- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by Bitbucket 07 Jan '13

07 Jan '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f51be0814ca/ changeset: 2f51be0814ca user: dan date: 2013-01-07 17:45:26 summary: Fix for workflow editor when a missing tool is connected to a valid tool. Javascript error would cause the 'Loading worflow editor...' modal window to spin indefinitely. affected #: 1 file diff -r eb4dac39eed53cc0ef1550ee63486358fd53ad59 -r 2f51be0814cafc106de5ef39878afd3333c90a35 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -80,9 +80,13 @@ $.extend( Connector.prototype, { connect: function ( t1, t2 ) { this.handle1 = t1; - this.handle1.connect( this ); + if ( this.handle1 ) { + this.handle1.connect( this ); + } this.handle2 = t2; - this.handle2.connect( this ); + if ( this.handle2 ) { + this.handle2.connect( this ); + } }, destroy : function () { if ( this.handle1 ) { https://bitbucket.org/galaxy/galaxy-central/commits/ce62bf5a91f8/ changeset: ce62bf5a91f8 user: dan date: 2013-01-07 17:45:30 summary: Pack scripts. affected #: 1 file diff -r 2f51be0814cafc106de5ef39878afd3333c90a35 -r ce62bf5a91f86d0c53764bda3df4975486d7512e static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(b,c,a){Terminal.call(this,b);this.datatypes=c;this.multiple=a}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1||this.multiple){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};if(!this.handle1||!this.handle2){return}var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(f,b,c,a){var d=this;$(f).each(function(){var g=this.terminal=new InputTerminal(this,c,a);g.node=d;g.name=b;$(this).bind("dropinit",function(h,i){return $(i.drag).hasClass("output-terminal")&&g.can_accept(i.drag.terminal)}).bind("dropstart",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#BBFFBB"}}).bind("dropend",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#FFFFFF"}}).bind("drop",function(h,i){(new Connector(i.drag.terminal,g)).redraw()}).bind("hover",function(){if(g.connectors.length>0){var h=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png").click(function(){$.each(g.connectors,function(j,i){if(i){i.destroy()}});h.remove()}))).bind("mouseleave",function(){$(this).remove()});h.css({top:$(this).offset().top-2,left:$(this).offset().left-h.width(),"padding-right":$(this).width()}).show()}});d.input_terminals[b]=g})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new 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a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions,f.multiple);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout "+f+"'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions,j.multiple);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b,a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0&&g==workflow.active_node){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(i,j){g[j.name]=null;var h=[];$.each(j.connectors,function(k,l){h[k]={id:l.handle1.node.id,output_name:l.handle1.name};g[j.name]=h})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node("tool",f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){if($.isArray(h)){$.each(h,function(m,k){var n=wf.nodes[k.id];var o=new Connector();o.connect(n.output_terminals[k.output_name],d.input_terminals[i]);o.redraw()})}else{var j=wf.nodes[h.id];var l=new Connector();l.connect(j.output_terminals[h.output_name],d.input_terminals[i]);l.redraw()}}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node 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b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_paths.attributes.image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",galaxy_paths.attributes.image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(b,c,a){Terminal.call(this,b);this.datatypes=c;this.multiple=a}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1||this.multiple){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;if(this.handle1){this.handle1.connect(this)}this.handle2=a;if(this.handle2){this.handle2.connect(this)}},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};if(!this.handle1||!this.handle2){return}var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(f,b,c,a){var d=this;$(f).each(function(){var g=this.terminal=new InputTerminal(this,c,a);g.node=d;g.name=b;$(this).bind("dropinit",function(h,i){return $(i.drag).hasClass("output-terminal")&&g.can_accept(i.drag.terminal)}).bind("dropstart",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#BBFFBB"}}).bind("dropend",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#FFFFFF"}}).bind("drop",function(h,i){(new Connector(i.drag.terminal,g)).redraw()}).bind("hover",function(){if(g.connectors.length>0){var h=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/delete_icon.png").click(function(){$.each(g.connectors,function(j,i){if(i){i.destroy()}});h.remove()}))).bind("mouseleave",function(){$(this).remove()});h.css({top:$(this).offset().top-2,left:$(this).offset().left-h.width(),"padding-right":$(this).width()}).show()}});d.input_terminals[b]=g})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions,f.multiple);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout "+f+"'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions,j.multiple);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b,a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0&&g==workflow.active_node){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(i,j){g[j.name]=null;var h=[];$.each(j.connectors,function(k,l){h[k]={id:l.handle1.node.id,output_name:l.handle1.name};g[j.name]=h})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node("tool",f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){if($.isArray(h)){$.each(h,function(m,k){var n=wf.nodes[k.id];var o=new Connector();o.connect(n.output_terminals[k.output_name],d.input_terminals[i]);o.redraw()})}else{var j=wf.nodes[h.id];var l=new Connector();l.connect(j.output_terminals[h.output_name],d.input_terminals[i]);l.redraw()}}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_paths.attributes.image_path+"/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_paths.attributes.image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div 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f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var 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j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Enhance Tool.check_and_update_param_values_helper() to check that the type of value provided is valid for the input parameter currently declared. Fixes issue where a server error would occur within workflows when parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input.
by Bitbucket 07 Jan '13

