- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 1494: Fix functional test for count tool and correct...
by greg＠scofield.bx.psu.edu 08 Sep '08

08 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/d427760f8fec changeset: 1494:d427760f8fec user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Sep 08 09:16:32 2008 -0400 description: Fix functional test for count tool and correct spelling errors in template. 1 file(s) affected in this change: tools/filters/uniq.xml diffs (33 lines): diff -r e85d660c46ee -r d427760f8fec tools/filters/uniq.xml --- a/tools/filters/uniq.xml Fri Sep 05 16:36:51 2008 -0400 +++ b/tools/filters/uniq.xml Mon Sep 08 09:16:32 2008 -0400 @@ -1,9 +1,9 @@ <tool id="Count1" name="Count"> - <description>occurences of each record</description> + <description>occurrences of each record</description> <command interpreter="python">uniq.py -i $input -o $out_file1 -c "$column" -d $delim</command> <inputs> <param name="input" type="data" format="tabular" label="from query" help="Query missing? See TIP below"/> - <param name="column" type="data_column" data_ref="input" multiple="True" numerical="False" label="Count occurencies of values in column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" /> + <param name="column" type="data_column" data_ref="input" multiple="True" numerical="False" label="Count occurrences of values in column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" /> <param name="delim" type="select" label="Delimited by"> <option value="T">Tab</option> <option value="Sp">Whitespace</option> @@ -21,7 +21,7 @@ <test> <param name="input" value="1.bed"/> <output name="out_file1" file="uniq_out.dat"/> - <param name="column" value="c1"/> + <param name="column" value="1"/> <param name="delim" value="T"/> </test> </tests> @@ -35,7 +35,7 @@ **Syntax** -This tool counts occurences of unique values in selected column(s). +This tool counts occurrences of unique values in selected column(s). - If multiple columns are selected, counting is performed on each unique group of all values in the selected columns. - The first column of the resulting query will be the count of unique values in the selected column(s) and will be followed by each value.

1 0

[hg] galaxy 1495: Update packed version of workflow editor scrip...
by greg＠scofield.bx.psu.edu 08 Sep '08

