- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: guerler: Pack scripts
by commits-noreply＠bitbucket.org 25 Nov '13

25 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9165deb80084/ Changeset: 9165deb80084 User: guerler Date: 2013-11-25 15:25:31 Summary: Pack scripts Affected #: 2 files diff -r 5dfc0b3bf0351e7274cd3a5bdeab921752215973 -r 9165deb8008461d43107c2b1cd99b750bcb0508f static/scripts/packed/galaxy.grids.js --- a/static/scripts/packed/galaxy.grids.js +++ b/static/scripts/packed/galaxy.grids.js @@ -1,1 +1,1 @@ -jQuery.ajaxSettings.traditional=true;var Grid=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(a){return _.indexOf(this.attributes.async_ops,a)!==-1},add_filter:function(e,f,b){if(b){var c=this.attributes.filters[e],a;if(c===null||c===undefined){a=f}else{if(typeof(c)=="string"){if(c=="All"){a=f}else{var d=[];d[0]=c;d[1]=f;a=d}}else{a=c;a.push(f)}}this.attributes.filters[e]=a}else{this.attributes.filters[e]=f}},remove_filter:function(b,e){var a=this.attributes.filters[b];if(a===null||a===undefined){return false}var d=true;if(typeof(a)==="string"){if(a=="All"){d=false}else{delete this.attributes.filters[b]}}else{var c=_.indexOf(a,e);if(c!==-1){a.splice(c,1)}else{d=false}}return d},get_url_data:function(){var a={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes};if(this.attributes.operation){a.operation=this.attributes.operation}if(this.attributes.item_ids){a.id=this.attributes.item_ids}var b=this;_.each(_.pairs(b.attributes.filters),function(c){a["f-"+c[0]]=c[1]});return a}});var GridView=Backbone.View.extend({grid:null,initialize:function(a){this.grid=a;this.init_grid_elements();this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var a=this;$(".sort-link").each(function(){$(this).click(function(){a.set_sort_condition($(this).attr("sort_key"));return false})});$(".page-link > a").each(function(){$(this).click(function(){a.set_page($(this).attr("page_num"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){a.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var e=$(this).attr("column_key");var d=$("#input-"+e+"-filter");var f=d.val();d.val("");a.add_filter_condition(e,f,true);return false})});var b=$("#input-tags-filter");if(b.length){b.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var c=$("#input-name-filter");if(c.length){c.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})},init_grid_elements:function(){$(".grid").each(function(){var c=$(this).find("input.grid-row-select-checkbox");var b=$(this).find("span.grid-selected-count");var d=function(){b.text($(c).filter(":checked").length)};$(c).each(function(){$(this).change(d)});d()});var a=this;$(".label").each(function(){var b=$(this).attr("href");if(b!==undefined&&b.indexOf("operation=")!=-1){$(this).click(function(){a.do_operation_from_href($(this).attr("href"));return false})}});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}make_popup_menus()},go_page_one:function(){var a=this.grid.get("cur_page");if(a!==null&&a!==undefined&&a!=="all"){this.grid.set("cur_page",1)}},add_filter_condition:function(d,f,a){if(f===""){return false}this.grid.add_filter(d,f,a);var e=$("<span>"+f+"<a href='javascript:void(0);'><span class='delete-search-icon' /></a></span>");e.addClass("text-filter-val");var c=this;e.click(function(){c.grid.remove_filter(d,f);$(this).remove();c.go_page_one();c.update_grid()});var b=$("#"+d+"-filtering-criteria");b.append(e);this.go_page_one();this.update_grid()},set_sort_condition:function(f){var e=this.grid.get("sort_key");var d=f;if(e.indexOf(f)!==-1){if(e.substring(0,1)!=="-"){d="-"+f}else{}}$(".sort-arrow").remove();var c=(d.substring(0,1)=="-")?"↑":"↓";var a=$("<span>"+c+"</span>").addClass("sort-arrow");var b=$("#"+f+"-header");b.append(a);this.grid.set("sort_key",d);this.go_page_one();this.update_grid()},set_categorical_filter:function(c,e){var b=this.grid.get("categorical_filters")[c],d=this.grid.get("filters")[c];var a=this;$("."+c+"-filter").each(function(){var i=$.trim($(this).text());var g=b[i];var h=g[c];if(h==e){$(this).empty();$(this).addClass("current-filter");$(this).append(i)}else{if(h==d){$(this).empty();var f=$("<a href='#'>"+i+"</a>");f.click(function(){a.set_categorical_filter(c,h)});$(this).removeClass("current-filter");$(this).append(f)}}});this.grid.add_filter(c,e);this.go_page_one();this.update_grid()},set_page:function(a){var b=this;$(".page-link").each(function(){var h=$(this).attr("id"),f=parseInt(h.split("-")[2],10),d=b.grid.get("cur_page"),g;if(f===a){g=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(g)}else{if(f===d){g=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var e=$("<a href='#'>"+g+"</a>");e.click(function(){set_page(f)});$(this).append(e)}}});var c=true;if(a==="all"){this.grid.set("cur_page",a);c=false}else{this.grid.set("cur_page",parseInt(a,10))}this.update_grid(c)},do_operation:function(b,a){b=b.toLowerCase();this.grid.set({operation:b,item_ids:a});if(this.grid.can_async_op(b)){this.update_grid(true)}else{this.go_to_URL()}},do_operation_from_href:function(c){var f=c.split("?");if(f.length>1){var a=f[1];var e=a.split("&");var b=null;var g=-1;for(var d=0;d<e.length;d++){if(e[d].indexOf("operation")!=-1){b=e[d].split("=")[1]}else{if(e[d].indexOf("id")!=-1){g=e[d].split("=")[1]}}}this.do_operation(b,g);return false}},go_to_URL:function(){this.grid.set("async",false);window.location=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data());this.grid.set({operation:undefined,item_ids:undefined})},update_grid:function(b){if(!this.grid.get("async")){this.go_to_URL();return}var c=(this.grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();var a=this;$.ajax({type:c,url:a.grid.get("url_base"),data:a.grid.get_url_data(),error:function(){alert("Grid refresh failed")},success:function(e){var d=e.split("*****");$("#grid-table-body").html(d[0]);$("#grid-table-footer").html(d[1]);$("#grid-table-body").trigger("update");a.init_grid_elements();make_popup_menus();$(".loading-elt-overlay").hide();var f=$.trim(d[2]);if(f!==""){$("#grid-message").html(f).show();setTimeout(function(){$("#grid-message").hide()},5000)}},complete:function(){a.grid.set({operation:undefined,item_ids:undefined})}})},check_all_items:function(){var a=document.getElementById("check_all"),b=document.getElementsByTagName("input"),d=0,c;if(a.checked===true){for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=true;d++}}}else{for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=false}}}this.init_grid_elements()},submit_operation:function(d,e){var c=$('input[name="id"]:checked').length;if(!c>0){return false}if(e!="None"&&e!=""){if(!confirm(e)){return false}}var b=$(d).val();var a=[];$("input[name=id]:checked").each(function(){a.push($(this).val())});this.do_operation(b,a);return true}}); \ No newline at end of file +jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var c={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes};if(this.attributes.operation){c.operation=this.attributes.operation}if(this.attributes.item_ids){c.id=this.attributes.item_ids}var d=this;_.each(_.pairs(d.attributes.filters),function(e){c["f-"+e[0]]=e[1]});return c}});var b=Backbone.View.extend({grid:null,initialize:function(c){this.init_grid(c);this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},init_grid:function(c){this.grid=c;this.init_grid_elements()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h,true);return false})});var d=$("#input-tags-filter");if(d.length){d.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var e=$("#input-name-filter");if(e.length){e.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})},init_grid_elements:function(){$(".grid").each(function(){var j=$(this).find("input.grid-row-select-checkbox");var i=$(this).find("span.grid-selected-count");var q=function(){i.text($(j).filter(":checked").length)};$(j).each(function(){$(this).change(q)});q()});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}var p=this.grid.attributes;var o=this;$(".page-link > a").each(function(){$(this).click(function(){o.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(i){o.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(i){o.execute({href:$(this).attr("href")});return false})});for(var h in p.items){var k=$("#grid-"+h+"-popup");k.off();var d=new PopupMenu(k);var n=p.items[h];for(var g in p.operations){var e=p.operations[g];var l=e.label;var c=n.operation_config[l];var f=n.encode_id;if(c.allowed&&e.allow_popup){var m={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};m.func=function(q){q.preventDefault();var j=$(q.target).html();var i=this.findItemByHtml(j);o.execute(i)};d.addItem(m)}}}},add_filter_condition:function(f,h,c){if(h===""){return false}this.grid.add_filter(f,h,c);var g=$("<span>"+h+"<a href='javascript:void(0);'><span class='delete-search-icon' /></a></span>");g.addClass("text-filter-val");var e=this;g.click(function(){e.grid.remove_filter(f,h);$(this).remove();e.go_page_one();e.execute()});var d=$("#"+f+"-filtering-criteria");d.append(g);this.go_page_one();this.execute()},set_sort_condition:function(h){var g=this.grid.get("sort_key");var f=h;if(g.indexOf(h)!==-1){if(g.substring(0,1)!=="-"){f="-"+h}else{}}$(".sort-arrow").remove();var e=(f.substring(0,1)=="-")?"↑":"↓";var c=$("<span>"+e+"</span>").addClass("sort-arrow");var d=$("#"+h+"-header");d.append(c);this.grid.set("sort_key",f);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;$("."+e+"-filter").each(function(){var k=$.trim($(this).text());var i=d[k];var j=i[e];if(j==g){$(this).empty();$(this).addClass("current-filter");$(this).append(k)}else{if(j==f){$(this).empty();var h=$("<a href='#'>"+k+"</a>");h.click(function(){c.set_categorical_filter(e,j)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;$(".page-link").each(function(){var i=$(this).attr("id"),g=parseInt(i.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$("<a href='#'>"+h+"</a>");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(f,g){var e=$('input[name="id"]:checked').length;if(!e>0){return false}var d=$(f).val();var c=[];$("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:d,id:c,confirmation_text:g});return true},execute:function(l){var f=null;var e=null;var g=null;var c=null;var k=null;if(l){e=l.href;g=l.operation;f=l.id;c=l.confirmation_text;k=l.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var j=e.split("?");if(j.length>1){var i=j[1];var d=i.