07 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eb4dac39eed5/ changeset: eb4dac39eed5 user: dan date: 2013-01-07 17:07:52 summary: Enhance Tool.check_and_update_param_values_helper() to check that the type of value provided is valid for the input parameter currently declared. Fixes issue where a server error would occur within workflows when parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input. affected #: 1 file diff -r f93f509ca0c2a21acdf0ed17615d1caf839dcb98 -r eb4dac39eed53cc0ef1550ee63486358fd53ad59 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2181,7 +2181,12 @@ self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix ) else: # Regular tool parameter, no recursion needed - pass + try: + #this will fail when a parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input + input.value_from_basic( values[ input.name ], trans.app, ignore_errors=False ) + except: + messages[ input.name ] = "Value no longer valid for '%s%s', replaced with default" % ( prefix, input.label ) + values[ input.name ] = input.get_initial_value( trans, context ) def handle_unvalidated_param_values( self, input_values, app ): """ Find any instances of `UnvalidatedValue` within input_values and Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Handle tool panel locations appropriately for tool shed repositories and repository dependencies being installed or reinstalled into Galaxy.
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f93f509ca0c2/ changeset: f93f509ca0c2 user: greg date: 2013-01-04 22:10:26 summary: Handle tool panel locations appropriately for tool shed repositories and repository dependencies being installed or reinstalled into Galaxy. affected #: 2 files diff -r 8fe64f73835cd19274dcac65c935187d426b18ba -r f93f509ca0c2a21acdf0ed17615d1caf839dcb98 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -5,6 +5,7 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.webapps.community.util import container_util import shed_util_common as suc +import galaxy.tools from galaxy.tools.search import ToolBoxSearch from galaxy.tool_shed.tool_dependencies.install_util import create_or_update_tool_dependency, install_package, set_environment from galaxy.tool_shed import encoding_util @@ -175,14 +176,17 @@ # Attempt to ensure we're copying an appropriate file. if is_data_index_sample_file( filename ): suc.copy_sample_file( app, filename, dest_path=dest_path ) -def create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False, install_repository_dependencies=False ): +def create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False, install_repository_dependencies=False, + no_changes_checked=False, tool_panel_section=None, new_tool_panel_section=None ): """ Discover all repository dependencies and make sure all tool_shed_repository and associated repository_dependency records exist as well as the dependency relationships between installed repositories. This method is called when new repositories are being installed into a Galaxy instance and when uninstalled repositories are being reinstalled. """ message = '' + # There will be a one-to-one mapping between items in created_or_updated_tool_shed_repositories and tool_panel_section_keys. created_or_updated_tool_shed_repositories = [] + tool_panel_section_keys = [] # Repositories will be filtered (e.g., if already installed, etc), so filter the associated repo_info_dicts accordingly. filtered_repo_info_dicts = [] if install_repository_dependencies: @@ -204,6 +208,11 @@ installed_tool_shed_repository, installed_changeset_revision = \ repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple, clone_dir ) if installed_tool_shed_repository: + tool_section, new_tool_panel_section, tool_panel_section_key = handle_tool_panel_selection( trans=trans, + metadata=installed_tool_shed_repository.metadata, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) if reinstalling or install_repository_dependencies: if installed_tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR, trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: @@ -217,22 +226,23 @@ # There is a repository already installed which is a dependency of the repository being reinstalled. can_update = False else: - # An attempt is being made to install a tool shed repository into a Galaxy instance when the same repository was previously installed. - message += "Revision <b>%s</b> of tool shed repository <b>%s</b> owned by <b>%s</b> " % ( changeset_revision, name, repository_owner ) - if installed_changeset_revision != changeset_revision: - message += "was previously installed using changeset revision <b>%s</b>. " % installed_changeset_revision - else: - message += "was previously installed. " - if installed_tool_shed_repository.uninstalled: - message += "The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. " - elif installed_tool_shed_repository.deleted: - message += "The repository has been deactivated, however, so activate the original repository instead of installing it again. " - if installed_changeset_revision != changeset_revision: - message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's " - message += "<b>Repository Actions</b> pop-up menu. " if len( all_repo_info_dicts ) == 1: + # An attempt is being made to install a tool shed repository into a Galaxy instance when the same repository was previously installed. + message += "Revision <b>%s</b> of tool shed repository <b>%s</b> owned by <b>%s</b> " % ( changeset_revision, name, repository_owner ) + if installed_changeset_revision != changeset_revision: + message += "was previously installed using changeset revision <b>%s</b>. " % installed_changeset_revision + else: + message += "was previously installed. " + if installed_tool_shed_repository.uninstalled: + message += "The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. " + elif installed_tool_shed_repository.deleted: + message += "The repository has been deactivated, however, so activate the original repository instead of installing it again. " + if installed_changeset_revision != changeset_revision: + message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's " + message += "<b>Repository Actions</b> pop-up menu. " created_or_updated_tool_shed_repositories.append( installed_tool_shed_repository ) - return created_or_updated_tool_shed_repositories, all_repo_info_dicts, filtered_repo_info_dicts, message + tool_panel_section_keys.append( tool_panel_section_key ) + return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts, message else: can_update = True else: @@ -243,6 +253,36 @@ metadata_dict={} dist_to_shed = False if can_update: + if reinstalling or install_repository_dependencies: + # Get the repository metadata to see where it was previously located in the tool panel. + installed_tool_shed_repository = suc.get_repository_for_dependency_relationship( app=trans.app, + tool_shed=tool_shed_url, + name=name, + owner=repository_owner, + changeset_revision=changeset_revision ) + if installed_tool_shed_repository: + tool_section, new_tool_panel_section, tool_panel_section_key = \ + handle_tool_panel_selection( trans=trans, + metadata=installed_tool_shed_repository.metadata, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) + else: + if new_tool_panel_section: + section_id = new_tool_panel_section.lower().replace( ' ', '_' ) + tool_panel_section_key = 'section_%s' % str( section_id ) + elif tool_panel_section: + tool_panel_section_key = 'section_%s' % tool_panel_section + else: + tool_panel_section_key = None + else: + if new_tool_panel_section: + section_id = new_tool_panel_section.lower().replace( ' ', '_' ) + tool_panel_section_key = 'section_%s' % str( section_id ) + elif tool_panel_section: + tool_panel_section_key = 'section_%s' % tool_panel_section + else: + tool_panel_section_key = None tool_shed_repository = suc.create_or_update_tool_shed_repository( app=trans.app, name=name, description=description, @@ -255,8 +295,9 @@ owner=repository_owner, dist_to_shed=False ) created_or_updated_tool_shed_repositories.append( tool_shed_repository ) + tool_panel_section_keys.append( tool_panel_section_key ) filtered_repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) ) - return created_or_updated_tool_shed_repositories, all_repo_info_dicts, filtered_repo_info_dicts, message + return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts, message def create_repository_dict_for_proprietary_datatypes( tool_shed, name, owner, installed_changeset_revision, tool_dicts, converter_path=None, display_path=None ): return dict( tool_shed=tool_shed, repository_name=name, @@ -836,6 +877,60 @@ app.model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) return installed_tool_dependencies +def handle_tool_panel_selection( trans, metadata, no_changes_checked, tool_panel_section, new_tool_panel_section ): + """Handle the selected tool panel location for loading tools included in tool shed repositories when installing or reinstalling them.""" + # Get the location in the tool panel in which each tool was originally loaded. + tool_section = None + tool_panel_section_key = None + if 'tools' in metadata: + if 'tool_panel_section' in metadata: + tool_panel_dict = metadata[ 'tool_panel_section' ] + if not tool_panel_dict: + tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + else: + tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + # This forces everything to be loaded into the same section (or no section) in the tool panel. + tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] + tool_section_dict = tool_section_dicts[ 0 ] + original_section_id = tool_section_dict[ 'id' ] + original_section_name = tool_section_dict[ 'name' ] + if no_changes_checked: + if original_section_id: + tool_panel_section_key = 'section_%s' % str( original_section_id ) + if tool_panel_section_key in trans.app.toolbox.tool_panel: + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + # The section in which the tool was originally loaded used to be in the tool panel, but no longer is. + elem = Element( 'section' ) + elem.attrib[ 'name' ] = original_section_name + elem.attrib[ 'id' ] = original_section_id + elem.attrib[ 'version' ] = '' + tool_section = galaxy.tools.ToolSection( elem ) + trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section + else: + # The user elected to change the tool panel section to contain the tools. + if new_tool_panel_section: + section_id = new_tool_panel_section.lower().replace( ' ', '_' ) + tool_panel_section_key = 'section_%s' % str( section_id ) + if tool_panel_section_key in trans.app.toolbox.tool_panel: + # Appending a tool to an existing section in trans.app.toolbox.tool_panel + log.debug( "Appending to tool panel section: %s" % new_tool_panel_section ) + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + # Appending a new section to trans.app.toolbox.tool_panel + log.debug( "Loading new tool panel section: %s" % new_tool_panel_section ) + elem = Element( 'section' ) + elem.attrib[ 'name' ] = new_tool_panel_section + elem.attrib[ 'id' ] = section_id + elem.attrib[ 'version' ] = '' + tool_section = galaxy.tools.ToolSection( elem ) + trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section + elif tool_panel_section: + tool_panel_section_key = 'section_%s' % tool_panel_section + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + tool_section = None + return tool_section, new_tool_panel_section, tool_panel_section_key def handle_tool_versions( app, tool_version_dicts, tool_shed_repository ): """ Using the list of tool_version_dicts retrieved from the tool shed (one per changeset revison up to the currently installed changeset revision), diff -r 8fe64f73835cd19274dcac65c935187d426b18ba -r f93f509ca0c2a21acdf0ed17615d1caf839dcb98 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -396,7 +396,7 @@ if operation == "activate or reinstall": repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) if repository.uninstalled: - if repository.includes_tools: + if repository.includes_tools or repository.has_repository_dependencies: # Only allow selecting a different section in the tool panel if the repository was uninstalled. return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='reselect_tool_panel_section', @@ -835,17 +835,19 @@ @web.require_admin def install_tool_shed_repositories( self, trans, tool_shed_repositories, reinstalling=False, **kwd ): """Install specified tool shed