08 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/49fe600b9499 changeset: 1495:49fe600b9499 user: James Taylor <james(a)jamestaylor.org> date: Mon Sep 08 09:47:37 2008 -0400 description: Update packed version of workflow editor script (fix z-index problem again?) 1 file(s) affected in this change: static/scripts/packed/galaxy.workflow_editor.canvas.js diffs (8 lines): diff -r d427760f8fec -r 49fe600b9499 static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Mon Sep 08 09:16:32 2008 -0400 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Mon Sep 08 09:47:37 2008 -0400 @@ -1,1 +1,1 @@ -function Terminal(A){this.element=A;this.connectors=[]}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(){$.each(this.connectors.slice(),function(A,B){B.destroy()})}};function OutputTerminal(A,B){Terminal.call(this,A);this.datatype=B}OutputTerminal.prototype=new Terminal;function InputTerminal(A,B){Terminal.call(this,A);this.datatypes=B}InputTerminal.prototype=new Terminal;$.extend(InputTerminal.prototype,{can_accept:function(A){if(this.connectors.length<1){for(t in this.datatypes){if(A.datatype=="input"){return true}if(issubtype(A.datatype,this.datatypes[t])){return true}}}return false}});function Connector(B,A){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365"}$.extend(Connector.prototy pe,{connect:function(B,A){this.handle1=B;this.handle1.connect(this);this.handle2=A;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var C=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}C.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var L=function(S){return $(S).offset().left-C.offset().left};var G=function(S){return $(S).offset().top-C.offset().top};var F=L(this.handle1.element)+5;var E=G(this.handle1.element)+5;var N=L(this.handle2.element)+5;var K=G(this.handle2.element)+5;var D=100;var I=Math.min(F,N);var A=Math.max(F,N);var H=Math.min(E,K);var R=Math.max(E,K);var B=Math.min(Math.max(Math.abs(R-H)/2,100),300);var M=I-D;var Q=H-D;var O=A-I+2*D;var J=R-H+2*D;this.canvas.style.left=M+"px";this.canvas.styl e.top=Q+"px";this.canvas.setAttribute("width",O);this.canvas.setAttribute("height",J);F-=M;E-=Q;N-=M;K-=Q;var P=this.canvas.getContext("2d");P.lineCap="round";P.strokeStyle=this.outer_color;P.lineWidth=7;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke();P.strokeStyle=this.inner_color;P.lineWidth=5;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke()}});function Node(A){this.element=A;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new InputTerminal(this,B);D.node=node;D.name=A;$(this).droppable({tolerance:"intersect",accept:function(E){E=E.get(0);return(E.terminal)&&(D.can_accept(E.terminal))},activeClass:"input-terminal-active",over:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#BBFFBB"},out:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#FFFFFF"},drop:function(I ,G){var E=$(this).data("droppable");var F=G.draggable.get(0).terminal;var H=E.element.get(0).terminal;var J=new Connector();J.connect(F,H);J.redraw()}});$(this).hoverIntent(function(){if(D.connectors.length>0){var E=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(D.connectors,function(G,F){F.destroy()});E.remove()}))).bind("mouseleave",function(){$(this).remove()});E.css({top:$(this).offset().top-2,left:$(this).offset().left-E.width(),"padding-right":$(this).width()}).show()}},function(){});node.input_terminals[A]=D})},enable_output_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new OutputTerminal(this,B);D.node=node;D.name=A;$(this).draggable({scrollPanel:true,panel:$("#canvas-container"),helper:function(){var E=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container"). get(0);E.terminal=new OutputTerminal(E);var F=new Connector();this.drag_temp_connector=F;F.dragging=true;F.connect(this.terminal,E.terminal);return E},drag:function(F,E){h=E.helper.get(0);h.terminal.redraw()},stop:function(F,E){this.drag_temp_connector.destroy()}});node.output_terminals[A]=D})},redraw:function(){$.each(this.input_terminals,function(A,B){B.redraw()});$.each(this.output_terminals,function(A,B){B.redraw()})},destroy:function(){$.each(this.input_terminals,function(A,B){B.destroy();$(B.element).droppable("destroy")});$.each(this.output_terminals,function(A,B){B.destroy();$(B.element).draggable("destroy")});$(this.element).draggable("destroy").remove();workflow.remove_node(this)},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){$(this.element).removeClass("toolForm-active")},init_field_data:function(D){var C=this.element;if(D.type){this.type=D.type}this.form_html=D.form_html;this.tool_state=D.tool_state;this.tool_errors= D.tool_errors;if(this.tool_errors){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var B=this;var A=C.find(".toolFormBody");A.find("div").remove();var E=$("<div class='inputs'></div>").appendTo(A);$.each(D.data_inputs,function(H,F){var G=$("<div class='terminal input-terminal'></div>");B.enable_input_terminal(G,F.name,F.extensions);E.