=i.value}var k=new f(this.app,{label:i.label,default_value:i.default_value,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(!this.app.options.is_dynamic){i.info="Data input '"+i.name+"' ("+e.textify(i.extensions.toString())+")";i.value=null;return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,optional:i.optional,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(!this.app.options.is_dynamic&&j.is_dynamic){return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){if(!this.app.options.is_dynamic&&i.is_dynamic){return this._fieldText(i)}var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){if(i.options){i.area=i.multiple;if(!e.validate(i.value)){i.value=""}else{if(i.value instanceof Array){i.value=value.toString()}else{i.value=String(i.value).replace(/[\[\]'"\s]/g,"");if(i.multiple){i.value=i.value.replace(/,/g,"\n")}}}}var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls="ui-table-plain";i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs});o.$el.addClass("ui-table-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;var l=new c.View({title:p.title,title_new:p.title,min:p.min,max:p.max,onnew:function(){n(p.inputs);s.app.trigger("refresh")}});function n(i){var t=p.id+"-section-"+(q++);var u=new g(s.app,{inputs:i});l.add({id:t,$el:u.$el,ondel:function(){l.del(t);s.app.trigger("refresh")}})}var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o)}var k=new f(this.app,{label:p.title,help:p.help,field:l});this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);l.append($("<div/>").addClass("ui-table-form-info").html(i.help));var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;if(i.value===undefined){i.value=null}if(i.default_value===undefined){i.default_value=i.value}var j=this._createField(i);this.app.field_list[l]=j;var k=new f(this.app,{label:i.label,default_value:i.default_value,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(!this.app.options.is_dynamic){i.info="Data input '"+i.name+"' ("+e.textify(i.extensions.toString())+")";i.value=null;return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,optional:i.optional,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(!this.app.options.is_dynamic&&j.is_dynamic){return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){if(!this.app.options.is_dynamic&&i.is_dynamic){return this._fieldText(i)}var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){if(i.options){i.area=i.multiple;if(!e.validate(i.value)){i.value=""}else{if(i.value instanceof Array){i.value=value.toString()}else{i.value=String(i.value).replace(/[\[\]'"\s]/g,"");if(i.multiple){i.value=i.value.replace(/,/g,"\n")}}}}var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(g[u.type]){v=g[u.type](v)}if(t.skip){continue}if(t.validate&&!t.validate()){v=null}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(t.validate&&!t.validate()){v=null}if(g[u.type]){v=g[u.type](v)}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 static/scripts/packed/utils/metrics-logger.js --- a/static/scripts/packed/utils/metrics-logger.js +++ b/static/scripts/packed/utils/metrics-logger.js @@ -1,1 +1,1 @@ -define([],function(){function i(D){D=D||{};var C=this;C.userId=window.bootstrapped?window.bootstrapped.user.id:null;C.userId=C.userId||D.userId||null;C.consoleLogger=D.consoleLogger||null;C._init(D);return 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E.options.onServerResponse==="function"){E.options.onServerResponse(I)}E.cache.remove(G);E._postSize=E.options.postSize})};i.prototype._delayPost=function k(){var C=this;C._waiting=setTimeout(function(){C._waiting=null},C.options.delayPostInMs)};i.prototype._emitToConsole=function c(G,F,E){var C=this;if(!C.consoleLogger){return C}var