February 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: guerler: Merge
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/057069969de0/ Changeset: 057069969de0 User: guerler Date: 2014-02-19 19:18:37 Summary: Merge Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Grids: Fix negative page numbers
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0770af01a257/ Changeset: 0770af01a257 Branch: stable User: guerler Date: 2014-02-19 19:16:36 Summary: Grids: Fix negative page numbers Affected #: 2 files diff -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc -r 0770af01a257818ee82f11a191d4305880ea0b91 static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -847,7 +847,7 @@ var page_link_range = num_page_links / 2; var min_page = cur_page_num - page_link_range var min_offset = 0; - if (min_page == 0) { + if (min_page <= 0) { // Min page is too low. min_page = 1; min_offset = page_link_range - ( cur_page_num - min_page ); diff -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc -r 0770af01a257818ee82f11a191d4305880ea0b91 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;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,advanced_search: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,advanced_search:this.attributes.advanced_search};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},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(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")})})},handle_refresh:function(c){if(c){if($.inArray("history",c)>-1){if(top.Galaxy&&top.Galaxy.currHistoryPanel){top.Galaxy.currHistoryPanel.loadCurrentHistory()}}}},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;this.handle_refresh(d.refresh_frames);var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));if(d.use_hide_message){setTimeout(function(){$("#grid-message").html("")},5000)}}this.init_grid_elements();init_refresh_on_change()},init_grid_controls:function(){$(".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=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});var d=$("#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 s=$(this).find("input.grid-row-select-checkbox");var r=$(this).find("span.grid-selected-count");var t=function(){r.text($(s).filter(":checked").length)};$(s).each(function(){$(this).change(t)});t()});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}var q=this.grid.attributes;var p=this;$(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=$("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(t){t.preventDefault();var s=$(t.target).html();var r=this.findItemByHtml(s);p.execute(r)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$("<span>"+g+"<a href='javascript:void(0);'><span class='delete-search-icon' /></span></a>");f.addClass("text-filter-val");var d=this;f.click(function(){d.grid.remove_filter(e,g);$(this).remove();d.go_page_one();d.execute()});var c=$("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},set_sort_condition:function(h){var g=this.grid.get("sort_key");var f=h;if(g.indexOf(h)!==-1){if(g.substring(0,1)!=="-"){f="-"+h}else{}}$(".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;$("."+e+"-filter").each(function(){var m=$.trim($(this).text());var k=d[m];var l=k[e];if(l==g){$(this).empty();$(this).addClass("current-filter");$(this).append(m)}else{if(l==f){$(this).empty();var h=$("<a href='#'>"+m+"</a>");h.click(function(){c.set_categorical_filter(e,l)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;$(".page-link").each(function(){var k=$(this).attr("id"),g=parseInt(k.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($(this).val())});this.execute({operation:d,id:c,confirmation_text:g});return true},execute:function(n){var f=null;var e=null;var g=null;var c=null;var m=null;if(n){e=n.href;g=n.operation;f=n.id;c=n.confirmation_text;m=n.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var l=e.split("?");if(l.length>1){var k=l[1];var d=k.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"&&c!="null"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(m,"")}return false}if(e){this.go_to(m,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(m,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);advanced_search=$("#advanced-search").is(":visible");this.grid.set("advanced_search",advanced_search);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(e){c.init_grid($.parseJSON(e));$(".loading-elt-overlay").hide()},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)}},template_body:function(t){var m="";var u=0;var g=t.items.length;if(g==0){m+='<tr><td colspan="100"><em>No Items</em></td></tr>';u=1}for(var h in t.items){var r=t.items[h];var c=r.encode_id;var k="grid-"+h+"-popup";m+="<tr ";if(t.current_item_id==r.id){m+='class="current"'}m+=">";if(t.show_item_checkboxes){m+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+c+'" id="'+c+'" class="grid-row-select-checkbox" /></td>'}for(j in t.columns){var f=t.columns[j];if(f.visible){var e="";if(f.nowrap){e='style="white-space:nowrap;"'}var s=r.column_config[f.label];var l=s.link;var n=s.value;var q=s.inbound;if(jQuery.type(n)==="string"){n=n.replace(/\/\//g,"/")}var d="";var p="";if(f.attach_popup){d="grid-"+h+"-popup";p="menubutton";if(l!=""){p+=" split"}p+=" popup"}m+="<td "+e+">";if(l){if(t.operations.length!=0){m+='<div id="'+d+'" class="'+p+'" style="float: left;">'}var o="";if(q){o="use-inbound"}else{o="use-outbound"}m+='<a class="label '+o+'" href="'+l+'" onclick="return false;">'+n+"</a>";if(t.operations.length!=0){m+="</div>"}}else{m+='<div id="'+d+'" class="'+p+'"><label id="'+f.label_id_prefix+c+'" for="'+c+'">'+n+"</label></div>"}m+="</td>"}}m+="</tr>";u++}return m},template_footer:function(q){var m="";if(q.use_paging&&q.num_pages>1){var o=q.num_page_links;var c=q.cur_page_num;var p=q.num_pages;var l=o/2;var k=c-l;var g=0;if(k==0){k=1;g=l-(c-k)}var f=l+g;var e=c+f;if(e<=p){max_offset=0}else{e=p;max_offset=f-(e+1-c)}if(max_offset!=0){k-=max_offset;if(k<1){k=1}}m+='<tr id="page-links-row">';if(q.show_item_checkboxes){m+="<td></td>"}m+='<td colspan="100"><span id="page-link-container">Page:';if(k>1){m+='<span class="page-link" id="page-link-1"><a href="'+this.grid.get_url({page:n})+'" page_num="1" onclick="return false;">1</a></span> ...'}for(var n=k;n<e+1;n++){if(n==q.cur_page_num){m+='<span class="page-link inactive-link" id="page-link-'+n+'">'+n+"</span>"}else{m+='<span class="page-link" id="page-link-'+n+'"><a href="'+this.grid.get_url({page:n})+'" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}}if(e<p){m+='...