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(k,"")}return false}if(e){this.go_to(k,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(k,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);if(!d){d=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data())}this.grid.set({operation:undefined,item_ids:undefined,async:e});if(f){var c=$(".grid-header").closest(".inbound");if(c.length!==0){c.load(d);return}}window.location=d},update_grid:function(){var d=(this.grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();var c=this;$.ajax({type:d,url:c.grid.get("url_base"),data:c.grid.get_url_data(),error:function(e){alert("Grid refresh failed")},success:function(f){var e=f.split("*****");$("#grid-table-body").html(e[0]);$("#grid-table-footer").html(e[1]);$("#grid-table-body").trigger("update");$(".loading-elt-overlay").hide();var g=$.trim(e[2]);if(g!==""){$("#grid-message").html(g).show();setTimeout(function(){$("#grid-message").hide()},5000)}},complete:function(){c.grid.set({operation:undefined,item_ids:undefined})}})},check_all_items:function(){var c=document.getElementById("check_all"),d=document.getElementsByTagName("input"),f=0,e;if(c.checked===true){for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=true;f++}}}else{for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=false}}}this.init_grid_elements()},go_page_one:function(){var c=this.grid.get("cur_page");if(c!==null&&c!==undefined&&c!=="all"){this.grid.set("cur_page",1)}}});return{Grid:a,GridView:b}}); \ No newline at end of file diff -r 5dfc0b3bf0351e7274cd3a5bdeab921752215973 -r 9165deb8008461d43107c2b1cd99b750bcb0508f static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body");this.$el.css(this._getShownPosition(a));this._setUpCloseBehavior();this.$el.show()},render:function(){this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options));if(this.options.length){var a=this;this.$el.find("li").each(function(c,b){var d=a.options[c];if(d.func){$(this).children("a.popupmenu-option").click(function(e){d.func.call(a,e,d)})}})}return this},template:function(b,a){return['<ul id="',b,'-menu" class="dropdown-menu">',this._templateOptions(a),"</ul>"].join("")},_templateOptions:function(a){if(!a.length){return"<li>(no options)</li>"}return _.map(a,function(d){if(d.divider){return'<li class="divider"></li>'}else{if(d.header){return['<li class="head"><a href="javascript:void(0);">',d.html,"</a></li>"].join("")}}var c=d.href||"javascript:void(0);",e=(d.target)?(' target="'+d.target+'"'):(""),b=(d.checked)?('<span class="fa fa-check"></span>'):("");return['<li><a class="popupmenu-option" href="',c,'"',e,">",b,d.html,"</a></li>"].join("")}).join("")},_getShownPosition:function(b){var c=this.$el.width();var a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_setUpCloseBehavior:function(){var b=this;var a=function(c){c.one("click.close_popup",function(){b.remove()})};a($(window.document));a($(window.top.document));_.each(window.top.frames,function(c){a($(c.document))})},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(d.attr("href")){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a};var faIconButton=function(a){a=a||{};a.tooltipConfig=a.tooltipConfig||{placement:"bottom"};a.classes=["icon-btn"].concat(a.classes||[]);if(a.disabled){a.classes.push("disabled")}var b=['<a class="',a.classes.join(" "),'"',((a.title)?(' title="'+a.title+'"'):("")),((a.target)?(' target="'+a.target+'"'):("")),' href="',((a.href)?(a.href):("javascript:void(0);")),'">','<span class="fa ',a.faIcon,'"></span>',"</a>"].join("");var c=$(b).tooltip(a.tooltipConfig);if(_.isFunction(a.onclick)){c.click(a.onclick)}return c};var searchInput=function(k){var a=27,h=13,i=$("<div/>"),b={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onsearch:function(l){},minSearchLen:0,escWillClear:true,oninit:function(){}};if(jQuery.type(k)==="object"){k=jQuery.extend(true,b,k)}function d(l){var m=$(this).parent().children("input");m.val("");m.trigger("clear:searchInput");k.onclear()}function j(m,l){$(this).trigger("search:searchInput",l);k.onsearch(l)}function c(){return['<input type="text" name="',k.name,'" placeholder="',k.placeholder,'" ','class="search-query ',k.classes,'" ',"/>"].join("")}function g(){return $(c()).css({width:"100%","padding-right":"24px"}).focus(function(l){$(this).select()}).keyup(function(m){if(m.which===a&&k.escWillClear){d.call(this,m)}else{var l=$(this).val();if((m.which===h)||(k.minSearchLen&&l.length>=k.minSearchLen)){j.call(this,m,l)}else{if(!l.length){d.call(this,m)}}}}).val(k.initialVal)}function f(){return'<span class="search-clear fa fa-times-circle"></span>'}function e(){return $(f()).css({position:"absolute",right:"15px","font-size":"1.4em","line-height":"23px",color:"grey"}).click(function(l){d.call(this,l)})}return i.append([g(),e()])};function LoadingIndicator(a,c){var b=this;c=jQuery.extend({cover:false},c||{});function d(){var e=['<div class="loading-indicator">','<div class="loading-indicator-text">','<span class="fa fa-spinner fa-spin fa-lg"></span>','<span class="loading-indicator-message">loading...</span>',"</div>","</div>"].join("\n");var g=$(e).hide().css(c.css||{position:"fixed"}),f=g.children(".loading-indicator-text");if(c.cover){g.css({"z-index":2,top:a.css("top"),bottom:a.css("bottom"),left:a.css("left"),right:a.css("right"),opacity:0.5,"background-color":"white","text-align":"center"});f=g.children(".loading-indicator-text").css({"margin-top":"20px"})}else{f=g.children(".loading-indicator-text").css({margin:"12px 0px 0px 10px",opacity:"0.85",color:"grey"});f.children(".loading-indicator-message").css({margin:"0px 8px 0px 0px","font-style":"italic"})}return g}b.show=function(f,e,g){f=f||"loading...";e=e||"fast";b.$indicator=d().insertBefore(a);b.message(f);b.$indicator.fadeIn(e,g);return b};b.message=function(e){b.$indicator.find("i").text(e)};b.hide=function(e,f){e=e||"fast";if(b.$indicator&&b.$indicator.size()){b.$indicator.fadeOut(e,function(){b.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}; \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body");this.$el.css(this._getShownPosition(a));this._setUpCloseBehavior();this.$el.show()},render:function(){this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options));if(this.options.length){var a=this;this.$el.find("li").each(function(c,b){var d=a.options[c];if(d.func){$(this).children("a.popupmenu-option").mousedown(function(e){d.func.call(a,e,d)})}})}return this},template:function(b,a){return['<ul id="',b,'-menu" class="dropdown-menu">',this._templateOptions(a),"</ul>"].join("")},_templateOptions:function(a){if(!a.length){return"<li>(no options)</li>"}return _.map(a,function(d){if(d.divider){return'<li class="divider"></li>'}else{if(d.header){return['<li class="head"><a href="javascript:void(0);">',d.html,"</a></li>"].join("")}}var c=d.href||"javascript:void(0);",e=(d.target)?(' target="'+d.target+'"'):(""),b=(d.checked)?('<span class="fa fa-check"></span>'):("");return['<li><a class="popupmenu-option" href="',c,'"',e,">",b,d.html,"</a></li>"].join("")}).join("")},_getShownPosition:function(b){var c=this.$el.width();var a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_setUpCloseBehavior:function(){var b=this;var a=function(c){c.one("mousedown.close_popup",function(){b.remove()})};a($(window.document));a($(window.top.document));_.each(window.top.frames,function(c){a($(c.document))})},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(d.attr("href")){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a};var faIconButton=function(a){a=a||{};a.tooltipConfig=a.tooltipConfig||{placement:"bottom"};a.classes=["icon-btn"].concat(a.classes||[]);if(a.disabled){a.classes.push("disabled")}var b=['<a class="',a.classes.join(" "),'"',((a.title)?(' title="'+a.title+'"'):("")),((a.target)?(' target="'+a.target+'"'):("")),' href="',((a.href)?(a.href):("javascript:void(0);")),'">','<span class="fa ',a.faIcon,'"></span>',"</a>"].join("");var c=$(b).tooltip(a.tooltipConfig);if(_.isFunction(a.onclick)){c.click(a.onclick)}return c};var searchInput=function(k){var a=27,h=13,i=$("<div/>"),b={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onsearch:function(l){},minSearchLen:0,escWillClear:true,oninit:function(){}};if(jQuery.type(k)==="object"){k=jQuery.extend(true,b,k)}function d(l){var m=$(this).parent().children("input");m.val("");m.trigger("clear:searchInput");k.onclear()}function j(m,l){$(this).trigger("search:searchInput",l);k.onsearch(l)}function c(){return['<input type="text" name="',k.name,'" placeholder="',k.placeholder,'" ','class="search-query ',k.classes,'" ',"/>"].join("")}function g(){return $(c()).css({width:"100%","padding-right":"24px"}).focus(function(l){$(this).select()}).keyup(function(m){if(m.which===a&&k.escWillClear){d.call(this,m)}else{var l=$(this).val();if((m.which===h)||(k.minSearchLen&&l.length>=k.minSearchLen)){j.call(this,m,l)}else{if(!l.length){d.call(this,m)}}}}).val(k.initialVal)}function f(){return'<span class="search-clear fa fa-times-circle"></span>'}function e(){return $(f()).css({position:"absolute",right:"15px","font-size":"1.4em","line-height":"23px",color:"grey"}).click(function(l){d.call(this,l)})}return i.append([g(),e()])};function LoadingIndicator(a,c){var b=this;c=jQuery.extend({cover:false},c||{});function d(){var e=['<div class="loading-indicator">','<div class="loading-indicator-text">','<span class="fa fa-spinner fa-spin fa-lg"></span>','<span class="loading-indicator-message">loading...</span>',"</div>","</div>"].join("\n");var g=$(e).hide().css(c.css||{position:"fixed"}),f=g.children(".loading-indicator-text");if(c.cover){g.css({"z-index":2,top:a.css("top"),bottom:a.css("bottom"),left:a.css("left"),right:a.css("right"),opacity:0.5,"background-color":"white","text-align":"center"});f=g.children(".loading-indicator-text").css({"margin-top":"20px"})}else{f=g.children(".loading-indicator-text").css({margin:"12px 0px 0px 10px",opacity:"0.85",color:"grey"});f.children(".loading-indicator-message").css({margin:"0px 8px 0px 0px","font-style":"italic"})}return g}b.show=function(f,e,g){f=f||"loading...";e=e||"fast";b.$indicator=d().insertBefore(a);b.message(f);b.$indicator.fadeIn(e,g);return b};b.message=function(e){b.$indicator.find("i").text(e)};b.hide=function(e,f){e=e||"fast";if(b.$indicator&&b.$indicator.size()){b.$indicator.fadeOut(e,function(){b.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}; \ 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.