D=Array.prototype.slice.call(E,0);D.unshift(F);if(G>=i.METRIC&&typeof(C.consoleLogger.info)==="function"){return C.consoleLogger.info.apply(C.consoleLogger,D)}else{if(G>=i.ERROR&&typeof(C.consoleLogger.error)==="function"){return C.consoleLogger.error.apply(C.consoleLogger,D)}else{if(G>=i.WARN&&typeof(C.consoleLogger.warn)==="function"){C.consoleLogger.warn.apply(C.consoleLogger,D)}else{if(G>=i.INFO&&typeof(C.consoleLogger.info)==="function"){C.consoleLogger.info.apply(C.consoleLogger,D)}else{if(G>=i.DEBUG&&typeof(C.consoleLogger.debug)==="function"){C.consoleLogger.debug.apply(C.consoleLogger,D)}else{if(typeof(C.consoleLogger.log)==="function"){C.consoleLogger.log.apply(C.consoleLogger,D)}}}}}}return C};i.prototype.log=function h(){this.emit(1,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))};i.prototype.debug=function p(){this.emit(i.DEBUG,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))};i.prototype.info=function x(){this.emit(i.INFO,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))};i.prototype.warn=function w(){this.emit(i.WARN,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))};i.prototype.error=function t(){this.emit(i.ERROR,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))};i.prototype.metric=function r(){this.emit(i.METRIC,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))};function z(D){var C=this;return C._init(D||{})}z.defaultOptions={maxSize:5000};z.prototype._init=function j(C){if(!this._hasStorage()){throw new Error("LoggingCache needs localStorage")}if(!C.key){throw new Error("LoggingCache needs key for localStorage")}this.key=C.key;this._initStorage();this.maxSize=C.maxSize||z.defaultOptions.maxSize;return this};z.prototype._hasStorage=function A(){var D="test";try{localStorage.setItem(D,D);localStorage.removeItem(D);return true}catch(C){return false}};z.prototype._initStorage=function m(){if(localStorage.getItem(this.key)===null){return this.empty()}return this};z.prototype.add=function o(E){var D=this,F=D._fetchAndParse(),C=(F.length+1)-D.maxSize;if(C>0){F.splice(0,C)}F.push(E);D._unparseAndStore(F);return F.length};z.prototype._fetchAndParse=function g(){var C=this;return JSON.parse(localStorage.getItem(C.key))};z.prototype._unparseAndStore=function f(C){var D=this;return localStorage.setItem(D.key,JSON.stringify(C))};z.prototype.length=function e(){return this._fetchAndParse().length};z.prototype.get=function y(C){return this._fetchAndParse().slice(0,C)};z.prototype.remove=function B(C){var E=this._fetchAndParse(),D=E.splice(0,C);this._unparseAndStore(E);return D};z.prototype.empty=function l(){localStorage.setItem(this.key,"[]");return this};z.prototype.stringify=function s(C){return JSON.stringify(this.get(C))};z.prototype.print=function d(){console.log(JSON.stringify(this._fetchAndParse(),null," "))};return{MetricsLogger:i,LoggingCache:z}}); \ No newline at end of file +define([],function(){function i(D){D=D||{};var C=this;C.userId=(window.bootstrapped&&window.bootstrapped.user)?window.bootstrapped.user.id:null;C.userId=C.userId||D.userId||null;C.consoleLogger=D.consoleLogger||null;C._init(D);return C}i.ALL=0;i.DEBUG=10;i.INFO=20;i.WARN=30;i.ERROR=40;i.METRIC=50;i.NONE=100;i.defaultOptions={logLevel:i.NONE,consoleLevel:i.NONE,defaultNamespace:"Galaxy",clientPrefix:"client.",maxCacheSize:3000,postSize:1000,addTime:true,cacheKeyPrefix:"logs-",postUrl:"/api/metrics",delayPostInMs:1000*60*10,getPingData:undefined,onServerResponse:undefined};i.prototype._init=function j(E){var D=this;D.options={};for(var C in i.defaultOptions){if(i.defaultOptions.hasOwnProperty(C)){D.options[C]=(E.hasOwnProperty(C))?