repositories.""" - repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] ) tool_path = kwd[ 'tool_path' ] includes_tool_dependencies = util.string_as_bool( kwd[ 'includes_tool_dependencies' ] ) install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) - tool_panel_section_key = kwd.get( 'tool_panel_section_key', None ) - if tool_panel_section_key: - tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] - else: - tool_section = None - for tup in zip( tool_shed_repositories, repo_info_dicts ): - tool_shed_repository, repo_info_dict = tup + # There must be a one-to-one mapping between items in the 3 lists:tool_shed_repositories, tool_panel_section_keys, repo_info_dicts. + tool_panel_section_keys = util.listify( kwd[ 'tool_panel_section_keys' ] ) + repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] ) + for index, tool_shed_repository in enumerate( tool_shed_repositories ): + repo_info_dict = repo_info_dicts[ index ] + tool_panel_section_key = tool_panel_section_keys[ index ] + if tool_panel_section_key: + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + tool_section = None if isinstance( repo_info_dict, basestring ): repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict ) # Clone each repository to the configured location. @@ -1021,13 +1023,17 @@ encoded_kwd = kwd[ 'encoded_kwd' ] decoded_kwd = encoding_util.tool_shed_decode( encoded_kwd ) tsr_ids = decoded_kwd[ 'tool_shed_repository_ids' ] + tool_panel_section_keys = decoded_kwd[ 'tool_panel_section_keys' ] + filtered_tool_panel_section_keys = [] repositories_for_installation = [] - for tsr_id in tsr_ids: + for index, tsr_id in enumerate( tsr_ids ): repository = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) if repository.status in [ trans.model.ToolShedRepository.installation_status.NEW, trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: repositories_for_installation.append( repository ) + filtered_tool_panel_section_keys.append( tool_panel_section_keys[ index ] ) if repositories_for_installation: + decoded_kwd[ 'tool_panel_section_keys' ] = filtered_tool_panel_section_keys self.install_tool_shed_repositories( trans, repositories_for_installation, reinstalling=reinstalling, **decoded_kwd ) else: kwd[ 'message' ] = 'All selected tool shed repositories are already installed.' @@ -1154,6 +1160,7 @@ # Every repository will be installed into the same tool panel section or all will be installed outside of any sections. new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) tool_panel_section = kwd.get( 'tool_panel_section', '' ) + tool_panel_section_keys = [] # One or more repositories may include tools, but not necessarily all of them. includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) ) includes_tool_dependencies = util.string_as_bool( kwd.get( 'includes_tool_dependencies', False ) ) @@ -1191,13 +1198,16 @@ else: install_tool_dependencies = False tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ) - created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts, message = \ + created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False, - install_repository_dependencies=install_repository_dependencies ) + install_repository_dependencies=install_repository_dependencies, + no_changes_checked=False, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) if message and len( repo_info_dicts ) == 1: installed_tool_shed_repository = created_or_updated_tool_shed_repositories[ 0 ] message+= 'Click <a href="%s">here</a> to manage the repository. ' % \ @@ -1235,6 +1245,10 @@ tool_panel_section_key = None tool_section = None tsrids_list = [ trans.security.encode_id( tsr.id ) for tsr in created_or_updated_tool_shed_repositories ] + # Create a one-to-one mapping of tool shed repository id and tool panel section key. All tools contained in the repositories + # being installed will be loaded into the same section in the tool panel. + for tsr in created_or_updated_tool_shed_repositories: + tool_panel_section_keys.append( tool_panel_section_key ) new_kwd = dict( includes_tools=includes_tools, includes_repository_dependencies=includes_repository_dependencies, install_repository_dependencies=install_repository_dependencies, @@ -1245,7 +1259,8 @@ shed_tool_conf=shed_tool_conf, status=status, tool_path=tool_path, - tool_panel_section_key=tool_panel_section_key, + + tool_panel_section_keys=tool_panel_section_keys, tool_shed_repository_ids=tsrids_list, tool_shed_url=tool_shed_url ) encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) @@ -1369,66 +1384,25 @@ no_changes_checked = CheckboxField.is_checked( no_changes ) install_repository_dependencies = CheckboxField.is_checked( kwd.get( 'install_repository_dependencies', '' ) ) install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) - new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) - tool_panel_section = kwd.get( 'tool_panel_section', '' ) shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) clone_dir = os.path.join( tool_path, shed_util.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) tool_section = None + tool_panel_section = kwd.get( 'tool_panel_section', '' ) + new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) tool_panel_section_key = None + tool_panel_section_keys = [] metadata = tool_shed_repository.metadata if tool_shed_repository.includes_tools: - # Get the location in the tool panel in which each tool was originally loaded. - if 'tool_panel_section' in metadata: - tool_panel_dict = metadata[ 'tool_panel_section' ] - if not tool_panel_dict: - tool_panel_dict = shed_util.generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) - else: - tool_panel_dict = shed_util.generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) - # Fix this to handle the case where the tools are distributed across in more than 1 ToolSection - this assumes everything was loaded into 1 - # section (or no section) in the tool panel. - tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] - tool_section_dict = tool_section_dicts[ 0 ] - original_section_id = tool_section_dict[ 'id' ] - original_section_name = tool_section_dict[ 'name' ] - if no_changes_checked: - if original_section_id: - tool_panel_section_key = 'section_%s' % str( original_section_id ) - if tool_panel_section_key in trans.app.toolbox.tool_panel: - tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] - else: - # The section in which the tool was originally loaded used to be in the tool panel, but no longer is. - elem = Element( 'section' ) - elem.attrib[ 'name' ] = original_section_name - elem.attrib[ 'id' ] = original_section_id - elem.attrib[ 'version' ] = '' - tool_section = tools.ToolSection( elem ) - trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section - else: - # The user elected to change the tool panel section to contain the tools. - if new_tool_panel_section: - section_id = new_tool_panel_section.lower().replace( ' ', '_' ) - tool_panel_section_key = 'section_%s' % str( section_id ) - if tool_panel_section_key in trans.app.toolbox.tool_panel: - # Appending a tool to an existing section in trans.app.toolbox.tool_panel - log.debug( "Appending to tool panel section: %s" % new_tool_panel_section ) - tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] - else: - # Appending a new section to trans.app.toolbox.tool_panel - log.debug( "Loading new tool panel section: %s" % new_tool_panel_section ) - elem = Element( 'section' ) - elem.attrib[ 'name' ] = new_tool_panel_section - elem.attrib[ 'id' ] = section_id - elem.attrib[ 'version' ] = '' - tool_section = tools.ToolSection( elem ) - trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section - elif tool_panel_section: - tool_panel_section_key = 'section_%s' % tool_panel_section - tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] - else: - tool_section = None + # Handle the selected tool panel location for loading tools included in the tool shed repository. + tool_section, new_tool_panel_section, tool_panel_section_key = \ + shed_util.handle_tool_panel_selection( trans=trans, + metadata=metadata, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) # The repository's status must be updated from 'Uninstall' to 'New' when initiating reinstall so the repository_installation_updater will function. tool_shed_repository = suc.create_or_update_tool_shed_repository( trans.app, tool_shed_repository.name, @@ -1471,22 +1445,31 @@ repo_info_dict = encoding_util.tool_shed_encode( repo_info_dict ) repo_info_dicts.append( repo_info_dict ) # Make sure all tool_shed_repository records exist. - created_or_updated_tool_shed_repositories = [ tool_shed_repository ] if install_repository_dependencies: # This is a bit screwy because filtered_repo_info_dicts in this block is a list of tool_shed_encoded dictionaries, but # in the associated else block, it is a list of unencoded dictionaries - not sure if this should be corrected... - created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts, message = \ + created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=True, - install_repository_dependencies=install_repository_dependencies ) + install_repository_dependencies=install_repository_dependencies, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) if len( created_or_updated_tool_shed_repositories ) > 1: # Build repository dependency relationships. suc.build_repository_dependency_relationships( trans, repo_info_dicts, created_or_updated_tool_shed_repositories ) else: filtered_repo_info_dicts = [ repo_info_dict for repo_info_dict in repo_info_dicts ] + created_or_updated_tool_shed_repositories = [ tool_shed_repository ] + tool_panel_section_keys.append( tool_panel_section_key ) + # Defaulot the selected tool panel location for loading tools included in each newly installed required tool shed repository to the location + # selected for the repository selected for reinstallation. + for index, tps_key in enumerate( tool_panel_section_keys ): + if tps_key is None: + tool_panel_section_keys[ index ] = tool_panel_section_key encoded_repository_ids = [ trans.security.encode_id( r.id ) for r in created_or_updated_tool_shed_repositories ] new_kwd = dict( includes_tool_dependencies=tool_shed_repository.includes_tool_dependencies, includes_tools=tool_shed_repository.includes_tools, @@ -1498,7 +1481,7 @@ status=status, tool_panel_section=tool_panel_section, tool_path=tool_path, - tool_panel_section_key=tool_panel_section_key, + tool_panel_section_keys=tool_panel_section_keys, tool_shed_repository_ids=encoded_repository_ids, tool_shed_url=tool_shed_url ) encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) @@ -1530,6 +1513,7 @@ @web.expose @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): + """Select or change the tool panel section to contain the tools included in the tool shed repositories being reinstalled.""" message = '' repository_id = kwd[ 'id' ] tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: james_taylor: remove trailing comma
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8fe64f73835c/ changeset: 8fe64f73835c user: james_taylor date: 2013-01-04 20:42:28 summary: remove trailing comma affected #: 1 file diff -r 312ba8a948a1c678bea807f4a0d3320af8363968 -r 8fe64f73835cd19274dcac65c935187d426b18ba templates/root/index.mako --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -76,7 +76,7 @@ if( navigator.userAgent.match( /(iPhone|iPod|iPad)/i ) ) { $("iframe").parent().css( { "overflow": "scroll", - "-webkit-overflow-scrolling": "touch", + "-webkit-overflow-scrolling": "touch" }) } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: james_taylor: Fix for scrolling on iOS (thanks Carrie Ganote!)
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/312ba8a948a1/ changeset: 312ba8a948a1 user: james_taylor date: 2013-01-04 20:38:06 summary: Fix for scrolling on iOS (thanks Carrie Ganote!) affected #: 1 file diff -r 8676b55d191c6742e6e7b8864e47918719314f78 -r 312ba8a948a1c678bea807f4a0d3320af8363968 templates/root/index.mako --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -71,6 +71,15 @@ galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}"; } }); + + // Fix iFrame scrolling on iOS + if( navigator.userAgent.match( /(iPhone|iPod|iPad)/i ) ) { + $("iframe").parent().css( { + "overflow": "scroll", + "-webkit-overflow-scrolling": "touch", + }) + } + }); </script></%def> @@ -118,7 +127,9 @@ center_url = h.url_for( '/static/welcome.html' ) %> - <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe> + <div style="position: absolute; width: 100%; height: 100%"> + <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe> + </div></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Improve wording for item sharing.