1 0

commit/galaxy-central: guerler: Fix tagging mako
by commits-noreply＠bitbucket.org 25 Nov '13

25 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5dfc0b3bf035/ Changeset: 5dfc0b3bf035 User: guerler Date: 2013-11-25 06:16:41 Summary: Fix tagging mako Affected #: 1 file diff -r 6d8062a02641e8be1d1df7b9e87519662ac9c2d5 -r 5dfc0b3bf0351e7274cd3a5bdeab921752215973 templates/tagging_common.mako --- a/templates/tagging_common.mako +++ b/templates/tagging_common.mako @@ -135,7 +135,6 @@ ## Build script that augments tags using progressive javascript. <script type="text/javascript"> - $(function() { // // Set up autocomplete tagger. // @@ -213,8 +212,6 @@ }; $('#${elt_id}').autocomplete_tagging(options); - - }); </script> ## Use style to hide/display the tag area. 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: guerler: Grids: Fix for toolshed
by commits-noreply＠bitbucket.org 23 Nov '13

23 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6d8062a02641/ Changeset: 6d8062a02641 User: guerler Date: 2013-11-23 23:02:46 Summary: Grids: Fix for toolshed Affected #: 2 files diff -r 59c4b30557cd889472ad7162b1f1b5be3e01973a -r 6d8062a02641e8be1d1df7b9e87519662ac9c2d5 templates/webapps/tool_shed/category/grid.mako --- a/templates/webapps/tool_shed/category/grid.mako +++ b/templates/webapps/tool_shed/category/grid.mako @@ -7,6 +7,7 @@ ## TODO: This is very similar to this directory's valid_grid.mako, so see if we can re-use this code in a better way. <%def name="render_grid_header( grid, repo_grid, render_title=True)"> ${init()} + ${grid_javascripts()} <div class="grid-header"> %if render_title: ${grid_title()} diff -r 59c4b30557cd889472ad7162b1f1b5be3e01973a -r 6d8062a02641e8be1d1df7b9e87519662ac9c2d5 templates/webapps/tool_shed/category/valid_grid.mako --- a/templates/webapps/tool_shed/category/valid_grid.mako +++ b/templates/webapps/tool_shed/category/valid_grid.mako @@ -6,6 +6,7 @@ ## Render grid header. <%def name="render_grid_header( grid, repo_grid, render_title=True)"> ${init()} + ${grid_javascripts()} <div class="grid-header"> %if render_title: ${grid_title()} 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: guerler: Grids: Fix for Toolshed
by commits-noreply＠bitbucket.org 23 Nov '13

23 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/59c4b30557cd/ Changeset: 59c4b30557cd User: guerler Date: 2013-11-23 22:49:54 Summary: Grids: Fix for Toolshed Affected #: 2 files diff -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c -r 59c4b30557cd889472ad7162b1f1b5be3e01973a templates/webapps/tool_shed/category/grid.mako --- a/templates/webapps/tool_shed/category/grid.mako +++ b/templates/webapps/tool_shed/category/grid.mako @@ -48,7 +48,7 @@ ${render_grid_table( grid, show_item_checkboxes )} </%def> -<%def name="grid_body( grid )"> +<%def name="grid_body()"><% from tool_shed.grids.repository_grids import RepositoryGrid repo_grid = RepositoryGrid() diff -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c -r 59c4b30557cd889472ad7162b1f1b5be3e01973a templates/webapps/tool_shed/category/valid_grid.mako --- a/templates/webapps/tool_shed/category/valid_grid.mako +++ b/templates/webapps/tool_shed/category/valid_grid.mako @@ -47,7 +47,7 @@ ${render_grid_table( grid, show_item_checkboxes )} </%def> -<%def name="grid_body( grid )"> +<%def name="grid_body()"><% from tool_shed.grids.repository_grids import ValidRepositoryGrid repo_grid = ValidRepositoryGrid() 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: guerler: Grids: Unify operation handling, use new popups, refactor, bug fixes
by commits-noreply＠bitbucket.org 23 Nov '13

23 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3f630f92f598/ Changeset: 3f630f92f598 User: guerler Date: 2013-11-23 22:14:59 Summary: Grids: Unify operation handling, use new popups, refactor, bug fixes Affected #: 19 files diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -323,7 +323,7 @@ def __init__( self, label, key=None, model_class=None, method=None, format=None, \ link=None, attach_popup=False, visible=True, nowrap=False, \ # Valid values for filterable are ['standard', 'advanced', None] - filterable=None, sortable=True, label_id_prefix=None ): + filterable=None, sortable=True, label_id_prefix=None, inbound=False ): """Create a grid column.""" self.label = label self.key = key @@ -331,6 +331,7 @@ self.method = method self.format = format self.link = link + self.inbound = inbound self.nowrap = nowrap self.attach_popup = attach_popup self.visible = visible @@ -734,7 +735,7 @@ class GridOperation( object ): def __init__( self, label, key=None, condition=None, allow_multiple=True, allow_popup=True, target=None, url_args=None, async_compatible=False, confirm=None, - global_operation=None ): + global_operation=None, inbound=False ): self.label = label self.key = key self.allow_multiple = allow_multiple @@ -743,6 +744,7 @@ self.target = target self.url_args = url_args self.async_compatible = async_compatible + self.inbound = inbound # if 'confirm' is set, then ask before completing the operation self.confirm = confirm # specify a general operation that acts on the full grid @@ -772,9 +774,10 @@ return { 'action' : 'display_by_username_and_slug', 'username' : item.user.username, 'slug' : item.slug } class GridAction( object ): - def __init__( self, label=None, url_args=None ): + def __init__( self, label=None, url_args=None, inbound=False ): self.label = label self.url_args = url_args + self.inbound = inbound class GridColumnFilter( object ): def __init__( self, label, args=None ): diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -99,8 +99,8 @@ columns = [ grids.TextColumn( "Name", key="name", # Link name to dataset's history. - link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced", attach_popup=True ), - HistoryColumn( "History", key="history", sortable=False, + link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced", attach_popup=True, inbound=True ), + HistoryColumn( "History", key="history", sortable=False, inbound=True, link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), StatusColumn( "Status", key="deleted", attach_popup=False ), diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -34,14 +34,14 @@ for state in ( 'ok', 'running', 'queued', 'error' ): count = state_count_dict.get( state, 0 ) if count: - rval += '<div class="count-box state-color-%s">%s</div>' % (state, count) + rval += '<div class="count-box state-color-%s">%s</div> ' % (state, count) return rval class HistoryListNameColumn( NameColumn ): def get_link( self, trans, grid, history ): link = None if not history.deleted: - link = dict( operation="Switch", id=history.id, use_panels=grid.use_panels ) + link = dict( operation="Switch", id=history.id, use_panels=grid.use_panels, async_compatible=True ) return link @@ -85,10 +85,10 @@ key="free-text-search", visible=False, filterable="standard" ) ) operations = [ - grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), - grids.GridOperation( "View", allow_multiple=False ), + grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=True ), + grids.GridOperation( "View", allow_multiple=False, inbound=True ), grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), - grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), async_compatible=False ), + grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), async_compatible=False, inbound=True ), grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True ), grids.GridOperation( "Delete Permanently", condition=( lambda item: not item.purged ), confirm="History contents will be removed from disk, this cannot be undone. Continue?", async_compatible=True ), grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), async_compatible=True ), diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -95,7 +95,6 @@ # Grid definition. show_item_checkboxes = True template = "/page/select_items_grid.mako" - async_template = "/page/select_items_grid_async.mako" default_filter = { "deleted" : "False" , "sharing" : "All" } default_sort_key = "-update_time" use_async = True diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -56,7 +56,7 @@ datasets_action = 'list_history_datasets' datasets_param = "f-history" columns = [ - NameColumn( "History Name", key="name", filterable="standard" ), + NameColumn( "History Name", key="name", filterable="standard", inbound=True ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago, visible=False ), DbKeyPlaceholderColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=False ) ] @@ -77,7 +77,7 @@ datasets_action = 'list_library_datasets' datasets_param = "f-library" columns = [ - NameColumn( "Library Name", key="name", filterable="standard" ) + NameColumn( "Library Name", key="name", filterable="standard", inbound=True ) ] num_rows_per_page = 10 use_async = True @@ -196,15 +196,15 @@ key="free-text-search", visible=False, filterable="standard" ) ) global_actions = [ - grids.GridAction( "Create new visualization", dict( action='create' ) ) + grids.GridAction( "Create new visualization", dict( action='create' ), inbound=True ) ] operations = [ grids.GridOperation( "Open", allow_multiple=False, url_args=get_url_args ), grids.GridOperation( "Open in Circster", allow_multiple=False, condition=( lambda item: item.type == 'trackster' ), url_args=dict( action='circster' ) ), - grids.GridOperation( "Edit Attributes", allow_multiple=False, url_args=dict( action='edit') ), - grids.GridOperation( "Copy", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False, url_args=dict( action='copy') ), + grids.GridOperation( "Edit Attributes", allow_multiple=False, url_args=dict( action='edit'), inbound=True), + grids.GridOperation( "Copy", allow_multiple=False, condition=( lambda item: not item.deleted )), grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), - grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True, confirm="Are you sure you want to delete this visualization?" ), + grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), confirm="Are you sure you want to delete this visualization?" ), ] def apply_query_filter( self, trans, query, **kwargs ): return query.filter_by( user=trans.user, deleted=False ) @@ -327,6 +327,7 @@ @web.expose @web.require_login( "use Galaxy visualizations", use_panels=True ) def list( self, trans, *args, **kwargs ): + # Handle operation if 'operation' in kwargs and 'id' in kwargs: session = trans.sa_session @@ -338,6 +339,8 @@ item.deleted = True if operation == "share or publish": return self.sharing( trans, **kwargs ) + if operation == "copy": + self.copy( trans, **kwargs ) session.flush() # Build list of visualizations shared with user. @@ -350,8 +353,7 @@ .all() return trans.fill_template( "visualization/list.mako", grid=self._user_list_grid( trans, *args, **kwargs ), shared_by_others=shared_by_others ) - - + # # -- Functions for operating on visualizations. -- # @@ -364,7 +366,7 @@ @web.expose @web.require_login() - def copy(self, trans, id, *args, **kwargs): + def copy(self, trans, id, **kwargs): visualization = self.get_visualization( trans, id, check_ownership=False ) user = trans.get_user() owner = ( visualization.user == user ) @@ -381,7 +383,7 @@ # Display the management page trans.set_message( 'Created new visualization with name "%s"' % copied_viz.title ) - return self.list( trans ) + return @web.expose @web.require_login( "use Galaxy visualizations" ) diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -4,6 +4,9 @@ // not appended to the identifier of a nested array. jQuery.ajaxSettings.traditional = true; +// dependencies +define(['mvc/ui'], function() { + /** * A Galaxy grid. */ @@ -137,8 +140,7 @@ // Initialize initialize: function(grid) { - this.grid = grid; - this.init_grid_elements(); + this.init_grid(grid); this.init_grid_controls(); // Initialize text filters to select text on click and use normal font when user is typing. @@ -147,7 +149,14 @@ .keyup(function () { $(this).css("font-style", "normal"); }); }); }, - + + // Initialize + init_grid: function(grid) + { + this.grid = grid; + this.init_grid_elements(); + }, + // Initialize grid controls init_grid_controls: function() { // Initialize submit image elements. @@ -174,14 +183,6 @@ }); }); - // Initialize page links. - $('.page-link > a').each( function() { - $(this).click( function() { - self.set_page( $(this).attr('page_num') ); - return false; - }); - }); - // Initialize categorical filters. $('.categorical-filter > a').each( function() { $(this).click( function() { @@ -227,7 +228,6 @@ // Initialize grid elements. init_grid_elements : function() { - // Initialize grid selection checkboxes. $(".grid").each( function() { var checkboxes = $(this).find("input.grid-row-select-checkbox"); @@ -242,34 +242,94 @@ update_checked(); }); - // Initialize item labels. - var self = this; - $(".label").each( function() { - // If href has an operation in it, do operation when clicked. Otherwise do nothing. - var href = $(this).attr('href'); - if ( href !