(E[C]):(i.defaultOptions[C])}}D.options.logLevel=D._parseLevel(D.options.logLevel);D.options.consoleLevel=D._parseLevel(D.options.consoleLevel);D._sending=false;D._waiting=null;D._postSize=D.options.postSize;D._initCache();return D};i.prototype._initCache=function a(){try{this.cache=new z({maxSize:this.options.maxCacheSize,key:this.options.cacheKeyPrefix+this.userId})}catch(C){this._emitToConsole("warn","MetricsLogger",["Could not intitialize logging cache:",C]);this.options.logLevel=i.NONE}};i.prototype._parseLevel=function n(E){var D=typeof E;if(D==="number"){return E}if(D==="string"){var C=E.toUpperCase();if(i.hasOwnProperty(C)){return i[C]}}throw new Error("Unknown log level: "+E)};i.prototype.emit=function q(F,E,D){var C=this;E=E||C.options.defaultNamespace;if(!F||!D){return C}F=C._parseLevel(F);if(F>=C.options.logLevel){C._addToCache(F,E,D)}if(C.consoleLogger&&F>=C.options.consoleLevel){C._emitToConsole(F,E,D)}return C};i.prototype._addToCache=function b(H,E,D){this._emitToConsole("debug","MetricsLogger",["_addToCache:",arguments,this.options.addTime,this.cache.length()]);var C=this;try{var G=C.cache.add(C._buildEntry(H,E,D));if(G>=C._postSize){C._postCache()}}catch(F){C._emitToConsole("warn","MetricsLogger",["Metrics logger could not stringify 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E.options.onServerResponse==="function"){E.options.onServerResponse(I)}E.cache.remove(G);E._postSize=E.options.postSize})};i.prototype._delayPost=function k(){var C=this;C._waiting=setTimeout(function(){C._waiting=null},C.options.delayPostInMs)};i.prototype._emitToConsole=function c(G,F,E){var C=this;if(!C.consoleLogger){return C}var D=Array.prototype.slice.call(E,0);D.unshift(F);if(G>=i.METRIC&&typeof(C.consoleLogger.info)==="function"){return C.consoleLogger.info.apply(C.consoleLogger,D)}else{if(G>=i.ERROR&&typeof(C.consoleLogger.error)==="function"){return 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t(){this.emit(i.ERROR,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))};i.prototype.metric=function r(){this.emit(i.METRIC,this.options.defaultNamespace,Array.prototype.slice.call(arguments,0))};function z(D){var C=this;return C._init(D||{})}z.defaultOptions={maxSize:5000};z.prototype._init=function j(C){if(!this._hasStorage()){throw new Error("LoggingCache needs localStorage")}if(!C.key){throw new Error("LoggingCache needs key for localStorage")}this.key=C.key;this._initStorage();this.maxSize=C.maxSize||z.defaultOptions.maxSize;return this};z.prototype._hasStorage=function A(){var D="test";try{localStorage.setItem(D,D);localStorage.removeItem(D);return true}catch(C){return false}};z.prototype._initStorage=function m(){if(localStorage.getItem(this.key)===null){return this.empty()}return this};z.prototype.add=function o(E){var D=this,F=D._fetchAndParse(),C=(F.length+1)-D.maxSize;if(C>0){F.splice(0,C)}F.push(E);D._unparseAndStore(F);return F.length};z.prototype._fetchAndParse=function g(){var C=this;return JSON.parse(localStorage.getItem(C.key))};z.prototype._unparseAndStore=function f(C){var D=this;return localStorage.setItem(D.key,JSON.stringify(C))};z.prototype.length=function e(){return this._fetchAndParse().length};z.prototype.get=function y(C){return this._fetchAndParse().slice(0,C)};z.prototype.remove=function B(C){var E=this._fetchAndParse(),D=E.splice(0,C);this._unparseAndStore(E);return D};z.prototype.empty=function l(){localStorage.setItem(this.key,"[]");return this};z.prototype.stringify=function s(C){return JSON.stringify(this.get(C))};z.prototype.print=function d(){console.log(JSON.stringify(this._fetchAndParse(),null," "))};return{MetricsLogger:i,LoggingCache:z}}); \ No newline at end of file diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 static/scripts/utils/metrics-logger.js --- a/static/scripts/utils/metrics-logger.js +++ b/static/scripts/utils/metrics-logger.js @@ -34,7 +34,7 @@ var