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div>").prepend(G))});if((D.data_inputs.length>0)&&(D.data_outputs.length>0)){A.append($("<div class='rule'></div>"))}$.each(D.data_outputs,function(I,F){var H=$("<div class='terminal output-terminal'></div>");B.enable_output_terminal(H,F.name,F.extension);var G=F.name;if(F.extension!="input"){G=G+" ("+F.extension+")"}A.append($("<div class='form-row dataRow'>"+G+"</div>").append(H))});workflow.node_changed(this)},update_field_data:function(E){var C=$(this.element),D=this;this.tool_state=E.tool_state;this.form_html=E.form_html;this.tool_error s=E.tool_errors;if(this.tool_errors){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var F=C.find("div.inputs");var B=$("<div class='inputs'></div>");var A=F.find("div.input-data-row");$.each(E.data_inputs,function(I,G){var H=$("<div class='terminal input-terminal'></div>");D.enable_input_terminal(H,G.name,G.extensions);F.find("div[name="+G.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var J=this.terminal.connectors[0];if(J){H[0].terminal.connectors[0]=J;J.handle2=H[0].terminal}});$(this).remove()});B.append($("<div class='form-row dataRow input-data-row' name='"+G.name+"'>"+G.label+"</div>").prepend(H))});F.replaceWith(B);F.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(C){var A=$(this.element).find(".toolFormBody");A.find("div").remove();var B="<div style='color: red; text-style: italic;'>"+C+"</div>";this.form_html=B;A.html(B);workflow.node_change d(this)},changed:function(){workflow.node_changed(this)}});function Workflow(){this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(A){A.id=this.id_counter;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;$.each(this.nodes,function(B,A){A.destroy();wf.remove_node(A)})},to_simple:function(){var A={};$.each(this.nodes,function(B,D){var E={};$.each(D.input_terminals,function(F,G){E[G.name]=null;$.each(G.connectors,function(H,I){E[G.name]={id:I.handle1.node.id,output_name:I.handle1.name}})});var C={id:D.id,type:D.type,tool_id:D.tool_id,tool_state:D.tool_state,tool_errors:D.tool_errors,input_connections:E,position:$(D.element).position()};A[D.id]=C});return{steps:A}},from_simple:function(A){wf=this;var B=0;wf.name=A.name;$.each(A.steps,functio n(E,D){var C=prebuild_node("tool",D.name,D.tool_id);C.init_field_data(D);if(D.position){C.element.css({top:D.position.top,left:D.position.left})}C.id=D.id;wf.nodes[C.id]=C;B=Math.max(B,parseInt(E))});wf.id_counter=B+1;$.each(A.steps,function(E,D){var C=wf.nodes[E];$.each(D.input_connections,function(G,F){if(F){var H=wf.nodes[F.id];var I=new Connector();I.connect(H.output_terminals[F.output_name],C.input_terminals[G]);I.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive()}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(A){this.clear_active_node();parent.show_form_for_tool(A.form_html,A);A.make_active();this.active_node=A},node_changed:function(A){this.has_changes=true;if(this.active_node==A){this.activate_node(A)}}});function prebuild_node(H,F,K){var E=$("<div class='toolForm toolFormInCanvas'></div>");var C=new Node(E);C.type=H;if(H=="tool"){C.tool_id=K}var J=$("<div class='toolFormTitle unselectab le'>"+F+"</div>");E.append(J);E.css("left",$(window).scrollLeft()+20);E.css("top",$(window).scrollTop()+20);var I=$("<div class='toolFormBody'></div>");var D="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";I.append(D);C.form_html=D;E.append(I);var G=$("<div class='buttons' style='float: right;'></div>");G.append($("<img src='../images/delete_icon.png' />").click(function(L){C.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));zmax=$("#canvas-container").data("zmax");if(!zmax){zmax=0}E.css("zIndex",zmax+1);$("#canvas-container").data("zmax",zmax+1);E.appendTo("#canvas-container");var B=$("#canvas-container").position();E.css({left:(-B.left)+10,top:(-B.top)+10});var A=E.width();G.prependTo(J);A+=(G.width()+10);E.css("width",A);$(E).draggable({cursor:"move",scrollPanel:true,panel:$("#canvas-container"),scrollSensitivity:10, scrollSpeed:20,click:function(M,L){zmax=$("#canvas-container").data("zmax");$(this).css("zIndex",zmax+1);$("#canvas-container").data("zmax",zmax+1);workflow.activate_node(C)},start:function(M,L){workflow.activate_node(C);$(this).css("z-index",$("#canvas-container").data("zmax")+1000)},drag:function(M,L){$(this).find(".terminal").each(function(){this.terminal.redraw()})},stop:function(M,L){zmax=$("#canvas-container").data("zmax");$(this).css("zIndex",zmax+1);$("#canvas-container").data("zmax",zmax+1);$(this).find(".terminal").each(function(){this.terminal.redraw()});workflow.node_changed(this)}});return