== undefined && href.indexOf('operation=') != -1 ) { - $(this).click( function() { - self.do_operation_from_href( $(this).attr('href') ); - return false; - }); - } - }); - // Initialize ratings. if ($('.community_rating_star').length !== 0) $('.community_rating_star').rating({}); + + // get options + var options = this.grid.attributes; + var self = this; - // Initialize item menu operations. - make_popup_menus(); - }, - - // Go back to page one; this is useful when a filter is applied. - go_page_one: function () { - // Need to go back to page 1 if not showing all. - var cur_page = this.grid.get('cur_page'); - if (cur_page !== null && cur_page !== undefined && cur_page !== 'all') { - this.grid.set('cur_page', 1); - } + // + // add page click events + // + $('.page-link > a').each( function() { + $(this).click( function() { + self.set_page( $(this).attr('page_num') ); + return false; + }); + }); + + // + // add inbound/outbound events + // + $(".use-inbound").each( function() { + $(this).click( function(e) { + self.execute({ + href : $(this).attr('href'), + inbound : true + }); + return false; + + }); + }); + + $(".use-outbound").each( function() { + $(this).click( function(e) { + self.execute({ + href : $(this).attr('href') + }); + return false; + }); + }); + + // + // add operation popup menus + // + for (var i in options['items']) + { + // get identifiers + var button = $('#grid-' + i + '-popup'); + button.off(); + var popup = new PopupMenu(button); + + // load details + var item = options['items'][i]; + for (var j in options['operations']) + { + // get operation details + var operation = options['operations'][j]; + var operation_id = operation['label']; + var operation_settings = item['operation_config'][operation_id]; + var encode_id = item['encode_id']; + + // check + if (operation_settings['allowed'] && operation['allow_popup']) + { + // popup configuration + var popupConfig = + { + html : operation['label'], + href : operation_settings['url_args'], + target : operation_settings['target'], + confirmation_text : operation['confirm'], + inbound : operation['inbound'] + }; + + // add popup function + popupConfig.func = function(e) + { + e.preventDefault(); + var label = $(e.target).html(); + var options = this.findItemByHtml(label); + self.execute(options); + }; + + // add item + popup.addItem(popupConfig); + } + } + } }, // Add a condition to the grid filter; this adds the condition and refreshes the grid. @@ -294,14 +354,14 @@ $(this).remove(); self.go_page_one(); - self.update_grid(); + self.execute(); }); var container = $('#' + name + "-filtering-criteria"); container.append(t); this.go_page_one(); - this.update_grid(); + this.execute(); }, // Set sort condition for grid. @@ -331,7 +391,7 @@ // Update grid. this.grid.set('sort_key', new_sort); this.go_page_one(); - this.update_grid(); + this.execute(); }, // Set new value for categorical filter. @@ -366,7 +426,7 @@ // Update grid. this.grid.add_filter(name, new_value); this.go_page_one(); - this.update_grid(); + this.execute(); }, // Set page to view. @@ -394,88 +454,160 @@ $(this).removeClass("inactive-link"); var t = $("<a href='#'>" + text + "</a>"); t.click(function() { - set_page(page_num); + self.set_page(page_num); }); $(this).append(t); } }); - var maintain_page_links = true; if (new_page === "all") { this.grid.set('cur_page', new_page); - maintain_page_links = false; } else { this.grid.set('cur_page', parseInt(new_page, 10)); } - this.update_grid(maintain_page_links); + this.execute(); }, - // Perform a grid operation. - do_operation: function (operation, item_ids) { - operation = operation.toLowerCase(); - - // Update grid. - this.grid.set({ - operation: operation, - item_ids: item_ids + // confirmation/submission of operation request + submit_operation: function (selected_button, confirmation_text) + { + // verify in any item is selected + var number_of_checked_ids = $('input[name="id"]:checked').length; + if (!number_of_checked_ids > 0) + return false; + + // collect ids + var operation_name = $(selected_button).val(); + var item_ids = []; + $('input[name=id]:checked').each(function() { + item_ids.push( $(this).val() ); + }); + this.execute({ + operation: operation_name, + id: item_ids, + confirmation_text: confirmation_text }); - // Do operation. If operation cannot be performed asynchronously, redirect to location. - if (this.grid.can_async_op(operation)) { - this.update_grid(true); + // return + return true; + }, + + // execute operations and hyperlink requests + execute: function (options) { + // get url + var id = null; + var href = null; + var operation = null; + var confirmation_text = null; + var inbound = null; + + // check for options + if (options) + { + // get options + href = options.href; + operation = options.operation; + id = options.id; + confirmation_text = options.confirmation_text; + inbound = options.inbound; + + // check if input contains the operation tag + if (href !== undefined && href.indexOf('operation=') != -1) { + // Get operation, id in hyperlink's href. + var href_parts = href.split("?"); + if (href_parts.length > 1) { + var href_parms_str = href_parts[1]; + var href_parms = href_parms_str.split("&"); + for (var index = 0; index < href_parms.length; index++) { + if (href_parms[index].indexOf('operation') != -1) { + // Found operation parm; get operation value. + operation = href_parms[index].split('=')[1]; + operation = operation.replace (/\+/g, ' '); + } else if (href_parms[index].indexOf('id') != -1) { + // Found id parm; get id value. + id = href_parms[index].split('=')[1]; + } + } + } + } } - else { - this.go_to_URL(); + + // check for operation details + if (operation && id) { + // show confirmation box + if (confirmation_text && confirmation_text != '' && confirmation_text != 'None') + if(!confirm(confirmation_text)) + return false; + + // use small characters for operation?! + operation = operation.toLowerCase(); + + // Update grid. + this.grid.set({ + operation: operation, + item_ids: id + }); + + // Do operation. If operation cannot be performed asynchronously, redirect to location. + if (this.grid.can_async_op(operation)) { + this.update_grid(); + } else { + this.go_to(inbound, ''); + } + + // done + return false; } + + // check for href details + if (href) + { + this.go_to(inbound, href); + return false; + } + + // refresh grid + if (this.grid.get('async')) { + this.update_grid(); + } else { + this.go_to(inbound, ''); + } + + // done + return false; }, - // Perform a hyperlink click that initiates an operation. If there is no operation, ignore click. - do_operation_from_href: function (href) { - // Get operation, id in hyperlink's href. - var href_parts = href.split("?"); - if (href_parts.length > 1) { - var href_parms_str = href_parts[1]; - var href_parms = href_parms_str.split("&"); - var operation = null; - var id = -1; - for (var index = 0; index < href_parms.length; index++) { - if (href_parms[index].indexOf('operation') != -1) { - // Found operation parm; get operation value. - operation = href_parms[index].split('=')[1]; - } else if (href_parms[index].indexOf('id') != -1) { - // Found id parm; get id value. - id = href_parms[index].split('=')[1]; - } - } - // Do operation. - this.do_operation(operation, id); - return false; - } - }, - - // Navigate window to the URL defined by url_args. This method can be used to short-circuit grid AJAXing. - go_to_URL: function () { - // Not async request. + // go to url + go_to: function (inbound, href) { + + var async = this.grid.get('async'); this.grid.set('async', false); - // Go. - window.location = this.grid.get('url_base') + "?" + $.param(this.grid.get_url_data()); - + // get default url + if(!href) + href = this.grid.get('url_base') + "?" + $.param(this.grid.get_url_data()); + // Clear grid of transient request attributes. this.grid.set({ operation: undefined, - item_ids: undefined + item_ids: undefined, + async: async }); + + if (inbound) { + // this currently assumes that there is only a single grid shown at a time + var $div = $('.grid-header').closest('.inbound'); + if ($div.length !== 0) { + $div.load(href); + return; + } + } + + window.location = href; }, // Update grid. - update_grid: function (maintain_page_links) { - // If grid is not using async, then go to URL. - if (!this.grid.get('async')) { - this.go_to_URL(); - return; - } - + update_grid: function () { // If there's an operation, do POST; otherwise, do GET. var method = (this.grid.get('operation') ? "POST" : "GET" ); $('.loading-elt-overlay').show(); // Show overlay to indicate loading and prevent user actions. @@ -484,7 +616,7 @@ type: method, url: self.grid.get('url_base'), data: self.grid.get_url_data(), - error: function() { alert( "Grid refresh failed" ); }, + error: function(response) { alert( "Grid refresh failed" );}, success: function(response_text) { // HACK: use a simple string to separate the elements in the // response: (1) table body; (2) number of pages in table; and (3) message. @@ -498,11 +630,7 @@ // Trigger custom event to indicate grid body has changed. $('#grid-table-body').trigger('update'); - - // Init grid. - self.init_grid_elements(); - make_popup_menus(); - + // Hide loading overlay. $('.loading-elt-overlay').hide(); @@ -546,29 +674,20 @@ } this.init_grid_elements(); }, - - // confirmation/submission of operation request - submit_operation: function (selected_button, confirmation_text) - { - // verify in any item is selected - var number_of_checked_ids = $('input[name="id"]:checked').length; - if (!number_of_checked_ids > 0) - return false; - - // show confirmation box - if (confirmation_text != 'None' && confirmation_text != '') - if(!confirm(confirmation_text)) - return false; - - // collect ids - var operation_name = $(selected_button).val(); - var item_ids = []; - $('input[name=id]:checked').each(function() { - item_ids.push( $(this).val() ); - }); - this.do_operation(operation_name, item_ids); - - // return - return true; + + // Go back to page one; this is useful when a filter is applied. + go_page_one: function () { + // Need to go back to page 1 if not showing all. + var cur_page = this.grid.get('cur_page'); + if (cur_page !== null && cur_page !== undefined && cur_page !