self = this; ///** get the current user's id from bootstrapped data or options */ - self.userId = window.bootstrapped? window.bootstrapped.user.id: null; + self.userId = ( window.bootstrapped && window.bootstrapped.user )? window.bootstrapped.user.id: null; self.userId = self.userId || options.userId || null; /** the (optional) console to emit logs to */ diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -10,7 +10,7 @@ ## This avoids making two separate requests since the classic form requires the mako anyway. params = dict(trans.request.params) params['__dataset_id__'] = params.get('id', None) - self.form_config = tool.to_json(trans, **params) + self.form_config = tool.to_json(trans, params) self.form_config.update({ 'id' : tool.id, 'job_id' : trans.security.encode_id( job.id ) if job else None, diff -r 60ce4bb8e4cea17bf39b1799680b5bb45adf57b8 -r 01ac77bb90de2c285325abb27419f7e9880c8687 templates/webapps/galaxy/workflow/editor_tool_form.mako --- a/templates/webapps/galaxy/workflow/editor_tool_form.mako +++ b/templates/webapps/galaxy/workflow/editor_tool_form.mako @@ -6,11 +6,9 @@ ## TEMPORARY: create tool dictionary in mako while both tool forms are in use. ## This avoids making two separate requests since the classic form requires the mako anyway. from galaxy.tools.parameters import params_to_incoming - incoming = { - '__is_dynamic__' : False - } + incoming = {} params_to_incoming( incoming, tool.inputs, module.state.inputs, trans.app, to_html=False) - self.form_config = tool.to_json(trans, **incoming) + self.form_config = tool.to_json(trans, incoming, is_dynamic=False) self.form_config.update({ 'id' : tool.id, 'job_id' : trans.security.encode_id( job.id ) if job else None, https://bitbucket.org/galaxy/galaxy-central/commits/70b67e2355d0/ Changeset: 70b67e2355d0 User: dannon Date: 2015-02-09 17:16:01+00:00 Summary: Merge. Affected #: 2 files diff -r 01ac77bb90de2c285325abb27419f7e9880c8687 -r 70b67e2355d0bf455df62355807db413cca39c04 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -308,7 +308,7 @@ append_to_sniff_order() def load_build_sites( self, root ): - if root.find( 'build_sites' ): + if root.find( 'build_sites' ) is not None: for elem in root.find( 'build_sites' ).findall( 'site' ): if not (elem.get( 'type' ) and elem.get( 'file' )): self.log.exception( "Site is missing required 'type' and 'file' attributes: %s" ) diff -r 01ac77bb90de2c285325abb27419f7e9880c8687 -r 70b67e2355d0bf455df62355807db413cca39c04 lib/galaxy/webapps/galaxy/api/configuration.py --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -31,18 +31,25 @@ serialization_params = self._parse_serialization_params( kwd, 'all' ) return self.get_config_dict( trans, is_admin, **serialization_params ) - def get_config_dict( self, trans, return_admin=False, **kwargs ): + def get_config_dict( self, trans, return_admin=False, view=None, keys=None, default_view='all' ): + """ + Return a dictionary with (a subset of) current Galaxy settings. + + If `return_admin` also include a subset of more sensitive keys. + Pass in `view` (String) and comma seperated list of keys to control which + configuration settings are returned. + """ serializer = self.config_serializer if return_admin: #TODO: this should probably just be under a different route: 'admin/configuration' serializer = self.admin_config_serializer - if 'default_view' not in kwargs: - kwargs[ 'default_view' ] = serializer.default_view - serialized = serializer.serialize_to_view( trans, self.app.config, **kwargs ) + serialized = serializer.serialize_to_view( trans, self.app.config, + view=view, keys=keys, default_view=default_view ) return serialized +#TODO: for lack of a manager file for the config. May well be better in config.py? Circ imports? class