C}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(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}; \ No newline at end of file +function Terminal(A){this.element=A;this.connectors=[]}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(){$.each(this.connectors.slice(),function(A,B){B.destroy()})}};function OutputTerminal(A,B){Terminal.call(this,A);this.datatype=B}OutputTerminal.prototype=new Terminal;function InputTerminal(A,B){Terminal.call(this,A);this.datatypes=B}InputTerminal.prototype=new Terminal;$.extend(InputTerminal.prototype,{can_accept:function(A){if(this.connectors.length<1){for(t in this.datatypes){if(A.datatype=="input"){return true}if(issubtype(A.datatype,this.datatypes[t])){return true}}}return false}});function Connector(B,A){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365"}$.extend(Connector.prototy pe,{connect:function(B,A){this.handle1=B;this.handle1.connect(this);this.handle2=A;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var C=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}C.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var L=function(S){return $(S).offset().left-C.offset().left};var G=function(S){return $(S).offset().top-C.offset().top};var F=L(this.handle1.element)+5;var E=G(this.handle1.element)+5;var N=L(this.handle2.element)+5;var K=G(this.handle2.element)+5;var D=100;var I=Math.min(F,N);var A=Math.max(F,N);var H=Math.min(E,K);var R=Math.max(E,K);var B=Math.min(Math.max(Math.abs(R-H)/2,100),300);var M=I-D;var Q=H-D;var O=A-I+2*D;var J=R-H+2*D;this.canvas.style.left=M+"px";this.canvas.styl e.top=Q+"px";this.canvas.setAttribute("width",O);this.canvas.setAttribute("height",J);F-=M;E-=Q;N-=M;K-=Q;var P=this.canvas.getContext("2d");P.lineCap="round";P.strokeStyle=this.outer_color;P.lineWidth=7;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke();P.strokeStyle=this.inner_color;P.lineWidth=5;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke()}});function Node(A){this.element=A;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new InputTerminal(this,B);D.node=node;D.name=A;$(this).droppable({tolerance:"intersect",accept:function(E){E=E.get(0);return(E.terminal)&&(D.can_accept(E.terminal))},activeClass:"input-terminal-active",over:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#BBFFBB"},out:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#FFFFFF"},drop:function(I ,G){var E=$(this).data("droppable");var F=G.draggable.get(0).terminal;var H=E.element.get(0).terminal;var J=new Connector();J.connect(F,H);J.redraw()}});$(this).hoverIntent(function(){if(D.connectors.length>0){var E=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(D.connectors,function(G,F){F.destroy()});E.remove()}))).bind("mouseleave",function(){$(this).remove()});E.css({top:$(this).offset().top-2,left:$(this).offset().left-E.width(),"padding-right":$(this).width()}).show()}},function(){});node.input_terminals[A]=D})},enable_output_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new OutputTerminal(this,B);D.node=node;D.name=A;$(this).draggable({scrollPanel:true,panel:$("#canvas-container"),helper:function(){var E=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container"). get(0);E.terminal=new OutputTerminal(E);var F=new Connector();this.drag_temp_connector=F;F.dragging=true;F.connect(this.terminal,E.terminal);return E},drag:function(F,E){h=E.helper.get(0);h.terminal.redraw()},stop:function(F,E){this.drag_temp_connector.destroy()}});node.output_terminals[A]=D})},redraw:function(){$.each(this.input_terminals,function(A,B){B.redraw()});$.each(this.output_terminals,function(A,B){B.redraw()})},destroy:function(){$.each(this.input_terminals,function(A,B){B.destroy();$(B.element).droppable("destroy")});$.each(this.output_terminals,function(A,B){B.destroy();$(B.element).draggable("destroy")});workflow.remove_node(this);$(this.element).draggable("destroy").remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var A=this.element.get(0);(function(B){B.removeChild(A);B.appendChild(A)})(A.parentNode);$(A).removeClass("toolForm-active")},init_field_data:function(D){var C=this.element;if(D.type){this.type=D. type}this.form_html=D.form_html;this.tool_state=D.tool_state;this.tool_errors=D.tool_errors;if(this.tool_errors){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var B=this;var A=C.find(".toolFormBody");A.find("div").remove();var E=$("<div class='inputs'></div>").appendTo(A);$.each(D.data_inputs,function(H,F){var G=$("<div class='terminal input-terminal'></div>");B.enable_input_terminal(G,F.name,F.extensions);E.