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8676b55d191c/ changeset: 8676b55d191c user: jgoecks date: 2013-01-04 18:07:38 summary: Improve wording for item sharing. affected #: 1 file diff -r ad04a8d066e7092fb73d5469f1935196923b8ab3 -r 8676b55d191c6742e6e7b8864e47918719314f78 templates/sharing_base.mako --- a/templates/sharing_base.mako +++ b/templates/sharing_base.mako @@ -142,7 +142,7 @@ </form> %else: ## User has a public username, so private sharing and publishing options. - <h3>Making ${item_class_name} Accessible via Link and Publishing It</h3> + <h3>Make ${item_class_name} Accessible via Link and Publish It</h3><div> %if item.importable: @@ -214,7 +214,7 @@ ## ## Sharing with Galaxy users. ## - <h3>Sharing ${item_class_name} with Specific Users</h3> + <h3>Share ${item_class_name} with Individual Users</h3><div> %if item.users_shared_with: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: inithello: Tool shed functional tests for repositories with invalid tools, functional test enhancement for repositories with workflows.
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ad04a8d066e7/ changeset: ad04a8d066e7 user: inithello date: 2013-01-04 17:30:11 summary: Tool shed functional tests for repositories with invalid tools, functional test enhancement for repositories with workflows. affected #: 9 files diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -97,7 +97,7 @@ Loop through each tool dictionary in the repository metadata associated with the received changeset_revision. For each of these, check for a tools attribute, and load the tool metadata page if it exists, then display that tool's page. ''' - repository_metadata = test_db_util.get_repository_metadata_by_repository_id_changeset_revision( repository.id, changeset_revision ) + repository_metadata = self.get_repository_metadata_by_changeset_revision( repository, changeset_revision ) metadata = repository_metadata.metadata if 'tools' not in metadata: raise AssertionError( 'No tools in %s revision %s.' % ( repository.name, changeset_revision ) ) @@ -118,10 +118,9 @@ strings_not_displayed=[] ) def check_repository_invalid_tools_for_changeset_revision( self, repository, changeset_revision, strings_displayed=[], strings_not_displayed=[] ): '''Load the invalid tool page for each invalid tool associated with this changeset revision and verify the received error messages.''' - repository_metadata = test_db_util.get_repository_metadata_by_repository_id_changeset_revision( repository.id, changeset_revision ) + repository_metadata = self.get_repository_metadata_by_changeset_revision( repository, changeset_revision ) metadata = repository_metadata.metadata - if 'invalid_tools' not in metadata: - return + assert 'invalid_tools' in metadata, 'Metadata for changeset revision %s does not define invalid tools' % changeset_revision for tool_xml in metadata[ 'invalid_tools' ]: self.load_invalid_tool_page( repository, tool_xml=tool_xml, @@ -396,9 +395,11 @@ def get_repository_metadata( self, repository ): return [ metadata_revision for metadata_revision in repository.metadata_revisions ] def get_repository_metadata_by_changeset_revision( self, repository, changeset_revision ): - for metadata_revision in repository.metadata_revisions: + found = None + for metadata_revision in self.get_repository_metadata( repository ): if metadata_revision.changeset_revision == changeset_revision: - return metadata_revision + found = metadata_revision + return found def get_repository_metadata_revisions( self, repository ): return [ str( repository_metadata.changeset_revision ) for repository_metadata in repository.metadata_revisions ] def get_repository_tip( self, repository ): @@ -484,6 +485,8 @@ if not changeset_revision: changeset_revision = self.get_repository_tip( repository ) metadata = self.get_repository_metadata_by_changeset_revision( repository, changeset_revision ) + if not metadata: + raise AssertionError( 'Metadata not found for changeset revision %s.' % changeset_revision ) url = '/repository/generate_workflow_image?repository_metadata_id=%s&workflow_name=%s' % \ ( self.security.encode_id( metadata.id ), tool_shed_encode( workflow_name ) ) self.visit_url( url ) diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -2,8 +2,8 @@ import tool_shed.base.test_db_util as test_db_util repository_name = 'filtering_0000' -repository_description = "Galaxy's filtering tool" -repository_long_description = "Long description of Galaxy's filtering tool" +repository_description = "Galaxy's filtering tool for test 0000" +repository_long_description = "Long description of Galaxy's filtering tool for test 0000" class TestBasicRepositoryFeatures( ShedTwillTestCase ): diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_0060_workflows.py --- a/test/tool_shed/functional/test_0060_workflows.py +++ b/test/tool_shed/functional/test_0060_workflows.py @@ -2,9 +2,8 @@ import tool_shed.base.test_db_util as test_db_util repository_name = 'filtering_0060' -repository_description = "Galaxy's filtering tool" -repository_long_description = "Long description of Galaxy's filtering tool" -workflow_repository_name = 'filtering_workflow_0060' +repository_description="Galaxy's filtering tool for test 0060" +repository_long_description="Long description of Galaxy's filtering tool for test 0060" workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga' workflow_name = 'Workflow for 0060_filter_workflow_repository' @@ -54,6 +53,7 @@ 'filtering/filtering_2.2.0.tar', commit_message="Uploaded filtering 2.2.0", remove_repo_files_not_in_tar='No' ) +# raise Exception( self.get_repository_tip( repository ) ) self.load_workflow_image_in_tool_shed( repository, workflow_name, strings_not_displayed=[ '#EBBCB2' ] ) def test_0025_verify_repository_metadata( self ): '''Verify that resetting the metadata does not change it.''' diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_0070_invalid_tool.py --- a/test/tool_shed/functional/test_0070_invalid_tool.py +++ b/test/tool_shed/functional/test_0070_invalid_tool.py @@ -1,12 +1,13 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util -repository_name = 'freebayes_0070' -repository_description = "Galaxy's freebayes tool" -repository_long_description = "Long description of Galaxy's freebayes tool" +repository_name = 'bismark_0070' +repository_description = "Galaxy's bismark wrapper" +repository_long_description = "Long description of Galaxy's bismark wrapper" +category_name = 'Test 0070 Invalid Tool Revisions' -class TestFreebayesRepository( ShedTwillTestCase ): - '''Testing freebayes with tool data table entries, .loc files, and tool dependencies.''' +class TestBismarkRepository( ShedTwillTestCase ): + '''Testing bismark with valid and invalid tool entries.''' def test_0000_create_or_login_admin_user( self ): """Create necessary user accounts and login as an admin user.""" self.logout() @@ -19,14 +20,11 @@ admin_user = test_db_util.get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) - def test_0005_create_category( self ): - """Create a category for this test suite""" - self.create_category( name='Test 0070 Repository With Invalid Tool', description='Tests for a repository with an invalid tool.' ) - def test_0010_create_test_repository_and_upload_tool_xml( self ): - '''Create and populate a freebayes repository. After this test, it should contain one valid tool and one invalid tool.''' + def test_0005_create_category_and_repository( self ): + """Create a category for this test suite, then create and populate a bismark repository. It should contain at least one each valid and invalid tool.""" + category = self.create_category( name=category_name, description='Tests for a repository with invalid tool revisions.' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - category = test_db_util.get_category_by_name( 'Test 0070 Repository With Invalid Tool' ) repository = self.get_or_create_repository( name=repository_name, description=repository_description, long_description=repository_long_description, @@ -34,20 +32,18 @@ category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, - 'freebayes/freebayes.xml', + 'bismark/bismark.tar', valid_tools_only=False, strings_displayed=[], - commit_message='Uploaded the tool xml.' ) + commit_message='Uploaded the tool tarball.' ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Invalid tools' ] ) + invalid_revision = self.get_repository_tip( repository ) self.upload_file( repository, - 'filtering/filtering_1.1.0.tar', - valid_tools_only=False, + 'bismark/bismark_methylation_extractor.xml', + valid_tools_only=False, strings_displayed=[], - commit_message='Uploaded the tool xml.', - remove_repo_files_not_in_tar='No' ) - self.display_manage_repository_page( repository, strings_displayed=[ 'Valid tools', 'Invalid tools' ] ) - changeset_revision = self.get_repository_tip( repository ) - self.check_repository_tools_for_changeset_revision( repository, changeset_revision ) - self.check_repository_invalid_tools_for_changeset_revision( repository, - changeset_revision, - strings_displayed=[ 'requires an entry' ], - strings_not_displayed=[] ) + remove_repo_files_not_in_tar='No', + commit_message='Uploaded an updated tool xml.' ) + valid_revision = self.get_repository_tip( repository ) + self.check_repository_tools_for_changeset_revision( repository, valid_revision ) + self.check_repository_invalid_tools_for_changeset_revision( repository, invalid_revision ) diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_1060_install_repository_with_workflow.py --- a/test/tool_shed/functional/test_1060_install_repository_with_workflow.py +++ b/test/tool_shed/functional/test_1060_install_repository_with_workflow.py @@ -2,8 +2,8 @@ import tool_shed.base.test_db_util as test_db_util repository_name = 'filtering_0060' -repository_description = "Galaxy's filtering tool" -repository_long_description = "Long description of Galaxy's filtering tool" +repository_description="Galaxy's filtering tool for test 0060", +repository_long_description="Long description of Galaxy's filtering tool for test 0060", workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga' workflow_name = 'Workflow for 0060_filter_workflow_repository' diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_1070_invalid_tool.py --- a/test/tool_shed/functional/test_1070_invalid_tool.py +++ b/test/tool_shed/functional/test_1070_invalid_tool.py @@ -1,9 +1,10 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util -repository_name = 'freebayes_0070' -repository_description = "Galaxy's freebayes tool" -repository_long_description = "Long description of Galaxy's freebayes tool" +repository_name = 'bismark_0070' +repository_description = "Galaxy's bismark wrapper" +repository_long_description = "Long description of Galaxy's bismark wrapper" +category_name = 'Test 0070 Invalid Tool Revisions' class TestFreebayesRepository( ShedTwillTestCase ): '''Testing freebayes with tool data table entries, .loc files, and tool dependencies.''' @@ -26,11 +27,11 @@ admin_user_private_role = test_db_util.get_private_role( admin_user ) def test_0005_ensure_existence_of_repository_and_category( self ): '''Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool.''' - self.create_category( name='Test 0070 Repository With Invalid Tool', - description='Tests for a repository with an invalid tool.' ) + self.create_category( name=category_name, + description='Test 1070 for a repository with an invalid tool.' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - category = test_db_util.get_category_by_name( 'Test 0070 Repository With Invalid Tool' ) + category = test_db_util.get_category_by_name( category_name ) repository = self.get_or_create_repository( name=repository_name, description=repository_description, long_description=repository_long_description, @@ -39,27 +40,29 @@ strings_displayed=[] ) if self.repository_is_new( repository ): self.upload_file( repository, - 'freebayes/freebayes.xml', + 'bismark/bismark.tar', valid_tools_only=False, - commit_message='Uploaded the invalid tool xml.' ) + strings_displayed=[], + commit_message='Uploaded the tool tarball.' ) self.upload_file( repository, - 'filtering/filtering_1.1.0.tar', - valid_tools_only=False, - commit_message='Uploaded the valid tool xml.', - remove_repo_files_not_in_tar='No' ) + 'bismark/bismark_methylation_extractor.xml', + valid_tools_only=False, + strings_displayed=[], + remove_repo_files_not_in_tar='No', + commit_message='Uploaded an updated tool xml.' ) def test_0010_browse_tool_shed( self ): - """Browse the available tool sheds in this Galaxy instance and preview the freebayes repository.""" + """Browse the available tool sheds in this Galaxy instance and preview the bismark repository.""" self.galaxy_logout() self.galaxy_login( email=common.admin_email, username=common.admin_username ) - self.browse_tool_shed( url=self.url, strings_displayed=[ 'Test 0070 Repository With Invalid Tool' ] ) - category = test_db_util.get_category_by_name( 'Test 0070 Repository With Invalid Tool' ) + self.browse_tool_shed( url=self.url, strings_displayed=[ category_name ] ) + category = test_db_util.get_category_by_name( category_name ) self.browse_category( category, strings_displayed=[ repository_name ] ) self.preview_repository_in_tool_shed( repository_name, common.test_user_1_name, strings_displayed=[ repository_name ] ) def test_0015_install_freebayes_repository( self ): '''Install the test repository without installing tool dependencies.''' self.install_repository( repository_name, common.test_user_1_name, - 'Test 0070 Repository With Invalid Tool', + category_name, install_tool_dependencies=False, new_tool_panel_section='test_1070' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) @@ -70,11 +73,9 @@ installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'simple expressions', 'Invalid tools' ], - strings_not_displayed=[ 'variant detector' ] ) + strings_displayed=[ 'methylation extractor', 'Invalid tools' ], + strings_not_displayed=[ 'bisulfite mapper' ] ) self.verify_tool_metadata_for_installed_repository( installed_repository ) self.update_installed_repository( installed_repository, strings_displayed=[ "there are no updates available" ] ) - assert 'invalid_tools' in installed_repository.metadata, 'No invalid tools were defined in %s.' % installed_repository.name - def test_0020_verify_installed_repository_metadata( self ): - '''Verify that resetting the metadata on an installed repository does not change the metadata.''' - self.verify_installed_repository_metadata_unchanged( repository_name, common.test_user_1_name ) + assert 'invalid_tools' in installed_repository.metadata, 'No invalid tools were defined in %s.' % \ + installed_repository.name diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py --- a/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py +++ b/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py @@ -27,8 +27,8 @@ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = self.get_or_create_repository( name='filtering_0000', - description="Galaxy's filtering tool", - long_description="Long description of Galaxy's filtering tool", + description="Galaxy's filtering tool for test 0000", + long_description="Long description of Galaxy's filtering tool for test 0000", owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ) ) if self.repository_is_new( repository ): @@ -56,8 +56,8 @@ installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) self.uninstall_repository( installed_repository, remove_from_disk=True ) strings_not_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.installed_changeset_revision ] + installed_repository.description, + installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) def test_0020_reinstall_filtering_repository( self ): '''Reinstall the filtering repository.''' @@ -77,8 +77,8 @@ installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) self.uninstall_repository( installed_repository, remove_from_disk=False ) strings_not_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.installed_changeset_revision ] + installed_repository.description, + installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) def test_0030_reactivate_filtering_repository( self ): '''Reactivate the filtering repository and verify that it now shows up in the list of installed repositories.''' diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/test_data/bismark/bismark.tar Binary file test/tool_shed/test_data/bismark/bismark.tar has changed diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml --- /dev/null +++ b/test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml @@ -0,0 +1,306 @@ +<tool id="bismark_methylation_extractor" name="Bismark" version="0.7.7.3"> +  + <description>methylation extractor</description> +  + <requirements> + <requirement type="set_environment">SCRIPT_PATH</requirement> + <requirement type="package" version="0.12.8">bowtie</requirement> + <requirement type="package" version="2.0.0-beta7">bowtie2</requirement> + </requirements> + <parallelism method="basic"></parallelism> + <command interpreter="python"> + bismark_methylation_extractor.py + + --infile $input + + --bismark_path \$SCRIPT_PATH + + #if $singlePaired.sPaired == "single": + --single-end + #else: + --paired-end + $no_overlap + #end if + + #if str($ignore_bps) != "0": + --ignore $ignore_bps + #end if + + #if $report: + --report-file $o_report + #end if + + #if $comprehensive: + --comprehensive + #end if + + #if $merge_non_cpg: + --merge-non-cpg + #end if + + #if $compress: + --compress $compressed_output + #else: + #if $comprehensive == False and $merge_non_cpg == False: + ##twelfe files + --cpg_ot $cpg_ot + --chg_ot $chg_ot + --chh_ot $chh_ot + --cpg_ctot $cpg_ctot + --chg_ctot $chg_ctot + --chh_ctot $chh_ctot + --cpg_ob $cpg_ob + --chg_ob $chg_ob + --chh_ob $chh_ob + --cpg_ctob $cpg_ctob + --chg_ctob $chg_ctob + --chh_ctob $chh_ctob + #elif $merge_non_cpg and $comprehensive: + ## two files + --non_cpg_context $non_cpg_context + --cpg_context $cpg_context + #elif $comprehensive: + ## three files + --cpg_context $cpg_context + --chg_context $chg_context + --chh_context $chh_context + #elif $merge_non_cpg: + ## eight files + --non_cpg_context_ctot $non_cpg_context_ctot + --non_cpg_context_ot $non_cpg_context_ot + --non_cpg_context_ob $non_cpg_context_ob + --non_cpg_context_ctob $non_cpg_context_ctob + --cpg_ot $cpg_ot + --cpg_ctot $cpg_ctot + --cpg_ob $cpg_ob + --cpg_ctob $cpg_ctob + #end if + ## end compress + #end if + + </command> + <inputs> +  + <param name="input" type="data" format="sam" label="SAM file from Bismark bisulfid mapper" /> + <conditional name="singlePaired"> + <param name="sPaired" type="select" label="Is this library mate-paired?"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + </param> + <when value="single" /> + <when value="paired"> + <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="This option avoids scoring overlapping methylation calls twice, in case of overlapping read one and read two" help="" /> + </when> + </conditional> + + <param name="ignore_bps" type="integer" value="0" label="Ignore the first N bp when processing the methylation call string" /> + <param name="comprehensive" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all four possible strand-specific methylation info +into context-dependent output files" help="" /> + <param name="merge_non_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all non-CpG contexts into one file" help="This will produce eight strand-specific output files, or two output files in comprehensive mode." /> + <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Short methylation summary output" /> + <param name="compress" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Compress all result files and output one single file" /> + + </inputs> + <outputs> +  + <data format="tabular" name="o_report" label="${tool.name} on ${on_string}: Report file"> + <filter> ( report is True ) </filter> + </data> + +  + <data format="tabular" name="cpg_ot" label="${tool.name} on ${on_string}: CpG original top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chg_ot" label="${tool.name} on ${on_string}: CHG original top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chh_ot" label="${tool.name} on ${on_string}: CHH original top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="cpg_ctot" label="${tool.name} on ${on_string}: CpG complementary to top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chg_ctot" label="${tool.name} on ${on_string}: CHG complementary to top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chh_ctot" label="${tool.name} on ${on_string}: CHH complementary to top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + + <data format="tabular" name="cpg_ob" label="${tool.name} on ${on_string}: CpG original bottom strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chg_ob" label="${tool.name} on ${on_string}: CHG original bottom strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chh_ob" label="${tool.name} on ${on_string}: CHH original bottom strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="cpg_ctob" label="${tool.name} on ${on_string}: CpG complementary to bottom strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chg_ctob" label="${tool.name} on ${on_string}: CHG complementary to bottom strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chh_ctob" label="${tool.name} on ${on_string}: CHH complementary to bottom strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + +  + <data format="tabular" name="cpg_context" label="${tool.name} on ${on_string}: CpG context dependent"> + <filter> ( compress == False and comprehensive) </filter> + </data> + <data format="tabular" name="chg_context" label="${tool.name} on ${on_string}: CHG context dependent"> + <filter> ( compress == False and comprehensive and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chh_context" label="${tool.name} on ${on_string}: CHH context dependent"> + <filter> ( compress == False and comprehensive and merge_non_CpG == False) </filter> + </data> + + <data format="tabular" name="non_cpg_context" label="${tool.name} on ${on_string}: Non CpG context dependent"> + <filter> ( compress == False and comprehensive and merge_non_cpg) </filter> + </data> + + <data format="tabular" name="non_cpg_context_ot" label="${tool.name} on ${on_string}: Non CpG context dependent on original top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter> + </data> + <data format="tabular" name="non_cpg_context_ctot" label="${tool.name} on ${on_string}: Non CpG context dependent on complementary to top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter> + </data> + <data format="tabular" name="non_cpg_context_ob" label="${tool.name} on ${on_string}: Non CpG context dependent on bottom top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter> + </data> + <data format="tabular" name="non_cpg_context_ctob" label="${tool.name} on ${on_string}: Non CpG context dependent on complementary to bottom strand"> + <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter> + </data> + + <data format="gzipped" name="compressed_output" label="${tool.name} on ${on_string}: Result archive."> + <filter> ( compress ) </filter> + </data> + </outputs> + + <tests> + </tests> + + <help> + +**What it does** + +The following is a brief description of all options to control the Bismark_ +methylation extractor. The script reads in a bisulfite read alignment results file +produced by the Bismark bisulfite mapper and extracts the methylation information +for individual cytosines. This information is found in the methylation call field +which can contain the following characters: + + + - X = for methylated C in CHG context (was protected) + - x = for not methylated C CHG (was converted) + - H = for methylated C in CHH context (was protected) + - h = for not methylated C in CHH context (was converted) + - Z = for methylated C in CpG context (was protected) + - z = for not methylated C in CpG context (was converted) + - . = for any bases not involving cytosines + + +The methylation extractor outputs result files for cytosines in CpG, CHG and CHH +context (this distinction is actually already made in Bismark itself). As the methylation +information for every C analysed can produce files which easily have tens or even hundreds of +millions of lines, file sizes can become very large and more difficult to handle. The C +methylation info additionally splits cytosine methylation calls up into one of the four possible +strands a given bisulfite read aligned against: + + - OT = original top strand + - CTOT = complementary to original top strand + + - OB = original bottom strand + - CTOB = complementary to original bottom strand + +Thus, by default twelve individual output files are being generated per input file (unless +--comprehensive is specified, see below). The output files can be imported into a genome +viewer, such as SeqMonk, and re-combined into a single data group if desired (in fact +unless the bisulfite reads were generated preserving directionality it doesn't make any +sense to look at the data in a strand-specific manner). Strand-specific output files can +optionally be skipped, in which case only three output files for CpG, CHG or CHH context +will be generated. For both the strand-specific and comprehensive outputs there is also +the option to merge both non-CpG contexts (CHG and CHH) into one single non-CpG context. + + +.. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ + + +It is developed by Krueger F and Andrews SR. at the Babraham Institute. Krueger F, Andrews SR. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-2. + +------- + +**Bismark settings** + +All of the options have a default value. You can change any of them. If any Bismark function is missing please contact the tool author or your Galaxy admin. + +------ + +**Outputs** + +The output files are in the following format (tab delimited):: + + + Column Description + -------- -------------------------------------------------------- + 1 seq-ID + 2 strand + 3 chromosome + 4 position + 5 methylation call + + + * Methylated cytosines receive a '+' orientation, + * Unmethylated cytosines receive a '-' orientation. + +------ + +**OPTIONS** + +Input:: + + -s/--single-end Input file(s) are Bismark result file(s) generated from single-end + read data. Specifying either --single-end or --paired-end is + mandatory. + + -p/--paired-end Input file(s) are Bismark result file(s) generated from paired-end + read data. Specifying either --paired-end or --single-end is + mandatory. + + --no_overlap For paired-end reads it is theoretically possible that read_1 and + read_2 overlap. This option avoids scoring overlapping methylation + calls twice. Whilst this removes a bias towards more methylation calls + towards the center of sequenced fragments it can de facto remove + a good proportion of the data. + + --ignore INT Ignore the first INT bp at the 5' end of each read when processing the + methylation call string. This can remove e.g. a restriction enzyme site + at the start of each read. + +Output:: + + --comprehensive Specifying this option will merge all four possible strand-specific + methylation info into context-dependent output files. The default + contexts are: + - CpG context + - CHG context + - CHH context + + --merge_non_CpG This will produce two output files (in --comprehensive mode) or eight + strand-specific output files (default) for Cs in + - CpG context + - non-CpG context + + --report Prints out a short methylation summary as well as the paramaters used to run + this script. + + + </help> +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: history panel: panel was not showing deleted datasets when a dataset was purged (even when set to 'include deleted datasets') - fix by using purge_async; history panel: fix history-options menu checkbox with new font awesome class format; pack scripts
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eb67f0b3555d/ changeset: eb67f0b3555d user: carlfeberhard date: 2013-01-04 16:57:18 summary: history panel: panel was not showing deleted datasets when a dataset was purged (even when set to 'include deleted datasets') - fix by using purge_async; history panel: fix history-options menu checkbox with new font awesome class format; pack scripts affected #: 6 files diff -r 564c49962741608b073e9c3fb87b57f7e8aa454b -r eb67f0b3555df7e249c2d8715d75c598dc25055b static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -32,6 +32,38 @@ ]; }, + /** Set up js behaviors, event handlers for elements within the given container. + * Overridden from hda-base. + * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) + */ + _setUpBehaviors : function( $container ){ + //TODO: ideally this would be a DELETE call to the api + // using purge async for now + HDABaseView.prototype._setUpBehaviors.call( this, $container ); + + // use purge_async with an ajax call + var hdaView = this, + purge_url = this.urls.purge, + purge_link = $container.find( '#historyItemPurger-' + this.model.get( 'id' ) ); + if( purge_link ){ + //TODO: remove href from template + purge_link.attr( 'href', [ "javascript", "void(0)" ].join( ':' ) ); + purge_link.click( function( event ){ + //TODO??: confirm? + var ajaxPromise = jQuery.ajax( purge_url ); + ajaxPromise.success( function( message, status, responseObj ){ + hdaView.model.set( 'purged', true ); + }); + ajaxPromise.error( function( error, status, message ){ + //TODO: Exception messages are hidden within error page + //!NOTE: that includes the 'Removal of datasets by users is not allowed in this Galaxy instance.' + alert( '(' + error.status + ') Unable to purge this dataset:\n' + message ); + }); + }); + } + //TODO: same with undelete_async + }, + // ......................................................................... RENDER WARNINGS /** Render any hda warnings including: is deleted, is purged, is hidden. * Overrides _render_warnings to include links to further actions (undelete, etc.)). diff -r 564c49962741608b073e9c3fb87b57f7e8aa454b -r eb67f0b3555df7e249c2d8715d75c598dc25055b static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var 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';A=C.href;A=q["if"].call(C,A,{hash:{},inverse:p.noop,fn:p.program(13,v,B)});if(A||A===0){z+=A}z+=' class="popupmenu-option">\n ';A=C.checked;A=q["if"].call(C,A,{hash:{},inverse:p.noop,fn:p.program(15,u,B)});if(A||A===0){z+=A}z+="\n ";y=q.html;if(y){A=y.call(C,{hash:{}})}else{A=C.html;A=typeof A===d?A():A}if(A||A===0){z+=A}z+="\n </a></li>\n ";return z}function e(B,A){var z,y;y=q.href;if(y){z=y.call(B,{hash:{}})}else{z=B.href;z=typeof z===d?z():z}return c(z)}function w(z,y){return"javascript:void(0);"}function v(C,B){var z="",A,y;z+='target="';y=q.target;if(y){A=y.call(C,{hash:{}})}else{A=C.target;A=typeof A===d?A():A}z+=c(A)+'"';return z}function u(z,y){return'<span class="fa-icon-ok"></span>'}function t(z,y){return"\n <li>No Options.</li>\n"}r+='<ul id="';h=q.id;if(h){i=h.call(s,{hash:{}})}else{i=s.id;i=typeof i===d?i():i}r+=c(i)+'-menu" class="dropdown-menu">\n';i=s.options;i=i==null||i===false?i:i.length;i=q["if"].call(s,i,{hash:{},inverse:p.program(17,t,x),fn:p.program(1,o,x)});if(i||i===0){r+=i}r+="\n</ul>";return r})})(); \ No newline at end of file diff -r 564c49962741608b073e9c3fb87b57f7e8aa454b -r eb67f0b3555df7e249c2d8715d75c598dc25055b static/scripts/templates/compiled/template-popupmenu-menu.js --- a/static/scripts/templates/compiled/template-popupmenu-menu.js +++ b/static/scripts/templates/compiled/template-popupmenu-menu.js @@ -96,7 +96,7 @@ function program15(depth0,data) { - return "<span class=\"ficon ok\"></span>";} + return "<span class=\"fa-icon-ok\"></span>";} function program17(depth0,data) { diff -r 564c49962741608b073e9c3fb87b57f7e8aa454b -r eb67f0b3555df7e249c2d8715d75c598dc25055b static/scripts/templates/ui-templates.html --- a/static/scripts/templates/ui-templates.html +++ b/static/scripts/templates/ui-templates.html @@ -30,7 +30,7 @@ {{!NOTE: changed from # to void fn }} <li><a href="{{#if href }}{{ href }}{{else}}javascript:void(0);{{/if}}" {{#if href }}target="{{ target }}"{{/if}} class="popupmenu-option"> - {{#if checked }}<span class="ficon ok"></span>{{/if}} + {{#if checked }}<span class="fa-icon-ok"></span>{{/if}} {{{ html }}} </a></li> {{/if}} diff -r 564c49962741608b073e9c3fb87b57f7e8aa454b -r eb67f0b3555df7e249c2d8715d75c598dc25055b templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -124,7 +124,9 @@ url_dict = { # ................................................................ warning message links - 'purge' : h.url_for( controller='dataset', action='purge', + #'purge' : h.url_for( controller='dataset', action='purge', + # dataset_id=encoded_id_template ), + 'purge' : h.url_for( controller='dataset', action='purge_async', dataset_id=encoded_id_template ), #TODO: hide (via api) 'unhide' : h.url_for( controller='dataset', action='unhide', @@ -143,7 +145,6 @@ dataset_id=encoded_id_template ), #TODO: via api - #TODO: show deleted handled by history 'delete' : h.url_for( controller='dataset', action='delete_async', dataset_id=encoded_id_template ), # ................................................................ download links (and associated meta files), @@ -203,7 +204,6 @@ <%def name="get_hdas( history_id, hdas )"><% #BUG: one inaccessible dataset will error entire list - if not hdas: return '[]' # rather just use the history.id (wo the datasets), but... @@ -256,7 +256,6 @@ "mvc/dataset/hda-model", "mvc/dataset/hda-base", "mvc/dataset/hda-edit", - ##"mvc/dataset/hda-readonly", ##"mvc/tags", "mvc/annotations" @@ -302,9 +301,15 @@ $(function(){ galaxyPageSetUp(); - //Galaxy.historyFrame = window; - var debugging = ( new PersistantStorage( '__history_panel' ).get( 'debugging' ) || false ); + //NOTE: for debugging on non-local instances (main/test) + // 1. load history panel in own tab + // 2. from console: new PersistantStorage( '__history_panel' ).set( 'debugging', true ) + // -> history panel and hdas will display console logs in console + var debugging = false; + if( jQuery.jStorage.get( '__history_panel' ) ){ + debugging = new PersistantStorage( '__history_panel' ).get( 'debugging' ); + } // ostensibly, this is the App // LOAD INITIAL DATA IN THIS PAGE - since we're already sending it... Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Make sure metata is set for repositories in the tool shed that contain only invalid tools.
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/564c49962741/ changeset: 564c49962741 user: greg date: 2013-01-04 15:17:47 summary: Make sure metata is set for repositories in the tool shed that contain only invalid tools. affected #: 1 file diff -r 8d7d70348e526c64168392501922aa56f45d0a84 -r 564c49962741608b073e9c3fb87b57f7e8aa454b lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1056,6 +1056,7 @@ tool, valid, error_message = load_tool_from_config( app, full_path ) if tool is None: if not valid: + invalid_tool_configs.append( name ) invalid_file_tups.append( ( name, error_message ) ) else: invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_copy_paths ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Fix bugs that prevented creating a Circster visualization from a dataset.
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8d7d70348e52/ changeset: 8d7d70348e52 user: jgoecks date: 2013-01-04 04:07:55 summary: Fix bugs that prevented creating a Circster visualization from a dataset. affected #: 1 file diff -r d7475647cbb6a1c70218049fadc24ed1651d845a -r 8d7d70348e526c64168392501922aa56f45d0a84 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -725,12 +725,25 @@ Display a circster visualization. """ + # Get dataset to add. + if dataset_id: + dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) + # Get/create vis. if id: # Display existing viz. vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) else: # Create new viz. + if not dbkey: + # If dbkey not specified, use dataset's dbkey. + dbkey = dataset.dbkey + if not dbkey or dbkey == '?': + # Circster requires a valid dbkey. + return trans.show_error_message( "You must set the dataset's dbkey to view it. You can set " + "a dataset's dbkey by clicking on the pencil icon and editing " + "its attributes.", use_panels=True ) + vis = self.create_visualization( trans, type="genome", dbkey=dbkey, save=False ) # Get the vis config and work with it from here on out. Working with the @@ -739,12 +752,10 @@ viz_config = self.get_visualization_config( trans, vis ) # Add dataset if specified. - if dataset_id: - dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) + if dataset: viz_config[ 'tracks' ].append( self.get_new_track_config( trans, dataset ) ) # Get genome info. - dbkey = viz_config[ 'dbkey' ] chroms_info = self.app.genomes.chroms( trans, dbkey=dbkey ) genome = { 'dbkey': dbkey, 'chroms_info': chroms_info } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 12 new changesets
by Bitbucket 03 Jan '13