ConfigSerializer( base.ModelSerializer ): def __init__( self, app ): @@ -54,42 +61,42 @@ def default_serializer( self, trans, config, key ): return config.get( key, None ) - def _defaults_to( self, default ): - return lambda t, i, k: i.get( k, default ) + def add_serializers( self ): + def _defaults_to( default ): + return lambda t, i, k: i.get( k, default ) - def add_serializers( self ): self.serializers = { #TODO: this is available from user data, remove 'is_admin_user' : lambda *a: False, - 'brand' : lambda t, i, k: i.get( k, "" ), + 'brand' : _defaults_to( '' ), #TODO: this doesn't seem right - 'logo_url' : lambda t, i, k: self.url_for( i.get( k, '/') ), - 'terms_url' : lambda t, i, k: i.get( k, "" ), + 'logo_url' : lambda t, i, k: self.url_for( i.get( k, '/' ) ), + 'terms_url' : _defaults_to( '' ), #TODO: don't hardcode here - hardcode defaults once in config.py - 'wiki_url' : self._defaults_to( "http://galaxyproject.org/" ), - 'search_url' : self._defaults_to( "http://galaxyproject.org/search/usegalaxy/" ), - 'mailing_lists' : self._defaults_to( "http://wiki.galaxyproject.org/MailingLists" ), - 'screencasts_url' : self._defaults_to( "http://vimeo.com/galaxyproject" ), - 'citation_url' : self._defaults_to( "http://wiki.galaxyproject.org/CitingGalaxy" ), - 'support_url' : self._defaults_to( "http://wiki.galaxyproject.org/Support" ), - 'lims_doc_url' : self._defaults_to( "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), - 'biostar_url' : lambda t, i, k: i.biostar_url, + 'wiki_url' : _defaults_to( "http://galaxyproject.org/" ), + 'search_url' : _defaults_to( "http://galaxyproject.org/search/usegalaxy/" ), + 'mailing_lists' : _defaults_to( "http://wiki.galaxyproject.org/MailingLists" ), + 'screencasts_url' : _defaults_to( "http://vimeo.com/galaxyproject" ), + 'citation_url' : _defaults_to( "http://wiki.galaxyproject.org/CitingGalaxy" ), + 'support_url' : _defaults_to( "http://wiki.galaxyproject.org/Support" ), + 'lims_doc_url' : _defaults_to( "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), + 'biostar_url' : _defaults_to( '' ), 'biostar_url_redirect' : lambda *a: self.url_for( controller='biostar', action='biostar_redirect', - qualified=True ), + qualified=True ), - 'allow_user_creation' : lambda t, i, k: i.allow_user_creation, - 'use_remote_user' : lambda t, i, k: i.use_remote_user, - 'remote_user_logout_href' : lambda t, i, k: i.remote_user_logout_href, - 'enable_cloud_launch' : self._defaults_to( False ), - 'datatypes_disable_auto' : self._defaults_to( False ), - 'allow_user_dataset_purge' : self._defaults_to( False ), - 'enable_unique_workflow_defaults' : self._defaults_to( False ), + 'allow_user_creation' : _defaults_to( False ), + 'use_remote_user' : _defaults_to( None ), + 'remote_user_logout_href' : _defaults_to( '' ), + 'enable_cloud_launch' : _defaults_to( False ), + 'datatypes_disable_auto' : _defaults_to( False ), + 'allow_user_dataset_purge' : _defaults_to( False ), + 'enable_unique_workflow_defaults' : _defaults_to( False ), - 'nginx_upload_path' : self._defaults_to( self.url_for( controller='api', action='tools' ) ), - 'ftp_upload_dir' : self._defaults_to( None ), - 'ftp_upload_site' : self._defaults_to( None ), + 'nginx_upload_path' : _defaults_to( self.url_for( controller='api', action='tools' ) ), + 'ftp_upload_dir' : _defaults_to( None ), + 'ftp_upload_site' : _defaults_to( None ), } @@ -98,14 +105,16 @@ def add_serializers( self ): super( AdminConfigSerializer, self ).add_serializers() + def _defaults_to( default ): + return lambda t, i, k: i.get( k, default ) self.serializers.update({ #TODO: this is available from user data, remove 'is_admin_user' : lambda *a: True, - 'library_import_dir' : self._defaults_to( None ), - 