<span class="page-link" id="page-link-'+p+'"><a href="'+this.grid.get_url({page:p})+'" onclick="return false;" page_num="'+p+'">'+p+"</a></span>"}m+="</span>";m+='<span class="page-link" id="show-all-link-span"> | <a href="'+this.grid.get_url({page:"all"})+'" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(q.show_item_checkboxes){m+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView:b}}); \ 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,advanced_search: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,advanced_search:this.attributes.advanced_search};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},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(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")})})},handle_refresh:function(c){if(c){if($.inArray("history",c)>-1){if(top.Galaxy&&top.Galaxy.currHistoryPanel){top.Galaxy.currHistoryPanel.loadCurrentHistory()}}}},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;this.handle_refresh(d.refresh_frames);var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));if(d.use_hide_message){setTimeout(function(){$("#grid-message").html("")},5000)}}this.init_grid_elements();init_refresh_on_change()},init_grid_controls:function(){$(".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=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});var d=$("#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 s=$(this).find("input.grid-row-select-checkbox");var r=$(this).find("span.grid-selected-count");var t=function(){r.text($(s).filter(":checked").length)};$(s).each(function(){$(this).change(t)});t()});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}var q=this.grid.attributes;var p=this;$(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=$("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(t){t.preventDefault();var 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selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView: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.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d270d3cf7627/ Changeset: d270d3cf7627 Branch: stable User: greg Date: 2014-02-19 19:05:25 Summary: Make managing an in-memory registry of bi-directional installed repository dependency relationships a configurable option for Galaxy instances. Affected #: 6 files diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -95,6 +95,7 @@ self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) ) + self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', True ) ) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) self.hours_between_check = kwargs.get( 'hours_between_check', 12 ) try: diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -271,9 +271,10 @@ if remove_from_disk_checked: tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.UNINSTALLED tool_shed_repository.error_message = None - # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the - # installed_repository_manager. - trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository ) + if trans.app.config.manage_dependency_relationships: + # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the + # installed_repository_manager. + trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository ) else: tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.DEACTIVATED trans.install_model.context.add( tool_shed_repository ) diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -62,8 +62,9 @@ # whose values are a list of tuples defining tool_dependency objects (whose status is 'Installed') that require the key # at runtime. The value defines the entire tool dependency tree. self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {} - # Load defined dependency relationships for installed tool shed repositories and their contents. - self.load_dependency_relationships() + if app.config.manage_dependency_relationships: + # Load defined dependency relationships for installed tool shed repositories and their contents. + self.load_dependency_relationships() def add_entry_to_installed_repository_dependencies_of_installed_repositories( self, repository ): """ diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -602,8 +602,9 @@ suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.install_model.ToolShedRepository.installation_status.INSTALLED ) - # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager. - trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository ) + if trans.app.config.manage_dependency_relationships: + # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager. + trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository ) else: # An error occurred while cloning the repository, so reset everything necessary to enable another attempt. set_repository_attributes( trans, diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -507,8 +507,9 @@ if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED, app.install_model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) - # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. - app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + if app.config.manage_dependency_relationships: + # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. + app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) elif elem.tag == 'set_environment': # <set_environment version="1.0"> # <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -152,6 +152,11 @@ #enable_tool_shed_check = False #hours_between_check = 12 +# Enable use of an in-memory registry with bi-directional relationships +# between repositories (i.e., in addition to lists of dependencies for a +# repository, keep an in-memory registry of dependent items for each repository. +#manage_dependency_relationships = True + # XML config file that contains data table entries for the ToolDataTableManager. This file is manually # maintained by the Galaxy administrator. #tool_data_table_config_path = tool_data_table_conf.xml https://bitbucket.org/galaxy/galaxy-central/commits/ef0654f99261/ Changeset: ef0654f99261 User: inithello Date: 2014-02-19 19:09:03 Summary: Merge bugfix from stable. Affected #: 1 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: greg: Make managing an in-memory registry of bi-directional installed repository dependency relationships a configurable option for Galaxy instances.