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div>").prepend(G))});if((D.data_inputs.length>0)&&(D.data_outputs.length>0)){A.append($("<div class='rule'></div>"))}$.each(D.data_outputs,function(I,F){var H=$("<div class='terminal output-terminal'></div>");B.enable_output_terminal(H,F.name,F.extension);var G=F.name;if(F.extension!="input"){G=G+" ("+F.extension+")"}A.append($("<div class='form-row dataRow'>"+G+"</div>").append(H))});workflow.node_changed(this)},update_field_data:function(E){var C=$(this.element), D=this;this.tool_state=E.tool_state;this.form_html=E.form_html;this.tool_errors=E.tool_errors;if(this.tool_errors){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var F=C.find("div.inputs");var B=$("<div class='inputs'></div>");var A=F.find("div.input-data-row");$.each(E.data_inputs,function(I,G){var H=$("<div class='terminal input-terminal'></div>");D.enable_input_terminal(H,G.name,G.extensions);F.find("div[name="+G.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var J=this.terminal.connectors[0];if(J){H[0].terminal.connectors[0]=J;J.handle2=H[0].terminal}});$(this).remove()});B.append($("<div class='form-row dataRow input-data-row' name='"+G.name+"'>"+G.label+"</div>").prepend(H))});F.replaceWith(B);F.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(C){var A=$(this.element).find(".toolFormBody");A.find("div").remove();var B="<div style='color: red; tex t-style: italic;'>"+C+"</div>";this.form_html=B;A.html(B);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(){this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(A){A.id=this.id_counter;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;$.each(this.nodes,function(B,A){A.destroy();wf.remove_node(A)})},to_simple:function(){var A={};$.each(this.nodes,function(B,D){var E={};$.each(D.input_terminals,function(F,G){E[G.name]=null;$.each(G.connectors,function(H,I){E[G.name]={id:I.handle1.node.id,output_name:I.handle1.name}})});var C={id:D.id,type:D.type,tool_id:D.tool_id,tool_state:D.tool_state,tool_errors:D.tool_errors,input_connections:E,position:$(D.element).position()};A[D.id]=C});return{steps:A}} ,from_simple:function(A){wf=this;var B=0;wf.name=A.name;$.each(A.steps,function(E,D){var C=prebuild_node("tool",D.name,D.tool_id);C.init_field_data(D);if(D.position){C.element.css({top:D.position.top,left:D.position.left})}C.id=D.id;wf.nodes[C.id]=C;B=Math.max(B,parseInt(E))});wf.id_counter=B+1;$.each(A.steps,function(E,D){var C=wf.nodes[E];$.each(D.input_connections,function(G,F){if(F){var H=wf.nodes[F.id];var I=new Connector();I.connect(H.output_terminals[F.output_name],C.input_terminals[G]);I.redraw()}})})},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.clear_active_node();parent.show_form_for_tool(A.form_html,A);A.make_active();this.active_node=A}},node_changed:function(A){this.has_changes=true;if(this.active_node==A){parent.show_form_for_tool(A.form_html,A)}}});function prebuild_node(H,F,K){var E=$("<d iv class='toolForm toolFormInCanvas'></div>");var C=new Node(E);C.type=H;if(H=="tool"){C.tool_id=K}var J=$("<div class='toolFormTitle unselectable'>"+F+"</div>");E.append(J);E.css("left",$(window).scrollLeft()+20);E.css("top",$(window).scrollTop()+20);var I=$("<div class='toolFormBody'></div>");var D="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";I.append(D);C.form_html=D;E.append(I);var G=$("<div class='buttons' style='float: right;'></div>");G.append($("<img src='../images/delete_icon.png' />").click(function(L){C.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));E.appendTo("#canvas-container");var B=$("#canvas-container").position();E.css({left:(-B.left)+10,top:(-B.top)+10});var A=E.width();G.prependTo(J);A+=(G.width()+10);E.css("width",A);$(E).draggable({cursor:"move",scrollPanel:true,panel:$("#canvas-container"),s crollSensitivity:10,scrollSpeed:20,click:function(M,L){workflow.activate_node(C)},start:function(M,L){workflow.activate_node(C)},drag:function(M,L){$(this).find(".terminal").each(function(){this.terminal.redraw()})},stop:function(M,L){$(this).find(".terminal").each(function(){this.terminal.redraw()});workflow.node_changed(this)}});return C}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(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}; \ No newline at end of file