'user_library_import_dir' : self._defaults_to( None ), - 'allow_library_path_paste' : self._defaults_to( None ), - 'allow_user_creation' : self._defaults_to( False ), - 'allow_user_deletion' : self._defaults_to( False ), + 'library_import_dir' : _defaults_to( None ), + 'user_library_import_dir' : _defaults_to( None ), + 'allow_library_path_paste' : _defaults_to( False ), + 'allow_user_creation' : _defaults_to( False ), + 'allow_user_deletion' : _defaults_to( False ), }) https://bitbucket.org/galaxy/galaxy-central/commits/38717ecbec32/ Changeset: 38717ecbec32 User: dannon Date: 2015-02-09 19:49:35+00:00 Summary: Prevent last_action column from being populated with time.now() in the entire database and function correctly with null values here. Related bugfixes. Affected #: 4 files diff -r 70b67e2355d0bf455df62355807db413cca39c04 -r 38717ecbec32e88f43652bda0739a20ad7b3faf6 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2986,7 +2986,8 @@ current_history=None, session_key=None, is_valid=False, - prev_session_id=None ): + prev_session_id=None, + last_action=None ): self.id = id self.user = user self.remote_host = remote_host @@ -2997,7 +2998,7 @@ self.is_valid = is_valid self.prev_session_id = prev_session_id self.histories = [] - self.last_action = galaxy.model.orm.now.now() + self.last_action = last_action or datetime.now() def add_history( self, history, association=None ): if association is None: diff -r 70b67e2355d0bf455df62355807db413cca39c04 -r 38717ecbec32e88f43652bda0739a20ad7b3faf6 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -683,7 +683,8 @@ Column( "session_key", TrimmedString( 255 ), index=True, unique=True ), # unique 128 bit random number coerced to a string Column( "is_valid", Boolean, default=False ), Column( "prev_session_id", Integer ), # saves a reference to the previous session so we have a way to chain them together - Column( "disk_usage", Numeric( 15, 0 ), index=True ) ) + Column( "disk_usage", Numeric( 15, 0 ), index=True ), + Column( "last_action", DateTime) ) model.GalaxySessionToHistoryAssociation.table = Table( "galaxy_session_to_history", metadata, Column( "id", Integer, primary_key=True ), diff -r 70b67e2355d0bf455df62355807db413cca39c04 -r 38717ecbec32e88f43652bda0739a20ad7b3faf6 lib/galaxy/model/migrate/versions/0128_session_timeout.py --- a/lib/galaxy/model/migrate/versions/0128_session_timeout.py +++ b/lib/galaxy/model/migrate/versions/0128_session_timeout.py @@ -21,7 +21,7 @@ print __doc__ metadata.reflect() - lastaction_column = Column( "last_action", DateTime, default=now ) + lastaction_column = Column( "last_action", DateTime ) __add_column( lastaction_column, "galaxy_session", metadata ) diff -r 70b67e2355d0bf455df62355807db413cca39c04 -r 38717ecbec32e88f43652bda0739a20ad7b3faf6 lib/galaxy/web/framework/webapp.py --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -221,7 +221,13 @@ # Make sure we're not past the duration, and either log out or # update timestamp. now = datetime.datetime.now() - expiration_time = self.galaxy_session.update_time + datetime.timedelta(minutes=config.session_duration) + if self.galaxy_session.last_action: + expiration_time = self.galaxy_session.last_action + datetime.timedelta(minutes=config.session_duration) + else: + expiration_time = now + self.galaxy_session.last_action = now - datetime.timedelta(seconds=1) + self.sa_session.add(self.galaxy_session) + self.sa_session.flush() if expiration_time < now: # Expiration time has passed. self.handle_user_logout() @@ -236,7 +242,7 @@ status='info', use_panels=True ) ) else: - self.galaxy_session.update_time = datetime.datetime.now() + self.galaxy_session.last_action = now self.sa_session.add(self.galaxy_session) self.sa_session.flush() https://bitbucket.org/galaxy/galaxy-central/commits/e99cb7eea9d7/ Changeset: e99cb7eea9d7 User: dannon Date: 2015-02-09 19:50:00+00:00 Summary: Merge. Affected #: 3 files diff -r 38717ecbec32e88f43652bda0739a20ad7b3faf6 -r e99cb7eea9d785245398e33166e3f53606d24ed4 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2711,12 +2711,16 @@ error_message = "Dataset collection has no %s with key %s." % ( get_by_attribute, key ) raise KeyError( error_message ) - def copy( self ): + def copy( self, destination=None, element_destination=None ): new_collection = DatasetCollection( collection_type=self.collection_type, ) for element in self.elements: - element.copy_to_collection( new_collection ) + element.copy_to_collection( + new_collection, + destination=destination, + element_destination=element_destination, + ) object_session( self ).add( new_collection ) object_session( self ).flush() return new_collection @@ -2835,20 +2839,24 @@ break return matching_collection - def copy( self ): + def copy( self, element_destination=None ): """ Create a copy of this history dataset collection association. Copy underlying collection. """ hdca = HistoryDatasetCollectionAssociation( hid=self.hid, - collection=self.collection.copy(), + collection=None, visible=self.visible, deleted=self.deleted, name=self.name, copied_from_history_dataset_collection_association=self, ) - + collection_copy = self.collection.copy( + destination=hdca, + element_destination=element_destination, + ) + hdca.collection = collection_copy object_session( self ).add( hdca ) object_session( self ).flush() return hdca @@ -2957,9 +2965,26 @@ else: return element_object - def copy_to_collection( self, collection ): + def copy_to_collection( self, collection, destination=None, element_destination=None ): + element_object = self.element_object + if element_destination: + if self.is_collection: + element_object = element_object.copy( + destination=destination, + element_destination=element_destination + ) + else: + new_element_object = element_object.copy( copy_children=True ) + if destination is not None and element_object.hidden_beneath_collection_instance: + new_element_object.hidden_beneath_collection_instance = destination + # Ideally we would not need to give the following + # element an HID and it would exist in the history only + # as an element of the containing collection. + element_destination.add_dataset( new_element_object ) + element_object = new_element_object + new_element = DatasetCollectionElement( - element=self.element_object, + element=element_object, collection=collection, element_index=self.element_index, element_identifier=self.element_identifier, diff -r 38717ecbec32e88f43652bda0739a20ad7b3faf6 -r e99cb7eea9d785245398e33166e3f53606d24ed4 lib/galaxy/tools/deps/brew_exts.py --- a/lib/galaxy/tools/deps/brew_exts.py +++ b/lib/galaxy/tools/deps/brew_exts.py @@ -21,7 +21,10 @@ from __future__ import print_function -import argparse +try: + import argparse +except ImportError: + argparse = None import contextlib import json import glob diff -r 38717ecbec32e88f43652bda0739a20ad7b3faf6 -r e99cb7eea9d785245398e33166e3f53606d24ed4 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -1074,7 +1074,11 @@ if content.history_content_type == "dataset": hist.add_dataset( content.copy( copy_children=True ) ) else: - hist.add_dataset_collection( content.copy( ) ) + copy_collected_datasets = True + copy_kwds = {} + if copy_collected_datasets: + copy_kwds["element_destination"] = hist + hist.add_dataset_collection( content.copy( **copy_kwds ) ) if current_history in target_histories: refresh_frames = ['history'] trans.sa_session.flush() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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