== 'all') { + this.grid.set('cur_page', 1); + } } }); + +return { + Grid : Grid, + GridView : GridView +}; + +}); \ No newline at end of file diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -232,7 +232,7 @@ // if the option has 'func', call that function when the anchor is clicked if( option.func ){ - $( this ).children( 'a.popupmenu-option' ).click( function( event ){ + $( this ).children( 'a.popupmenu-option' ).mousedown( function( event ){ option.func.call( menu, event, option ); // bubble up so that an option click will call the close behavior //return false; @@ -292,7 +292,7 @@ // function to close popup and unbind itself var menu = this; var closePopupWhenClicked = function( $elClicked ){ - $elClicked.one( "click.close_popup", function(){ + $elClicked.one( "mousedown.close_popup", function(){ menu.remove(); }); }; diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c templates/admin/requests/sample_datasets_grid.mako --- a/templates/admin/requests/sample_datasets_grid.mako +++ b/templates/admin/requests/sample_datasets_grid.mako @@ -2,8 +2,8 @@ <%namespace file="/requests/common/common.mako" import="common_javascripts" /><%namespace file="/requests/common/common.mako" import="transfer_status_updater" /> -<%def name="javascripts()"> - ${parent.javascripts()} - ${common_javascripts()} - ${transfer_status_updater()} +<%def name="load()"> + ${parent.load()} + ${common_javascripts()} + ${transfer_status_updater()} </%def> diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -10,7 +10,7 @@ ${self.stylesheets()} ${self.javascripts()} </head> - <body> + <body class="inbound"> ${next.body()} </body></html> @@ -50,7 +50,8 @@ "libs/backbone/backbone-relational", "libs/handlebars.runtime", "galaxy.base", - "mvc/ui" + "mvc/ui", + 'libs/require' )} <script type="text/javascript"> @@ -69,6 +70,16 @@ error : function(){}, assert : function(){} }; + + ## configure require + require.config({ + baseUrl: "${h.url_for('/static/scripts') }", + shim: { + "libs/underscore": { exports: "_" }, + "libs/backbone/backbone": { exports: "Backbone" }, + "libs/backbone/backbone-relational": ["libs/backbone/backbone"] + } + }); </script> %if not form_input_auto_focus is UNDEFINED and form_input_auto_focus: diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -341,7 +341,7 @@ </div></div> %endif - <div id="center"> + <div id="center" class="inbound"> ${self.center_panel()} </div> %if self.has_right_panel: diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -16,6 +16,20 @@ <%namespace file="/refresh_frames.mako" import="handle_refresh_frames" /><%namespace file="/display_common.mako" import="get_class_plural" /> +<%def name="load(embedded = False)"> +<% + self.grid_javascripts() + if embedded: + self.init() + self.stylesheets() + self.render_grid_header( grid, False ) + self.render_grid_table( grid, show_item_checkboxes=show_item_checkboxes ) + else: + self.make_grid( grid ) + endif +%> +</%def> + <%def name="init()"><% self.has_left_panel = False @@ -47,7 +61,8 @@ 'get_class_plural' : get_class_plural( grid.model_class ).lower(), 'use_paging' : grid.use_paging, 'legend' : grid.legend, - 'current_item_id' : '' + 'current_item_id' : False, + 'use_panels' : context.get('use_panels') } ## add current item if exists @@ -94,6 +109,7 @@ 'target' : operation.target, 'label' : operation.label, 'confirm' : operation.confirm, + 'inbound' : operation.inbound, 'global_operation' : False }) if operation.allow_multiple: @@ -107,7 +123,8 @@ for action in grid.global_actions: self.grid_config['global_actions'].append({ 'url_args' : url(**action.url_args), - 'label' : action.label + 'label' : action.label, + 'inbound' : action.inbound }) endfor @@ -144,6 +161,9 @@ link = None endif + ## inbound + inbound = column.inbound + ## get value value = column.get_value( trans, grid, item ) @@ -158,7 +178,8 @@ ## Item dictionary item_dict['column_config'][column.label] = { 'link' : link, - 'value' : value + 'value' : value, + 'inbound' : inbound } endif endfor @@ -181,36 +202,29 @@ ## <%def name="center_panel()"> - ${self.grid_body( grid )} + ${self.grid_body()} </%def> ## Render the grid's basic elements. Each of these elements can be subclassed. <%def name="body()"> - ${self.grid_body( grid )} + ${self.grid_body()} </%def> ## Because body() is special and always exists even if not explicitly defined, ## it's not possible to override body() in the topmost template in the chain. ## Because of this, override grid_body() instead. -<%def name="grid_body( grid )"> - ${self.make_grid( grid )} +<%def name="grid_body()"> + ${self.load()} </%def><%def name="title()">${self.grid_config['title']}</%def> -<%def name="javascripts()"> - ${parent.javascripts()} - ${self.grid_javascripts()} -</%def> - <%def name="grid_javascripts()"> - ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", "libs/jquery/jquery.rating", "galaxy.grids" )} + ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", "libs/jquery/jquery.rating" )} ${handle_refresh_frames()} <script type="text/javascript"> - var gridView = null; - function add_tag_to_grid_filter (tag_name, tag_value) { // Put tag name and value together. @@ -218,23 +232,6 @@ $('#advanced-search').show('fast'); gridView.add_filter_condition("tags", tag, true); }; - - $(function() { - ## get configuration - var grid_config = ${ h.to_json_string( self.grid_config ) }; - - // Create grid. - var grid = new Grid(grid_config); - - // strip protocol and domain - var url = grid.get('url_base'); - url = url.replace(/^.*\/\/[^\/]+/, ''); - grid.set('url_base', url); - - // Create view. - gridView = new GridView(grid); - }); - </script></%def> @@ -290,16 +287,25 @@ %if self.grid_config['global_actions']: <ul class="manage-table-actions"> - %if len( self.grid_config['global_actions'] ) < 3: - %for action in self.grid_config['global_actions']: - <li><a class="action-button" href="${action['url_args']}">${action['label']}</a></li> - %endfor - %else: - <li><a class="action-button" id="action-8675309-popup" class="menubutton">Actions</a></li> - <div popupmenu="action-8675309-popup"> - %for action in self.grid_config['global_actions']: - <a class="action-button" href="${action['url_args']}">${action['label']}</a> - %endfor + <% + show_popup = len( self.grid_config['global_actions'] ) >= 3 + %> + %if show_popup: + <li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li> + <div popupmenu="popup-global-actions"> + %endif + %for action in self.grid_config['global_actions']: + <% + label_cls = "" + if action['inbound']: + label_cls = "use-inbound" + else: + label_cls = "use-outbound" + endif + %> + <li><a class="action-button ${label_cls}" href="${action['url_args']}" onclick="return false;">${action['label']}</a></li> + %endfor + %if show_popup: </div> %endif </ul> @@ -396,23 +402,21 @@ # load attributes link = column_settings['link'] value = column_settings['value'] + inbound = column_settings['inbound'] # check if formatting is defined value = str(value).replace('//', '/') # Attach popup menu? id = "" + cls = "" if column['attach_popup']: id = 'grid-%d-popup' % i - endif - - # Determine appropriate class - cls = "" - if column['attach_popup']: cls = "menubutton" if link: cls += " split" endif + cls += " popup" endif %><td ${nowrap}> @@ -420,7 +424,16 @@ %if len(self.grid_config['operations']) != 0: <div id="${id}" class="${cls}" style="float: left;"> %endif - <a class="label" href="${link}">${value}</a> + + <% + label_class = "" + if inbound: + label_class = "use-inbound" + else: + label_class = "use-outbound" + endif + %> + <a class="label ${label_class}" href="${link}" onclick="return false;">${value}</a> %if len(self.grid_config['operations']) != 0: </div> %endif @@ -430,32 +443,33 @@ </td> %endif %endfor - ## Actions column - <td> - <div popupmenu="${popupmenu_id}"> - %for operation in self.grid_config['operations']: - <% - operation_id = operation['label'] - operation_settings = item['operation_config'][operation_id] - %> - %if operation_settings['allowed'] and operation['allow_popup']: - <% - target = "" - if operation['target']: - target = "target='" + operation['target'] + "'" - %> - %if operation['confirm']: - <a class="action-button" ${target} confirm="${operation['confirm']}" href="${operation_settings['url_args']}">${operation_id}</a> - %else: - <a class="action-button" ${target} href="${operation_settings['url_args']}">${operation_id}</a> - %endif - %endif - %endfor - </div> - </td></tr><% num_rows_rendered += 1 %> %endfor + + ## update configuration + <script type="text/javascript"> + $(function() { + require(['galaxy.grids'], function(mod_grids) { + ## get configuration + var grid_config = ${ h.to_json_string( self.grid_config ) }; + + // Create grid. + var grid = new mod_grids.Grid(grid_config); + + // strip protocol and domain + var url = grid.get('url_base'); + url = url.replace(/^.*\/\/[^\/]+/, ''); + grid.set('url_base', url); + + // Create view. + if (!gridView) + gridView = new mod_grids.GridView(grid); + else + gridView.init_grid(grid); + }); + }); + </script></%def> ## Render grid table footer contents. @@ -510,24 +524,24 @@ %> Page: % if min_page > 1: - <span class='page-link' id="page-link-1"><a href="${url( page=1 )}" page_num="1">1</a></span> ... + <span class='page-link' id="page-link-1"><a href="${url( page=1 )}" page_num="1" onclick="return false;">1</a></span> ... % endif %for page_index in range(min_page, max_page + 1): %if page_index == cur_page_num: <span class='page-link inactive-link' id="page-link-${page_index}">${page_index}</span> %else: <% args = { 'page' : page_index } %> - <span class='page-link' id="page-link-${page_index}"><a href="${url( args )}" page_num='${page_index}'>${page_index}</a></span> + <span class='page-link' id="page-link-${page_index}"><a href="${url( args )}" onclick="return false;" page_num='${page_index}'>${page_index}</a></span> %endif %endfor %if max_page < num_pages: ... - <span class='page-link' id="page-link-${num_pages}"><a href="${url( page=num_pages )}" page_num="${num_pages}">${num_pages}</a></span> + <span class='page-link' id="page-link-${num_pages}"><a href="${url( page=num_pages )}" onclick="return false;" page_num="${num_pages}">${num_pages}</a></span> %endif </span> ## Show all link - <span class='page-link' id='show-all-link-span'> | <a href="${url( page='all' )}" page_num="all">Show All</a></span> + <span class='page-link' id='show-all-link-span'> | <a href="${url( page='all' )}" onclick="return false;" page_num="all">Show All</a></span></td></tr> %endif diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c templates/tagging_common.mako --- a/templates/tagging_common.mako +++ b/templates/tagging_common.mako @@ -135,6 +135,7 @@ ## Build script that augments tags using progressive javascript. <script type="text/javascript"> + $(function() { // // Set up autocomplete tagger. // @@ -212,6 +213,8 @@ }; $('#${elt_id}').autocomplete_tagging(options); + + }); </script> ## Use style to hide/display the tag area. diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c templates/user/openid_manage.mako --- a/templates/user/openid_manage.mako +++ b/templates/user/openid_manage.mako @@ -1,19 +1,10 @@ ## Template generates a grid that enables user to select items. -<%namespace file="../grid_base.mako" import="make_grid" /> +<%inherit file="../grid_base.mako" /> + <%namespace file="login.mako" import="render_openid_form" /> -<%inherit file="../grid_base.mako" /> - -<%def name="grid_body( grid )"> - ${make_grid( grid )} +<%def name="load()"> + ${parent.load()} <h2>Associate more OpenIDs</h2> ${render_openid_form( kwargs['redirect'], True, kwargs['openid_providers'] )} -</%def> - -<%def name="center_panel()"> - <div style="overflow: auto; height: 100%"> - <div class="page-container" style="padding: 10px;"> - ${grid_body( grid )} - </div> - </div> -</%def> +</%def> \ No newline at end of file diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c templates/webapps/galaxy/history/grid.mako --- a/templates/webapps/galaxy/history/grid.mako +++ b/templates/webapps/galaxy/history/grid.mako @@ -1,7 +1,7 @@ <%inherit file="../grid_base.mako"/> -<%def name="grid_body( grid )"> - ${self.make_grid( grid )} +<%def name="load()"> + ${parent.load()} <br/><div class="toolParamHelp" style="clear: both;"> Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted. diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c templates/webapps/galaxy/page/select_items_grid.mako --- a/templates/webapps/galaxy/page/select_items_grid.mako +++ b/templates/webapps/galaxy/page/select_items_grid.mako @@ -1,7 +1,3 @@ ## Template generates a grid that enables user to select items. <%namespace