1 0

[hg] galaxy 1493: More fixes for twill 0.9, the annotation profi...
by greg＠scofield.bx.psu.edu 08 Sep '08

08 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/e85d660c46ee changeset: 1493:e85d660c46ee user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Sep 05 16:36:51 2008 -0400 description: More fixes for twill 0.9, the annotation profiler tests do not yet pass, but all else should work now, more tests coming soon. 7 file(s) affected in this change: test/base/twilltestcase.py test/functional/__init__.py test/functional/test_metadata_editing.py tools/annotation_profiler/annotation_profiler.xml tools/filters/joiner.xml tools/new_operations/intersect.xml tools/new_operations/subtract.xml diffs (289 lines): diff -r d7e7804572fd -r e85d660c46ee test/base/twilltestcase.py --- a/test/base/twilltestcase.py Thu Sep 04 12:19:32 2008 -0400 +++ b/test/base/twilltestcase.py Fri Sep 05 16:36:51 2008 -0400 @@ -1,8 +1,7 @@ import pkg_resources -pkg_resources.require('twill') +pkg_resources.require( "twill==0.9" ) -import StringIO -import os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile +import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile from itertools import * import twill @@ -18,7 +17,7 @@ # Dial ClientCookie logging down (very noisy) logging.getLogger( "ClientCookie.cookies" ).setLevel( logging.WARNING ) -#log = logging.getLogger( __name__ ) +log = logging.getLogger( __name__ ) class TwillTestCase( unittest.TestCase ): @@ -244,8 +243,14 @@ self.assertEqual(len(elems), 1) self.visit_page( "delete?id=%s" % elems[0].get('id') ) - def edit_metadata( self, hid=None, form=1, **kwd ): - """Edits the metadata associated with a history item. There are currently 3 forms on the edit page.""" + def edit_metadata( self, hid=None, form_no=0, **kwd ): + """ + Edits the metadata associated with a history item.""" + # There are currently 4 forms on the edit page: + # 0. name="edit_attributes" + # 1. name="auto_detect" + # 2. name="convert_data" + # 3. name="change_datatype" data_list = self.get_history() self.assertTrue( data_list ) if hid is None: # take last hid @@ -253,12 +258,16 @@ hid = elem.get('hid') self.assertTrue( hid ) self.visit_page( 'edit?hid=%d' % hid ) - if form == 1: button = "save" #Edit Attributes form - elif form == 2: button = "detect" #Auto-detect Metadata Attributes - elif form == 3: button = "convert_data" #Convert to new format form - elif form == 4: button = "change" #Change data type form + if form_no == 0: + button = "save" #Edit Attributes form + elif form_no == 1: + button = "detect" #Auto-detect Metadata Attributes + elif form_no == 2: + button = "convert_data" #Convert to new format form + elif form_no == 3: + button = "change" #Change data type form if kwd: - self.submit_form(form=form, button=button, **kwd) + self.submit_form( form_no=form_no, button=button, **kwd) def get_dataset_ids_in_history( self ): """Returns the ids of datasets in a history""" @@ -406,23 +415,24 @@ def showforms( self ): """Shows form, helpful for debugging new tests""" - return tc.browser.showforms() + return tc.showforms() - def submit_form( self, form=1, button="runtool_btn", **kwd ): - """Populates and submits a form from the keyword arguments""" - #Check for onchange attribute, submit a change if required - for i, f in enumerate( tc.showforms() ): - if i == form - 1: + def submit_form( self, form_no=0, button="runtool_btn", **kwd ): + """Populates and submits a form from the keyword arguments.""" + for i, f in enumerate( self.showforms() ): + if i == form_no: break + # An HTMLForm contains a sequence of Controls. Supported control classes are: + # TextControl, FileControl, ListControl, RadioControl, CheckboxControl, SelectControl, + # SubmitControl, ImageControl for i, control in enumerate( f.controls ): try: + # Check for refresh_on_change attribute, submit a change if required if 'refresh_on_change' in control.attrs.keys(): changed = False for elem in kwd[control.name]: - """ - For DataToolParameter, control.value is the index of the DataToolParameter select list, - but elem is the filename. The following loop gets the filename of that index. - """ + # For DataToolParameter, control.value is the index of the DataToolParameter select list, + # but elem is the filename. The following loop gets the filename of that index. param_text = '' for param in tc.show().split('<select'): param = ('<select' + param.split('select>')[0] + 'select>').replace('selected', 'selected="yes"') @@ -433,52 +443,56 @@ param_text = option.text.strip() break break - if elem not in control.value and param_text.find(elem) == -1 : changed = True break if changed: - # Clear Control and set to proper value - the command: - # formvalue <formnum> <fieldname> <value> - # sets the given field in the given form to the given value. - # For read-only form widgets/controls, the click may be recorded for use by submit, - # but the value is not changed unless the 'config' command has changed the default behavior. + # Clear Control and set to proper value control.clear() - for elem in kwd[control.name]: - tc.formvalue(str(form), str(i+1), str(elem) ) - #Create a new submit control, allows form to refresh, instead of going to next page - control = ClientForm.SubmitControl('SubmitControl','___refresh_grouping___',{'name':'refresh_grouping'}) + # kwd[control.name] should be a singlelist + for elem in kwd[ control.name ]: + tc.fv( f.name, control.name, str( elem ) ) + # Create a new submit control, allows form to refresh, instead of going to next page + control = ClientForm.SubmitControl( 'SubmitControl', '___refresh_grouping___', {'name':'refresh_grouping'} ) control.add_to_form( f ) control.fixup() - #submit for refresh - tc.submit('___refresh_grouping___') - #start over submit_form() - return self.submit_form(form, button, **kwd) + # Submit for refresh + tc.submit( '___refresh_grouping___' ) + return self.submit_form( form_no=form_no, button=button, **kwd ) except Exception, e: - # Log.debug("In submit_form, caught exception: %s" %str( e )) + log.debug( "In submit_form, continuing, but caught exception: %s" % str( e ) ) continue - for key, value in kwd.items(): - # needs to be able to handle multiple values per key - if not isinstance(value, list): - value = [ value ] - for i, control in enumerate( f.controls ): - if control.name == key: - control.clear() - if control.is_of_kind("text"): - # set the given field in the given form to the given value. - tc.formvalue(str(form), str(i+1), ",".join(value) ) - else: - try: - for elem in value: - tc.formvalue(str(form), str(i+1), str(elem) ) - except Exception, exc: - errmsg = "Attempting to set field '%s' to value '%s' threw exception: '%s'\n" % ( str( key ), str( elem ), str( exc ) ) - errmsg += "control: %s\n" % str( control ) - errmsg += "If the above control is a DataToolparameter whose data type class does not include a sniff() method,\n" - errmsg += "make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.