03 Jan '13

12 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/de91f945a824/ changeset: de91f945a824 user: natefoo date: 2013-01-03 22:29:11 summary: Backed out 9ec94e5d6a28 affected #: 1 file <HgDiff de91f945a824:4c96179f6fe1 ['lib/galaxy/jobs/runners/lwr.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/de8a5f5e064e/ changeset: de8a5f5e064e user: natefoo date: 2013-01-03 22:29:41 summary: backout 2f5544be71d1 affected #: 1 file <HgDiff de8a5f5e064e:de91f945a824 ['lib/galaxy/jobs/runners/lwr.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/b78fc8715c33/ changeset: b78fc8715c33 user: natefoo date: 2013-01-03 22:30:07 summary: Backout 875ac898df00 affected #: 2 files <HgDiff b78fc8715c33:de8a5f5e064e ['lib/galaxy/jobs/runners/lwr.py']><HgDiff b78fc8715c33:de8a5f5e064e ['lib/galaxy/jobs/runners/lwr_client/__init__.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/09152e37a3e5/ changeset: 09152e37a3e5 user: natefoo date: 2013-01-03 22:30:21 summary: backout 6265bf3f27ad affected #: 1 file <HgDiff 09152e37a3e5:b78fc8715c33 ['lib/galaxy/jobs/runners/lwr_client/__init__.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/01ac1286291b/ changeset: 01ac1286291b user: natefoo date: 2013-01-03 22:30:32 summary: backout 5822038f8c96 affected #: 3 files <HgDiff 01ac1286291b:09152e37a3e5 ['lib/galaxy/jobs/runners/__init__.py']><HgDiff 01ac1286291b:09152e37a3e5 ['lib/galaxy/jobs/runners/lwr.py']><HgDiff 01ac1286291b:09152e37a3e5 ['lib/galaxy/jobs/runners/lwr_client/__init__.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/1e8a57a3004d/ changeset: 1e8a57a3004d user: natefoo date: 2013-01-03 22:30:42 summary: backout 50c1edba7fe0 affected #: 1 file <HgDiff 1e8a57a3004d:01ac1286291b ['lib/galaxy/jobs/runners/lwr_client/__init__.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/77e141b92b59/ changeset: 77e141b92b59 user: natefoo date: 2013-01-03 22:32:06 summary: backout 93dd6202175a affected #: 2 files <HgDiff 77e141b92b59:1e8a57a3004d ['lib/galaxy/jobs/runners/lwr.py']><HgDiff 77e141b92b59:1e8a57a3004d ['lib/galaxy/jobs/runners/lwr_client/__init__.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/f5477485ee0c/ changeset: f5477485ee0c user: natefoo date: 2013-01-03 22:32:17 summary: backout e4adc9ad0bb7 affected #: 1 file <HgDiff f5477485ee0c:77e141b92b59 ['lib/galaxy/jobs/runners/lwr.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/9ca4a534c126/ changeset: 9ca4a534c126 user: natefoo date: 2013-01-03 22:32:29 summary: backout e6676636cfe7 affected #: 1 file <HgDiff 9ca4a534c126:f5477485ee0c ['lib/galaxy/jobs/runners/lwr.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/adb5231d1a5c/ changeset: adb5231d1a5c user: natefoo date: 2013-01-03 22:32:43 summary: backout 8c6cf637058a affected #: 1 file <HgDiff adb5231d1a5c:9ca4a534c126 ['lib/galaxy/jobs/runners/lwr.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/c382028a4f5b/ changeset: c382028a4f5b user: natefoo date: 2013-01-03 22:32:55 summary: backout ab827b2c7907 affected #: 1 file <HgDiff c382028a4f5b:adb5231d1a5c ['lib/galaxy/jobs/runners/__init__.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/d7475647cbb6/ changeset: d7475647cbb6 user: natefoo date: 2013-01-03 22:34:40 summary: merge affected #: 1 file <HgDiff d7475647cbb6:c382028a4f5b ['templates/workflow/editor.mako']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: james_taylor: workflow: tool search always on, fix tool menu padding, using cog icon for options menu
by Bitbucket 03 Jan '13

03 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e81e8298d157/ changeset: e81e8298d157 user: james_taylor date: 2013-01-03 22:21:57 summary: workflow: tool search always on, fix tool menu padding, using cog icon for options menu affected #: 1 file <HgDiff e81e8298d157:4c96179f6fe1 ['templates/workflow/editor.mako']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Add missing import to visualization controller.
by Bitbucket 03 Jan '13

03 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4c96179f6fe1/ changeset: 4c96179f6fe1 user: jgoecks date: 2013-01-03 21:12:51 summary: Add missing import to visualization controller. affected #: 1 file <HgDiff 4c96179f6fe1:3fb6035cdc66 ['lib/galaxy/webapps/galaxy/controllers/visualization.py']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Enable BBI data provider to work even when chromosome naming conventions are mixed.
by Bitbucket 03 Jan '13