file="../grid_base.mako" import="*" /> -${init()} -${grid_javascripts()} -${stylesheets()} -${render_grid_header( grid, False )} -${render_grid_table( grid, show_item_checkboxes=True )} +${load(True)} \ No newline at end of file diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c templates/webapps/galaxy/page/select_items_grid_async.mako --- a/templates/webapps/galaxy/page/select_items_grid_async.mako +++ /dev/null @@ -1,9 +0,0 @@ -<%namespace file="../grid_base.mako" import="*" /> -<%namespace file="/display_common.mako" import="render_message" /> -${init()} -## Always show item checkboxes so that users can select items. -${render_grid_table_body_contents( grid, show_item_checkboxes=show_item_checkboxes )} -***** -${num_pages} -***** -${render_message( message, status )} \ No newline at end of file diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c templates/webapps/galaxy/tracks/add_to_viz.mako --- a/templates/webapps/galaxy/tracks/add_to_viz.mako +++ b/templates/webapps/galaxy/tracks/add_to_viz.mako @@ -1,8 +1,3 @@ ## Template generates a grid that enables user to add tracks <%namespace file="../grid_base.mako" import="*" /> -${init()} -${stylesheets()} -${grid_javascripts()} -${render_grid_header( grid, False )} -${render_grid_table( grid, show_item_checkboxes=True )} - +${load(True)} diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c templates/webapps/galaxy/tracks/add_tracks.mako --- a/templates/webapps/galaxy/tracks/add_tracks.mako +++ b/templates/webapps/galaxy/tracks/add_tracks.mako @@ -1,7 +1,3 @@ ## Template generates a grid that enables user to add tracks <%namespace file="../grid_base.mako" import="*" /> -${init()} -${stylesheets()} -${grid_javascripts()} -${render_grid_header( grid, False )} -${render_grid_table( grid, show_item_checkboxes=True )} \ No newline at end of file +${load(True)} \ No newline at end of file diff -r 82e91d215acf573d96d3d377620ed8815368c86d -r 3f630f92f5983c28e1aedff312e7ff7e598fe23c templates/webapps/galaxy/tracks/history_select_grid.mako --- a/templates/webapps/galaxy/tracks/history_select_grid.mako +++ b/templates/webapps/galaxy/tracks/history_select_grid.mako @@ -3,19 +3,15 @@ ## can be easily subclassed. Importing methods like this template does ## not make it possible to easily subclass templates. ## -<%namespace file="../grid_base.mako" import="*" /> -${init()} -${stylesheets()} -${grid_javascripts()} +<%namespace name="grid_base" file="../grid_base.mako" import="*" /><%def name="select_header()"><script type="text/javascript"> // Load all grid URLs into modal-body element so that // grid + links stays embedded. $(document).ready(function() { - $(".addtracktab, #grid-table a").off(); - $(".addtracktab, #grid-table a").click(function() { - var modal_body = $(".modal-body"); + $(".addtracktab").click(function() { + var modal_body = $(this).closest('.inbound'); if (modal_body.length !== 0) { modal_body.load($(this).attr("href")); return false; @@ -78,12 +74,11 @@ <div class="divider"></div></%def> -${select_header()} ## Need to define title so that it can be overridden by child templates. <%def name="title()"></%def> -${self.title()} - -${render_grid_header( grid, False )} -${render_grid_table( grid, show_item_checkboxes=show_item_checkboxes )} - +<div class='inbound'> + ${select_header()} + ${self.title()} + ${grid_base.load(True)} +</div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for tool shed install and test framework.
by commits-noreply＠bitbucket.org 23 Nov '13

23 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/82e91d215acf/ Changeset: 82e91d215acf User: greg Date: 2013-11-23 19:17:30 Summary: Fix for tool shed install and test framework. Affected #: 1 file diff -r 13bd960b94141a2974d0c968c26fc046e05e1d14 -r 82e91d215acf573d96d3d377620ed8815368c86d test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -672,12 +672,12 @@ repository_status_dict[ 'installation_errors' ][ 'current_repository' ] = error_message # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. - log.debug( 'Attempting to uninstall repository %s' % str( name ) ) + log.debug( 'Attempting to uninstall repository %s owned by %s.' % ( name, owner ) ) try: repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - except: - log.exception( 'No installed repository found.' ) - error_message = '%s\n%s' % ( error_message, extract_log_data( result, from_tool_test=False ) ) + except Exception, e: + error_message = 'Unable to find installed repository %s owned by %s: %s.' % ( name, owner, str( e ) ) + log.exception( error_message ) test_result = dict( tool_shed=galaxy_tool_shed_url, name=name, owner=owner, 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: Dave Bouvier: Correct typo in test framework.
by commits-noreply＠bitbucket.org 23 Nov '13

23 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/13bd960b9414/ Changeset: 13bd960b9414 User: Dave Bouvier Date: 2013-11-23 06:37:44 Summary: Correct typo in test framework. Affected #: 1 file diff -r a73e13655a942f83d9c475d522a861fb32b0148d -r 13bd960b94141a2974d0c968c26fc046e05e1d14 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -506,7 +506,7 @@ ( str( dependency.name ), str( dependency.type ), str( dependency.version ), unicodify( dependency.error_message ) ) ) test_result = dict( type=dependency.type, name=dependency.name, - version=sdependency.version, + version=dependency.version, error_message=dependency.error_message ) repository_status_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) for dependency in repository.missing_repository_dependencies: 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: More fixes for the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 22 Nov '13

22 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a73e13655a94/ Changeset: a73e13655a94 User: greg Date: 2013-11-22 23:27:10 Summary: More fixes for the tool shed's install and test framework. Affected #: 1 file diff -r f7a0ac415489fb3d58f46872f4aa5f19712e6cab -r a73e13655a942f83d9c475d522a861fb32b0148d test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -504,19 +504,19 @@ for dependency in repository.missing_tool_dependencies: log.debug( 'Missing tool dependency %s of type %s version %s: %s' % \ ( str( dependency.name ), str( dependency.type ), str( dependency.version ), unicodify( dependency.error_message ) ) ) - test_result = dict( type=str( dependency.type ), - name=str( dependency.name ), - version=str( dependency.version ), - error_message=unicodify( dependency.error_message ) ) + test_result = dict( type=dependency.type, + name=dependency.name, + version=sdependency.version, + error_message=dependency.error_message ) repository_status_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) for dependency in repository.missing_repository_dependencies: log.debug( 'Missing repository dependency %s changeset revision %s owned by %s: %s' % \ ( str( dependency.name ), str( dependency.changeset_revision ), str( dependency.owner ), unicodify( dependency.error_message ) ) ) - test_result = dict( tool_shed=str( dependency.tool_shed ), - name=str( dependency.name ), - owner=str( dependency.owner ), - changeset_revision=str( dependency.changeset_revision ), - error_message=unicodify( dependency.error_message ) ) + test_result = dict( tool_shed=dependency.tool_shed, + name=dependency.name, + owner=dependency.owner, + changeset_revision=dependency.changeset_revision, + error_message=dependency.error_message ) repository_status_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) # Record the status of this repository in the tool shed. params = dict( tools_functionally_correct=False, @@ -727,7 +727,14 @@ try: results_dict = test_repository_tools( app, repository, repository_dict, repository_status_dict, results_dict ) except Exception, e: - log.exception( 'Error executing tests for repository %s: %s' % ( name, str( e ) ) ) + exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) + log.exception( exception_message ) + repository_status_dict[ 'failed_tests' ].append( exception_message ) + # Record the status of this repository in the tool shed. + params = dict( tools_functionally_correct=False, + do_not_test=False, + test_install_error=False ) + register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) total_repositories_tested += 1 results_dict[ 'total_repositories_tested' ] = total_repositories_tested @@ -909,7 +916,7 @@ register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed and passed functional tests.' % ( str( changeset_revision ), str( name ) ) ) else: - repository_status_dict[ 'failed_tests' ] = extract_log_data( result, from_tool_test=True ) + repository_status_dict[ 'failed_tests' ].append( extract_log_data( result, from_tool_test=True ) ) # Call the register_test_result method, which executes a PUT request to the repository_revisions API controller with the outcome # of the tests, and updates tool_test_results with the relevant log data. # This also sets the do_not_test and tools_functionally correct flags to the appropriate values, and updates the time_last_tested 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: More code cleanup, fixes and additional exception handling for the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 22 Nov '13

22 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f7a0ac415489/ Changeset: f7a0ac415489 User: greg Date: 2013-11-22 22:19:18 Summary: More code cleanup, fixes and additional exception handling for the tool shed's install and test framework. Affected #: 2 files diff -r 14746e61b979fcf17e9fc9039ce2f5bd5621790a -r f7a0ac415489fb3d58f46872f4aa5f19712e6cab lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -114,6 +114,10 @@ app.model.RepositoryMetadata.table.c.includes_tools == True, app.model.RepositoryMetadata.table.c.do_not_test == False, not_( app.model.RepositoryMetadata.table.c.id.in_( skip_metadata_ids ) ) ) ): + # Clear any old invalid tests for this metadata revision, since this could lead to duplication of invalid test rows, + # or tests incorrectly labeled as invalid. + missing_test_components = [] + repository = repository_metadata.repository records_checked += 1 # Create the repository_status dictionary, using the dictionary from the previous test run if available. if repository_metadata.tool_test_results: @@ -143,12 +147,12 @@ print '# Now checking revision %s of %s, owned by %s.' % ( changeset_revision, name, owner ) # If this changeset revision has no tools, we don't need to do anything here, the install and test script has a filter for returning # only repositories that contain tools. - tool_dicts = repository_metadata.get( 'tools', None ) + tool_dicts = metadata.get( 'tools', None ) if tool_dicts is not None: has_test_data = False testable_revision_found = False # Clone the repository up to the changeset revision we're checking. - repo_dir = repository_metadata.repository.repo_path( app ) + repo_dir = repository.repo_path( app ) repo = hg.repository( get_configured_ui(), repo_dir ) work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-cafr" ) cloned_ok, error_message = clone_repository( repo_dir, work_dir, changeset_revision ) diff -r 14746e61b979fcf17e9fc9039ce2f5bd5621790a -r f7a0ac415489fb3d58f46872f4aa5f19712e6cab test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -267,9 +267,9 @@ remove_generated_tests( app ) sa_session = app.model.context.current # The dict contains the only repository the app should have installed at this point. - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( repository_dict[ 'name' ], - repository_dict[ 'owner' ], - repository_dict[ 'changeset_revision' ] ) + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( str( repository_dict[ 'name' ] ), + str( repository_dict[ 'owner' ] ), + str( repository_dict[ 'changeset_revision' ] ) ) # We have to do this through Twill, in order to maintain app.toolbox and shed_tool_conf.xml in a state that is valid for future tests. for required_repository in