\n" - raise AssertionError( errmsg ) - break - tc.submit(button) + # No refresh_on_change attribute found in current form, so process as usual + for control_name, control_value in kwd.items(): + if not isinstance( control_value, list ): + control_value = [ control_value ] + try: + control = f.find_control( name=control_name ) + except: + # This assumes we always want the first control of the given name, + # which may not be ideal... + control = f.find_control( name=control_name, nr=0 ) + control.clear() + if control.is_of_kind( "text" ): + tc.fv( f.name, control.name, ",".join( control_value ) ) + elif control.is_of_kind( "list" ): + try: + if control.is_of_kind( "multilist" ): + for elem in control_value: + control.get( name=elem ).selected = True + else: # control.is_of_kind( "singlelist" ) + for elem in control_value: + tc.fv( f.name, control.name, str( elem ) ) + except Exception, exc: + errmsg = "Attempting to set field '%s' to value '%s' in form '%s' threw exception: %s\n" % ( control_name, str( control_value ), f.name, str( exc ) ) + errmsg += "control: %s\n" % str( control ) + errmsg += "If the above control is a DataToolparameter whose data type class does not include a sniff() method,\n" + errmsg += "make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.\n" + raise AssertionError( errmsg ) + else: + # Add conditions for other control types here when necessary. + pass + tc.submit( button ) def visit_page( self, page ): tc.go("./%s" % page) @@ -493,8 +507,8 @@ tool_id = tool_id.replace(" ", "+") """Runs the tool 'tool_id' and passes it the key/values from the *kwd""" self.visit_url( "%s/tool_runner/index?tool_id=%s" % (self.url, tool_id) ) - tc.find('runtool_btn') - self.submit_form(**kwd) + tc.find( 'runtool_btn' ) + self.submit_form( **kwd ) def wait( self, maxiter=20 ): """Waits for the tools to finish""" diff -r d7e7804572fd -r e85d660c46ee test/functional/__init__.py --- a/test/functional/__init__.py Thu Sep 04 12:19:32 2008 -0400 +++ b/test/functional/__init__.py Fri Sep 05 16:36:51 2008 -0400 @@ -2,7 +2,7 @@ import pkg_resources -pkg_resources.require( "twill==0.8.3" ) +pkg_resources.require( "twill==0.9" ) pkg_resources.require( "Paste" ) pkg_resources.require( "PasteDeploy" ) pkg_resources.require( "Cheetah" ) diff -r d7e7804572fd -r e85d660c46ee test/functional/test_metadata_editing.py --- a/test/functional/test_metadata_editing.py Thu Sep 04 12:19:32 2008 -0400 +++ b/test/functional/test_metadata_editing.py Fri Sep 05 16:36:51 2008 -0400 @@ -9,17 +9,17 @@ self.check_history_for_string('\? bed') self.check_metadata_for_string('1.bed uploaded file unspecified (\?) chromCol value="1" selected endCol value="3" is_strandCol value="true" checked', hid=1) """test editing attributes""" - self.edit_metadata(hid=1, form=1, name='Testdata', info="Uploaded my file", dbkey='hg16', startCol='6') + self.edit_metadata(hid=1, form_no=0, name='Testdata', info="Uploaded my file", dbkey='hg16', startCol='6') self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="6" selected', hid=1) """test Auto-detecting attributes""" - self.edit_metadata(hid=1, form=2) + self.edit_metadata(hid=1, form_no=1) self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="2" selected', hid=1) """test converting formats""" - self.edit_metadata(hid=1, form=3, target_type='gff') + self.edit_metadata(hid=1, form_no=2, target_type='gff') self.check_history_for_string('hg16 Testdata Convert BED to GFF') self.check_metadata_for_string('"gff" selected="yes"', hid=1) """test changing data type""" - self.edit_metadata(hid=1, form=4, datatype='gff3') + self.edit_metadata(hid=1, form_no=3, datatype='gff3') self.check_history_for_string('hg16 Testdata Convert BED to GFF format: gff3') self.delete_history_item( 1 ) def test_9999_clean_up( self ): diff -r d7e7804572fd -r e85d660c46ee tools/annotation_profiler/annotation_profiler.xml --- a/tools/annotation_profiler/annotation_profiler.xml Thu Sep 04 12:19:32 2008 -0400 +++ b/tools/annotation_profiler/annotation_profiler.xml Fri Sep 05 16:36:51 2008 -0400 @@ -30,7 +30,7 @@ <test> <param name="input1" value="3.bed" dbkey="hg18"/> <param name="keep_empty" value=""/> - <param name="summary" value="-S"/> + <param name="summary" value="Summary"/> <param name="table_names" value="acembly,affyGnf1h,affyHuEx1,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/> <output name="out_file1" file="annotation_profiler_2.out" /> </test> diff -r d7e7804572fd -r e85d660c46ee tools/filters/joiner.xml --- a/tools/filters/joiner.xml Thu Sep 04 12:19:32 2008 -0400 +++ b/tools/filters/joiner.xml Fri Sep 05 16:36:51 2008 -0400 @@ -33,8 +33,8 @@ <param name="input2" value="2.bed"/> <param name="field1" value="2"/> <param name="field2" value="2"/> - <param name="unmatched" value="-u"/> - <param name="partial" value="-p"/> + <param name="unmatched" value="Yes"/> + <param name="partial" value="Yes"/> <output name="out_file1" file="joiner_out2.bed"/> </test> </tests> diff -r d7e7804572fd -r e85d660c46ee tools/new_operations/intersect.xml --- a/tools/new_operations/intersect.xml Thu Sep 04 12:19:32 2008 -0400 +++ b/tools/new_operations/intersect.xml Fri Sep 05 16:36:51 2008 -0400 @@ -33,7 +33,7 @@ <param name="input1" value="1.bed" /> <param name="input2" value="2.bed" /> <param name="min" value="10" /> - <param name="returntype" value="-p" /> + <param name="returntype" value="Overlapping pieces of Intervals" /> <output name="output" file="gops_intersect_p_out.bed" /> </test> <test> diff -r d7e7804572fd -r e85d660c46ee tools/new_operations/subtract.xml --- a/tools/new_operations/subtract.xml Thu Sep 04 12:19:32 2008 -0400 +++ b/tools/new_operations/subtract.xml Fri Sep 05 16:36:51 2008 -0400 @@ -43,7 +43,7 @@ <param name="input1" value="1.bed" /> <param name="input2" value="2.bed" /> <param name="min" value="10" /> - <param name="returntype" value="-p" /> + <param name="returntype" value="Non-overlapping pieces of intervals" /> <output name="output" file="gops-subtract-p.dat" /> </test> </tests>