03 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3fb6035cdc66/ changeset: 3fb6035cdc66 user: jgoecks date: 2013-01-03 20:54:50 summary: Enable BBI data provider to work even when chromosome naming conventions are mixed. affected #: 1 file <HgDiff 3fb6035cdc66:ddccdd0341f7 ['lib/galaxy/visualization/data_providers/genome.py']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Restrict discovery of repository dependencies to those occasions where the user chose to install them.
by Bitbucket 03 Jan '13

03 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ddccdd0341f7/ changeset: ddccdd0341f7 user: greg date: 2013-01-03 20:48:26 summary: Restrict discovery of repository dependencies to those occasions where the user chose to install them. affected #: 2 files <HgDiff ddccdd0341f7:b3a3660604f7 ['lib/galaxy/util/shed_util.py']><HgDiff ddccdd0341f7:b3a3660604f7 ['lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 3 new changesets
by Bitbucket 03 Jan '13

03 Jan '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/11870bfc1795/ changeset: 11870bfc1795 user: james_taylor date: 2013-01-03 20:17:59 summary: styles: update to latest boostrap (2.2.2) and Font-Awesome (3.0) affected #: 51 files <HgDiff 11870bfc1795:8acc7bfa21a2 ['static/images/fonts/fontawesome-webfont.eot']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/images/fonts/fontawesome-webfont.ttf']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/images/fonts/fontawesome-webfont.woff']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/base.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/blue/base.css']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/accordion.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/alerts.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/bootstrap.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/breadcrumbs.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/button-groups.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/buttons.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/carousel.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/close.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/code.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/component-animations.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/dropdowns.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/forms.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/grid.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/hero-unit.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/labels-badges.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/layouts.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/media.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/mixins.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/modals.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/navbar.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/navs.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/pager.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/pagination.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/popovers.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/progress-bars.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/reset.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/responsive-1200px-min.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/responsive-767px-max.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/responsive-768px-979px.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/responsive-navbar.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/responsive-utilities.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/responsive.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/scaffolding.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/sprites.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/tables.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/thumbnails.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/tooltip.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/type.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/utilities.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/variables.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/bootstrap/wells.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/fontawesome/font-awesome.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/galaxy_bootstrap.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['static/june_2007_style/galaxy_bootstrap_variables.less']><HgDiff 11870bfc1795:8acc7bfa21a2 ['templates/root/history_common.mako']><HgDiff 11870bfc1795:8acc7bfa21a2 ['templates/root/index.mako']> https://bitbucket.org/galaxy/galaxy-central/changeset/4e20f8e109e6/ changeset: 4e20f8e109e6 user: james_taylor date: 2013-01-03 20:25:48 summary: admin: fix scrolling for admin left menu affected #: 1 file <HgDiff 4e20f8e109e6:11870bfc1795 ['templates/webapps/galaxy/admin/index.mako']> https://bitbucket.org/galaxy/galaxy-central/changeset/b3a3660604f7/ changeset: b3a3660604f7 user: james_taylor date: 2013-01-03 20:28:41 summary: styles: remove old font-awesome svg fonts affected #: 2 files <HgDiff b3a3660604f7:4e20f8e109e6 ['static/images/fonts/fontawesome-webfont.svg']><HgDiff b3a3660604f7:4e20f8e109e6 ['static/images/fonts/fontawesome-webfont.svgz']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Functional tests for installing a repository that contains a workflow.
by Bitbucket 03 Jan '13

03 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8acc7bfa21a2/ changeset: 8acc7bfa21a2 user: inithello date: 2013-01-03 20:31:09 summary: Functional tests for installing a repository that contains a workflow. affected #: 2 files <HgDiff 8acc7bfa21a2:5521bfd71d8b ['test/tool_shed/base/twilltestcase.py']><HgDiff 8acc7bfa21a2:5521bfd71d8b ['test/tool_shed/functional/test_1060_install_repository_with_workflow.py']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Fix for installing repository without repository dependencies.
by Bitbucket 03 Jan '13

03 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5521bfd71d8b/ changeset: 5521bfd71d8b user: inithello date: 2013-01-03 19:28:12 summary: Fix for installing repository without repository dependencies. affected #: 1 file <HgDiff 5521bfd71d8b:1d0fe5115b85 ['lib/galaxy/util/shed_util.py']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for discovering repository dependencies for a tool shed repository being installed into Galaxy.
by Bitbucket 03 Jan '13

03 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1d0fe5115b85/ changeset: 1d0fe5115b85 user: greg date: 2013-01-03 17:29:01 summary: Fix for discovering repository dependencies for a tool shed repository being installed into Galaxy. affected #: 2 files <HgDiff 1d0fe5115b85:86e6bf3b9934 ['lib/galaxy/util/shed_util.py']><HgDiff 1d0fe5115b85:86e6bf3b9934 ['lib/galaxy/util/shed_util_common.py']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Make Galaxy Q&A URL optional and disable by default.
by Bitbucket 03 Jan '13

03 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/86e6bf3b9934/ changeset: 86e6bf3b9934 user: jgoecks date: 2013-01-03 15:43:53 summary: Make Galaxy Q&A URL optional and disable by default. affected #: 3 files <HgDiff 86e6bf3b9934:7424f6498807 ['templates/webapps/community/base_panels.mako']><HgDiff 86e6bf3b9934:7424f6498807 ['templates/webapps/galaxy/base_panels.mako']><HgDiff 86e6bf3b9934:7424f6498807 ['universe_wsgi.ini.sample']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for discovering all repository dependencies for a tool shed repository being installed into Galaxy.
by Bitbucket 02 Jan '13

02 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7424f6498807/ changeset: 7424f6498807 user: greg date: 2013-01-02 23:02:25 summary: Fix for discovering all repository dependencies for a tool shed repository being installed into Galaxy. affected #: 3 files <HgDiff 7424f6498807:9ee9956888d7 ['lib/galaxy/tool_shed/install_manager.py']><HgDiff 7424f6498807:9ee9956888d7 ['lib/galaxy/util/shed_util.py']><HgDiff 7424f6498807:9ee9956888d7 ['lib/galaxy/util/shed_util_common.py']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for displaying an installed tool shed repository in an error state.
by Bitbucket 02 Jan '13

02 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9ee9956888d7/ changeset: 9ee9956888d7 user: greg date: 2013-01-02 22:35:02 summary: Fix for displaying an installed tool shed repository in an error state. affected #: 1 file <HgDiff 9ee9956888d7:5764598c6509 ['templates/admin/tool_shed_repository/manage_repository.mako']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: history_contents, index & show: add force_history_refresh key/value; history panel: fix broken addHdas when used via the updater, add force_history_refresh to reload the history panel when an hda/tool requests it; pack scripts
by Bitbucket 02 Jan '13

02 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5764598c6509/ changeset: 5764598c6509 user: carlfeberhard date: 2013-01-02 22:30:24 summary: history_contents, index & show: add force_history_refresh key/value; history panel: fix broken addHdas when used via the updater, add force_history_refresh to reload the history panel when an hda/tool requests it; pack scripts affected #: 5 files <HgDiff 5764598c6509:9ec94e5d6a28 ['lib/galaxy/webapps/galaxy/api/history_contents.py']><HgDiff 5764598c6509:9ec94e5d6a28 ['static/scripts/mvc/history/history-model.js']><HgDiff 5764598c6509:9ec94e5d6a28 ['static/scripts/mvc/history/history-panel.js']><HgDiff 5764598c6509:9ec94e5d6a28 ['static/scripts/packed/mvc/history/history-model.js']><HgDiff 5764598c6509:9ec94e5d6a28 ['static/scripts/packed/mvc/history/history-panel.js']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Fix additional exception in shutdown method of LWR.
by Bitbucket 02 Jan '13

02 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9ec94e5d6a28/ changeset: 9ec94e5d6a28 user: inithello date: 2013-01-02 22:20:14 summary: Fix additional exception in shutdown method of LWR. affected #: 1 file <HgDiff 9ec94e5d6a28:4cbb80bbed37 ['lib/galaxy/jobs/runners/lwr.py']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes for rendering tool dependencies and repository dependencies for tool shed repositories being installed into Galaxy.
by Bitbucket 02 Jan '13

02 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4cbb80bbed37/ changeset: 4cbb80bbed37 user: greg date: 2013-01-02 22:05:08 summary: Fixes for rendering tool dependencies and repository dependencies for tool shed repositories being installed into Galaxy. affected #: 6 files <HgDiff 4cbb80bbed37:019fd7e8a757 ['lib/galaxy/util/shed_util.py']><HgDiff 4cbb80bbed37:019fd7e8a757 ['lib/galaxy/util/shed_util_common.py']><HgDiff 4cbb80bbed37:019fd7e8a757 ['lib/galaxy/webapps/community/util/container_util.py']><HgDiff 4cbb80bbed37:019fd7e8a757 ['lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py']><HgDiff 4cbb80bbed37:019fd7e8a757 ['templates/admin/tool_shed_repository/common.mako']><HgDiff 4cbb80bbed37:019fd7e8a757 ['templates/webapps/community/repository/common.mako']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0