repository.repository_dependencies: repository_dict = dict( name=required_repository.name, @@ -278,13 +278,13 @@ # Generate a test method to uninstall this repository through the embedded Galaxy application's web interface. test_install_repositories.generate_deactivate_or_uninstall_method( repository_dict, deactivate=True ) log.debug( 'Changeset revision %s of %s repository %s selected for deactivation.' % \ - ( required_repository.changeset_revision, required_repository.status, required_repository.name ) ) + ( str( required_repository.changeset_revision ), str( required_repository.status ), str( required_repository.name ) ) ) repository_dict = dict( name=repository.name, owner=repository.owner, changeset_revision=repository.changeset_revision ) test_install_repositories.generate_deactivate_or_uninstall_method( repository_dict, deactivate=True ) log.debug( 'Changeset revision %s of %s repository %s selected for deactivation.' % \ - ( repository.changeset_revision, repository.status, repository.name ) ) + ( str( repository.changeset_revision ), str( repository.status ), str( repository.name ) ) ) # Set up nose to run the generated uninstall method as a functional test. test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) test_config.configure( sys.argv ) @@ -292,7 +292,8 @@ # repository and delete it from disk. result, _ = run_tests( test_config ) success = result.wasSuccessful() - return success + if not success: + log.debug( 'Failed deactivation of repository %s.' % str( repository.name ) ) def extract_log_data( test_result, from_tool_test=True ): '''Extract any useful data from the test_result.failures and test_result.errors attributes.''' @@ -411,15 +412,6 @@ error_message = '' latest_revision_only = '-check_all_revisions' not in sys.argv repository_dicts = [] - results_dict = {} - # We are testing deprecated repositories because it is possible that a deprecated repository contains valid tools that - # someone has previously installed. Deleted repositories have never been installed, so should not be tested. If they are - # undeleted, this script will then test them the next time it runs. We don't need to check if a repository has been deleted - # here because our call to the Tool Shed API filters by downloadable='true', in which case deleted will always be False. - if os.path.exists( exclude_list_file ): - log.debug( 'Loading the list of repositories excluded from testing from the file %s...', exclude_list_file ) - exclude_list = parse_exclude_list( exclude_list_file ) - results_dict[ 'exclude_list' ] = exclude_list params = urllib.urlencode( dict( do_not_test='false', downloadable='true', malicious='false', @@ -502,61 +494,53 @@ return {}, error_message return tool_test_results, error_message -def handle_missing_dependencies( app, repository, metadata_revision_id, missing_tool_dependencies, repository_dict, repository_status_dict, results_dict ): +def handle_missing_dependencies( app, repository, missing_tool_dependencies, repository_dict, repository_status_dict, results_dict ): """Handle missing repository or tool dependencies for an installed repository.""" # If a tool dependency fails to install correctly, this should be considered an installation error, # and functional tests should be skipped, since the tool dependency needs to be correctly installed # for the test to be considered reliable. log.debug( 'The following dependencies of this repository are missing, so skipping functional tests.' ) - params = {} # In keeping with the standard display layout, add the error message to the dict for each tool individually. for dependency in repository.missing_tool_dependencies: log.debug( 'Missing tool dependency %s of type %s version %s: %s' % \ ( str( dependency.name ), str( dependency.type ), str( dependency.version ), unicodify( dependency.error_message ) ) ) - test_result = dict( type=dependency.type, - name=dependency.name, - version=dependency.version, - error_message=dependency.error_message ) + test_result = dict( type=str( dependency.type ), + name=str( dependency.name ), + version=str( dependency.version ), + error_message=unicodify( dependency.error_message ) ) repository_status_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) for dependency in repository.missing_repository_dependencies: log.debug( 'Missing repository dependency %s changeset revision %s owned by %s: %s' % \ ( str( dependency.name ), str( dependency.changeset_revision ), str( dependency.owner ), unicodify( dependency.error_message ) ) ) - test_result = dict( tool_shed=dependency.tool_shed, - name=dependency.name, - owner=dependency.owner, - changeset_revision=dependency.changeset_revision, - error_message=dependency.error_message ) + test_result = dict( tool_shed=str( dependency.tool_shed ), + name=str( dependency.name ), + owner=str( dependency.owner ), + changeset_revision=str( dependency.changeset_revision ), + error_message=unicodify( dependency.error_message ) ) repository_status_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) # Record the status of this repository in the tool shed. - params[ 'tools_functionally_correct' ] = False - params[ 'do_not_test' ] = False - params[ 'test_install_error' ] = True - register_test_result( galaxy_tool_shed_url, - metadata_revision_id, - repository_status_dict, - repository_dict, - params ) - # Since this repository is missing components, we do not want to test it. Deactivate this repository. + params = dict( tools_functionally_correct=False, + do_not_test=False, + test_install_error=True ) + register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) + # Since this repository is missing components, we do not want to test it, so deactivate it or uninstall it. # The deactivate flag is set to True if the environment variable GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES # is set to 'true'. deactivate = asbool( os.environ.get( 'GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES', False ) ) if deactivate: - log.debug( 'Due to the above missing tool dependencies, we are now uninstalling the following tool dependencies but not changing their repositories.' ) for missing_tool_dependency in missing_tool_dependencies: uninstall_tool_dependency( app, missing_tool_dependency ) # We are deactivating this repository and all of its repository dependencies. - log.debug( 'Due to the above missing repository dependencies, we are now deactivating the following repositories.' ) deactivate_repository( app, repository_dict ) else: # We are uninstalling this repository and all of its repository dependencies. - log.debug( 'Due to the above missing repository dependencies, we are now uninstalling the following repositories.' ) uninstall_repository( app, repository_dict ) results_dict[ 'repositories_failed_install' ].append( dict( name=str( repository.name ), owner=str( repository.owner ), changeset_revision=str( repository.changeset_revision ) ) ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox - return repository_status_dict, results_dict + return results_dict def initialize_results_dict(): # Initialize a dictionary for the summary that will be printed to stdout. @@ -565,7 +549,6 @@ results_dict[ 'repositories_passed' ] = [] results_dict[ 'repositories_failed' ] = [] results_dict[ 'repositories_failed_install' ] = [] - results_dict[ 'exclude_list' ] = [] return results_dict def install_repository( app, repository_dict ): @@ -596,15 +579,32 @@ return repository, error_message def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): + results_dict = initialize_results_dict() error_message = '' # Allow the option to keep or delete tool dependencies when a repository has been tested. deactivate = asbool( os.environ.get( 'GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES', False ) ) # Initialize a dictionary for the summary that will be printed to stdout. - results_dict = initialize_results_dict() total_repositories_tested = results_dict[ 'total_repositories_tested' ] repositories_to_install, error_message = get_repositories_to_install( galaxy_tool_shed_url ) if error_message: return None, error_message + # Handle repositories not to be tested. + if os.path.exists( exclude_list_file ): + # Entries in the exclude_list look something like this. + # { 'reason': The default reason or the reason specified in this section, + # 'repositories': + # [( name, owner, changeset revision if changeset revision else None ), + # ( name, owner, changeset revision if changeset revision else None )] } + # If changeset revision is None, that means the entire repository is excluded from testing, otherwise only the specified + # revision should be skipped. + # We are testing deprecated repositories because it is possible that a deprecated repository contains valid tools that + # someone has previously installed. Deleted repositories have never been installed, so should not be tested. If they are + # undeleted, this script will then test them the next time it runs. We don't need to check if a repository has been deleted + # here because our call to the Tool Shed API filters by downloadable='true', in which case deleted will always be False. + log.debug( 'Loading the list of repositories excluded from testing from the file %s...', exclude_list_file ) + exclude_list = parse_exclude_list( exclude_list_file ) + else: + exclude_list = [] # Generate a test method that will use Twill to install each repository into the embedded Galaxy application that was # started up, installing repository and tool dependencies. Upon successful installation, generate a test case for each # functional test defined for each tool in the repository and execute the test cases. Record the result of the tests. @@ -629,14 +629,13 @@ # "tool_shed_url": "http://toolshed.local:10001", # "url": "/api/repository_revisions/529fd61ab1c6cc36", # "user_id": "529fd61ab1c6cc36" } - params = {} - changeset_revision = repository_dict.get( 'changeset_revision', None ) metadata_revision_id = repository_dict.get( 'id', None ) # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. repository_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url # Get the name and owner out of the repository info dict. name = str( repository_dict[ 'name' ] ) owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) # Populate the repository_status_dict. repository_status_dict, error_message = get_tool_test_results_from_api( galaxy_tool_shed_url, metadata_revision_id ) if error_message: @@ -651,15 +650,7 @@ repository_status_dict[ 'failed_tests' ] = [] repository_status_dict[ 'skip_reason' ] = None repository_status_dict[ 'installation_errors' ] = dict( current_repository=[], repository_dependencies=[], tool_dependencies=[] ) - # Handle repositories not to be tested. - exclude_list = results_dict[ 'exclude_list' ] - # Entries in the exclude_list look something like this. - # { 'reason': The default reason or the reason specified in this section, - # 'repositories': - # [( name, owner, changeset revision if changeset revision else None ), - # ( name, owner, changeset revision if changeset revision else None )] } - # If changeset revision is None, that means the entire repository is excluded from testing, otherwise only the specified - # revision should be skipped. + # See if this repository should be skipped for any reason. skip_this_repository = False skip_reason = None for exclude_dict in exclude_list: @@ -671,10 +662,10 @@ break if skip_this_repository: repository_status_dict[ 'not_tested' ] = dict( reason=skip_reason ) - params[ 'tools_functionally_correct' ] = False - params[ 'do_not_test' ] = False - register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status_dict, repository_dict, params ) - log.debug( "Not testing revision %s of repository %s owned by %s." % ( str( changeset_revision ), str( name ), str( owner ) ) ) + params = dict( tools_functionally_correct=False, + do_not_test=False ) + register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) + log.debug( "Not