1 0

[hg] galaxy 1492: Fix for save link of history items.
by greg＠scofield.bx.psu.edu 08 Sep '08

08 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/d7e7804572fd changeset: 1492:d7e7804572fd user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Sep 04 12:19:32 2008 -0400 description: Fix for save link of history items. 1 file(s) affected in this change: templates/root/history_common.mako diffs (12 lines): diff -r 9b8d06eea5b7 -r d7e7804572fd templates/root/history_common.mako --- a/templates/root/history_common.mako Wed Sep 03 12:06:33 2008 -0400 +++ b/templates/root/history_common.mako Thu Sep 04 12:19:32 2008 -0400 @@ -57,7 +57,7 @@ <div class="info">Info: ${data.display_info()} </div> <div> %if data.has_data: - <a href="${h.url_for( action='display', id=data.id, tofile='yes', toext='data.ext' )}" target="_blank">save</a> + <a href="${h.url_for( action='display', id=data.id, tofile='yes', toext=data.ext )}" target="_blank">save</a> %for display_app in data.datatype.get_display_types(): <% display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> %if len( display_links ) > 0:

1 0

[hg] galaxy 1491: Fix for GMAJ tool when species chromosomes are...
by greg＠scofield.bx.psu.edu 08 Sep '08

08 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/9b8d06eea5b7 changeset: 1491:9b8d06eea5b7 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Sep 03 12:06:33 2008 -0400 description: Fix for GMAJ tool when species chromosomes are not specified. Error appears in paster.log as 'TypeError: iterable argument required' 1 file(s) affected in this change: tools/visualization/GMAJ.xml diffs (12 lines): diff -r cefbb71490a2 -r 9b8d06eea5b7 tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Sun Aug 31 21:14:06 2008 -0400 +++ b/tools/visualization/GMAJ.xml Wed Sep 03 12:06:33 2008 -0400 @@ -82,7 +82,7 @@ #set $seq_count = 0 #for $spec_count, $annotation in $enumerate( $annotations ): -#if $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]: +#if $maf_input.metadata.species_chromosomes and $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]: #set $seq_names = [ "%s.%s" % ( $annotation['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation['species'].value]] #else #set $seq_names = [$annotation['species'].value]

1 0

Adding new interval datatype
by Assaf Gordon 05 Sep '08

05 Sep '08

Hello, I'd like to add a new datatype to galaxy. This datatype is just an textual interval file, with non-default columns assignment. For example, the chromosome is on column 4, start/end at columns 6/7. Is there a way to achieve this without inheriting a new class in "/lib/galaxy/datatypes/interval.py" ? I was hoping for something along the lines of adding the following in "datatypes_conf.xml": <datatype extension="MyNewType" type="galaxy.datatypes.interval:Interval" mimetype="text/text" display_in_upload="true"> <metadata name="chromCol" value="4" /> <metadata name="startCol" value="6" /> <metadata name="endCol" value="7" /> </datatype> If this isn't possible yet, and if I may suggest a code fragment, then at "/lib/galaxy/datatypes/registry.py", line 53, I'd add something like: ------------------- for metadata in elem.findall( 'metadata ): name = metadata.get( 'name', None ) value = metadata.get( 'value', None ) if name and value: self.somehow_change_metadata_value ( name, value) ------------------- Thanks, Gordon.

1 0

Test is at rev 1553:5468a480c0d8
by Greg Von Kuster 04 Sep '08

04 Sep '08

1 0

Test is at rev 1552:3af945fa486b
by Greg Von Kuster 03 Sep '08

03 Sep '08

1 0

Test is at rev 1545:dcaed9f80caf
by Greg Von Kuster 02 Sep '08

02 Sep '08

1 0

Main is at rev 1490:cefbb71490a2
by Greg Von Kuster 02 Sep '08

02 Sep '08

1 0