testing revision %s of repository %s owned by %s." % ( changeset_revision, name, owner ) ) else: repository, error_message = install_repository( app, repository_dict ) if error_message: @@ -693,26 +684,19 @@ changeset_revision=changeset_revision, error_message=error_message ) repository_status_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) - params[ 'tools_functionally_correct' ] = False - params[ 'test_install_error' ] = True - params[ 'do_not_test' ] = False - register_test_result( galaxy_tool_shed_url, - metadata_revision_id, - repository_status_dict, - repository_dict, - params ) + params = dict( tools_functionally_correct=False, + test_install_error=True, + do_not_test=False ) + register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) try: if deactivate: # We are deactivating this repository and all of its repository dependencies. - success = deactivate_repository( app, repository_dict ) + deactivate_repository( app, repository_dict ) else: # We are uninstalling this repository and all of its repository dependencies. - success = uninstall_repository( app, repository_dict ) + uninstall_repository( app, repository_dict ) except: - log.exception( 'Encountered error attempting to deactivate or uninstall %s.', repository_dict[ 'name' ] ) - success = False - if not success: - log.error( 'Repository %s failed to uninstall.', name ) + log.exception( 'Encountered error attempting to deactivate or uninstall %s.', str( repository_dict[ 'name' ] ) ) results_dict[ 'repositories_failed_install' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) log.debug( 'Repository %s failed to install correctly.' % str( name ) ) else: @@ -729,25 +713,22 @@ repository_status_dict[ 'missing_test_components' ] = [] missing_tool_dependencies = get_missing_tool_dependencies( repository ) if missing_tool_dependencies or repository.missing_repository_dependencies: - repository_status_dict, results_dict = handle_missing_dependencies( app, - repository, - metadata_revision_id, - missing_tool_dependencies, - repository_dict, - repository_status_dict, - results_dict ) + results_dict = handle_missing_dependencies( app, + repository, + missing_tool_dependencies, + repository_dict, + repository_status_dict, + results_dict ) else: # If the repository has a test-data directory we write the generated shed_tools_dict to a file, so the functional # test framework can find it. file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) log.debug( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( str( galaxy_shed_tools_dict ), str( shed_tools_dict ) ) ) - params, repository_status_dict, results_dict = test_repository_tools( app, - repository, - params, - metadata_revision_id, - repository_dict, - repository_status_dict, - results_dict ) + try: + results_dict = test_repository_tools( app, repository, repository_dict, repository_status_dict, results_dict ) + except Exception, e: + log.exception( 'Error executing tests for repository %s: %s' % ( name, str( e ) ) ) + results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) total_repositories_tested += 1 results_dict[ 'total_repositories_tested' ] = total_repositories_tested return results_dict, error_message @@ -805,17 +786,20 @@ log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) ) return exclude_list -def register_test_result( url, metadata_id, test_results_dict, repository_dict, params ): +def register_test_result( url, test_results_dict, repository_dict, params ): """Update the repository metadata tool_test_results and appropriate flags using the API.""" - params[ 'tool_test_results' ] = test_results_dict if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: return {} else: - url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', metadata_id ) ) - return update( tool_shed_api_key, - url, - params, - return_formatted=False ) + metadata_revision_id = repository_dict.get( 'id', None ) + if metadata_revision_id is not None: + params[ 'tool_test_results' ] = test_results_dict + url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) + try: + return update( tool_shed_api_key, url, params, return_formatted=False ) + except Exception, e: + log.exception( 'Error attempting to register test results: %s' % str( e ) ) + return {} def remove_generated_tests( app ): """ @@ -885,7 +869,8 @@ for repository in repositories_by_owner[ owner ]: print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) -def test_repository_tools( app, repository, params, metadata_revision_id, repository_dict, repository_status_dict, results_dict ): +def test_repository_tools( app, repository, repository_dict, repository_status_dict, results_dict ): + """Test tools contained in the received repository.""" name = str( repository.name ) owner = str( repository.owner ) changeset_revision = str( repository.changeset_revision ) @@ -918,14 +903,10 @@ # controller with the status of the test. This also sets the do_not_test and tools_functionally correct flags, and # updates the time_last_tested field to today's date. results_dict[ 'repositories_passed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - params[ 'tools_functionally_correct' ] = True - params[ 'do_not_test' ] = False - params[ 'test_install_error' ] = False - register_test_result( galaxy_tool_shed_url, - metadata_revision_id, - repository_status_dict, - repository_dict, - params ) + params = dict( tools_functionally_correct=True, + do_not_test=False, + test_install_error=False ) + register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed and passed functional tests.' % ( str( changeset_revision ), str( name ) ) ) else: repository_status_dict[ 'failed_tests' ] = extract_log_data( result, from_tool_test=True ) @@ -935,14 +916,10 @@ # field to today's date. results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_dict ) - params[ 'tools_functionally_correct' ] = False - params[ 'test_install_error' ] = False - params[ 'do_not_test' ] = str( set_do_not_test ) - register_test_result( galaxy_tool_shed_url, - metadata_revision_id, - repository_status_dict, - repository_dict, - params ) + params = dict( tools_functionally_correct=False, + test_install_error=False, + do_not_test=str( set_do_not_test ) ) + register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed successfully but did not pass functional tests.' % \ ( str( changeset_revision ), str( name ) ) ) # Run the uninstall method. This removes tool functional test methods from the test_toolbox module and uninstalls the @@ -951,25 +928,26 @@ if deactivate: log.debug( 'Deactivating changeset revision %s of repository %s' % ( str( changeset_revision ), str( name ) ) ) # We are deactivating this repository and all of its repository dependencies. - success = deactivate_repository( app, repository_dict ) + deactivate_repository( app, repository_dict ) else: log.debug( 'Uninstalling changeset revision %s of repository %s' % ( str( changeset_revision ), str( name ) ) ) # We are uninstalling this repository and all of its repository dependencies. - success = uninstall_repository( app, repository_dict ) - if not success: - log.debug( 'Repository %s failed to uninstall.' % str( name ) ) + uninstall_repository( app, repository_dict ) + # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox - return params, repository_status_dict, results_dict + return results_dict def uninstall_repository( app, repository_dict ): + """Attempt to uninstall a repository.""" + sa_session = app.model.context.current # Clean out any generated tests. This is necessary for Twill. remove_generated_tests( app ) - sa_session = app.model.context.current # The dict contains the only repository the app should have installed at this point. - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( repository_dict[ 'name' ], - repository_dict[ 'owner' ], - repository_dict[ 'changeset_revision' ] ) + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) # We have to do this through Twill, in order to maintain app.toolbox and shed_tool_conf.xml in a state that is valid for future tests. for required_repository in repository.repository_dependencies: repository_dict = dict( name=str( required_repository.name ), @@ -979,12 +957,9 @@ test_install_repositories.generate_deactivate_or_uninstall_method( repository_dict, deactivate=False ) log.debug( 'Changeset revision %s of %s repository %s selected for uninstallation.' % \ ( str( required_repository.changeset_revision ), str( required_repository.status ), str( required_repository.name ) ) ) - repository_dict = dict( name=str( repository.name ), - owner=str( repository.owner ), - changeset_revision=str( repository.changeset_revision ) ) + repository_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) test_install_repositories.generate_deactivate_or_uninstall_method( repository_dict, deactivate=False ) - log.debug( 'Changeset revision %s of %s repository %s selected for uninstallation.' % \ - ( str( repository.changeset_revision ), str( repository.status ), str( repository.name ) ) ) + log.debug( 'Changeset revision %s of %s repository %s selected for uninstallation.' % ( changeset_revision, str( repository.status ), name ) ) # Set up nose to run the generated uninstall method as a functional test. test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) test_config.configure( sys.argv ) @@ -992,9 +967,12 @@ # repository and delete it from disk. result, _ = run_tests( test_config ) success = result.wasSuccessful() - return success + if not success: + log.debug( 'Repository %s failed to uninstall.' % str( name ) ) def uninstall_tool_dependency( app, tool_dependency ): + """Attempt to uninstall a tool dependency.""" + sa_session = app.model.context.current # Clean out any generated tests. This is necessary for Twill. tool_dependency_install_path = tool_dependency.installation_directory( app ) uninstalled, error_message = tool_dependency_util.remove_tool_dependency( app, tool_dependency ) @@ -1003,7 +981,6 @@ log.debug( error_message ) else: log.debug( 'Successfully removed tool dependency installation directory: %s' % str( tool_dependency_install_path ) ) - sa_session = app.model.context.current if not uninstalled or tool_dependency.status != app.model.ToolDependency.installation_status.UNINSTALLED: tool_dependency.status = app.model.ToolDependency.installation_status.UNINSTALLED sa_session.add( tool_dependency ) @@ -1213,7 +1190,6 @@ repositories_passed = results_dict[ 'repositories_passed' ] repositories_failed = results_dict[ 'repositories_failed' ] repositories_failed_install = results_dict[ 'repositories_failed_install' ] - exclude_list = results_dict[ 'exclude_list' ] now = strftime( "%Y-%m-%d %H:%M:%S" ) print "####################################################################################" print "# %s - repository installation and testing script completed." % now Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: Dave Bouvier: Fix undefined variable.
by commits-noreply＠bitbucket.org 22 Nov '13

22 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/14746e61b979/ Changeset: 14746e61b979 User: Dave Bouvier Date: 2013-11-22 20:52:28 Summary: Fix undefined variable. Affected #: 1 file diff -r 31138346d9ecb87887223e7940877b7949059a56 -r 14746e61b979fcf17e9fc9039ce2f5bd5621790a test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -508,6 +508,7 @@ # and functional tests should be skipped, since the tool dependency needs to be correctly installed # for the test to be considered reliable. log.debug( 'The following dependencies of this repository are missing, so skipping functional tests.' ) + params = {} # In keeping with the standard display layout, add the error message to the dict for each tool individually. for dependency in repository.missing_tool_dependencies: log.debug( 'Missing tool dependency %s of type %s version %s: %s' % \ 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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