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4df1be355e4f/ Changeset: 4df1be355e4f User: greg Date: 2014-02-19 19:05:25 Summary: Make managing an in-memory registry of bi-directional installed repository dependency relationships a configurable option for Galaxy instances. Affected #: 6 files diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -95,6 +95,7 @@ self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) ) + self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', True ) ) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) self.hours_between_check = kwargs.get( 'hours_between_check', 12 ) try: diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -271,9 +271,10 @@ if remove_from_disk_checked: tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.UNINSTALLED tool_shed_repository.error_message = None - # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the - # installed_repository_manager. - trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository ) + if trans.app.config.manage_dependency_relationships: + # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the + # installed_repository_manager. + trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository ) else: tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.DEACTIVATED trans.install_model.context.add( tool_shed_repository ) diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -62,8 +62,9 @@ # whose values are a list of tuples defining tool_dependency objects (whose status is 'Installed') that require the key # at runtime. The value defines the entire tool dependency tree. self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {} - # Load defined dependency relationships for installed tool shed repositories and their contents. - self.load_dependency_relationships() + if app.config.manage_dependency_relationships: + # Load defined dependency relationships for installed tool shed repositories and their contents. + self.load_dependency_relationships() def add_entry_to_installed_repository_dependencies_of_installed_repositories( self, repository ): """ diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -602,8 +602,9 @@ suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.install_model.ToolShedRepository.installation_status.INSTALLED ) - # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager. - trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository ) + if trans.app.config.manage_dependency_relationships: + # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager. + trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository ) else: # An error occurred while cloning the repository, so reset everything necessary to enable another attempt. set_repository_attributes( trans, diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -507,8 +507,9 @@ if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED, app.install_model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) - # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. - app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + if app.config.manage_dependency_relationships: + # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. + app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) elif elem.tag == 'set_environment': # <set_environment version="1.0"> # <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -152,6 +152,11 @@ #enable_tool_shed_check = False #hours_between_check = 12 +# Enable use of an in-memory registry with bi-directional relationships +# between repositories (i.e., in addition to lists of dependencies for a +# repository, keep an in-memory registry of dependent items for each repository. +#manage_dependency_relationships = True + # XML config file that contains data table entries for the ToolDataTableManager. This file is manually # maintained by the Galaxy administrator. #tool_data_table_config_path = tool_data_table_conf.xml 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: 3 new changesets
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1298d3f6aca5/ Changeset: 1298d3f6aca5 Branch: stable User: natefoo Date: 2014-02-19 19:00:33 Summary: Stop jobs when all output datasets are deleted via the API. Affected #: 3 files diff -r 44968207ddd283d0023c72e3d25fd39b1c71eb99 -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -849,6 +849,18 @@ break return job + def stop_hda_creating_job( self, hda ): + """ + Stops an HDA's creating job if all the job's other outputs are deleted. + """ + if hda.parent_id is None and len( hda.creating_job_associations ) > 0: + # Mark associated job for deletion + job = hda.creating_job_associations[0].job + if job.state in [ self.app.model.Job.states.QUEUED, self.app.model.Job.states.RUNNING, self.app.model.Job.states.NEW ]: + # Are *all* of the job's other output datasets deleted? + if job.check_if_output_datasets_deleted(): + job.mark_deleted( self.app.config.track_jobs_in_database ) + self.app.job_manager.job_stop_queue.put( job.id ) class UsesLibraryMixin: diff -r 44968207ddd283d0023c72e3d25fd39b1c71eb99 -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -278,6 +278,8 @@ # get_dataset can return a string during an error if hda and isinstance( hda, trans.model.HistoryDatasetAssociation ): changed = self.set_hda_from_dict( trans, hda, payload ) + if payload.get( 'deleted', False ): + self.stop_hda_creating_job( hda ) except Exception, exception: log.error( 'Update of history (%s), HDA (%s) failed: %s', history_id, id, str( exception ), exc_info=True ) @@ -347,6 +349,8 @@ trans.sa_session.flush() rval[ 'purged' ] = True + self.stop_hda_creating_job( hda ) + trans.sa_session.flush() rval[ 'deleted' ] = True diff -r 44968207ddd283d0023c72e3d25fd39b1c71eb99 -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -839,14 +839,7 @@ hda.mark_deleted() hda.clear_associated_files() trans.log_event( "Dataset id %s marked as deleted" % str(id) ) - if hda.parent_id is None and len( hda.creating_job_associations ) > 0: - # Mark associated job for deletion - job = hda.creating_job_associations[0].job - if job.state in [ self.app.model.Job.states.QUEUED, self.app.model.Job.states.RUNNING, self.app.model.Job.states.NEW ]: - # Are *all* of the job's other output datasets deleted? - if job.check_if_output_datasets_deleted(): - job.mark_deleted( self.app.config.track_jobs_in_database ) - self.app.job_manager.job_stop_queue.put( job.id ) + self.stop_hda_creating_job( hda ) trans.sa_session.flush() except Exception, e: msg = 'HDA deletion failed (encoded: %s, decoded: %s)' % ( dataset_id, id ) https://bitbucket.org/galaxy/galaxy-central/commits/0db8172d6d36/ Changeset: 0db8172d6d36 User: natefoo Date: 2014-02-19 19:01:03 Summary: merge. Affected #: 3 files diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -892,6 +892,18 @@ break return job + def stop_hda_creating_job( self, hda ): + """ + Stops an HDA's creating job if all the job's other outputs are deleted. + """ + if hda.parent_id is None and len( hda.creating_job_associations ) > 0: + # Mark associated job for deletion + job = hda.creating_job_associations[0].job + if job.state in [ self.app.model.Job.states.QUEUED, self.app.model.Job.states.RUNNING, self.app.model.Job.states.NEW ]: + # Are *all* of the job's other output datasets deleted? + if job.check_if_output_datasets_deleted(): + job.mark_deleted( self.app.config.track_jobs_in_database ) + self.app.job_manager.job_stop_queue.put( job.id ) class UsesLibraryMixin: diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -280,6 +280,8 @@ # get_dataset can return a string during an error if hda and isinstance( hda, trans.model.HistoryDatasetAssociation ): changed = self.set_hda_from_dict( trans, hda, payload ) + if payload.get( 'deleted', False ): + self.stop_hda_creating_job( hda ) except Exception, exception: log.error( 'Update of history (%s), HDA (%s) failed: %s', history_id, id, str( exception ), exc_info=True ) @@ -349,6 +351,8 @@ trans.sa_session.flush() rval[ 'purged' ] = True + self.stop_hda_creating_job( hda ) + trans.sa_session.flush() rval[ 'deleted' ] = True diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -839,14 +839,7 @@ hda.mark_deleted() hda.clear_associated_files() trans.log_event( "Dataset id %s marked as deleted" % str(id) ) - if hda.parent_id is None and len( hda.creating_job_associations ) > 0: - # Mark associated job for deletion - job = hda.creating_job_associations[0].job - if job.state in [ self.app.model.Job.states.QUEUED, self.app.model.Job.states.RUNNING, self.app.model.Job.states.NEW ]: - # Are *all* of the job's other output datasets deleted? - if job.check_if_output_datasets_deleted(): - job.mark_deleted( self.app.config.track_jobs_in_database ) - self.app.job_manager.job_stop_queue.put( job.id ) + self.stop_hda_creating_job( hda ) trans.sa_session.flush() except Exception, e: msg = 'HDA deletion failed (encoded: %s, decoded: %s)' % ( dataset_id, id ) https://bitbucket.org/galaxy/galaxy-central/commits/e51429649b44/ Changeset: e51429649b44 User: natefoo Date: 2014-02-19 19:02:12 Summary: merge. Affected #: 6 files diff -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -843,35 +843,6 @@ history. <br>You can <a href="%s">continue and import this history</a> or %s. """ % ( web.url_for(controller='history', action='imp', id=id, confirm=True, referer=trans.request.referer ), referer_message ), use_panels=True ) - # Replaced with view (below) but kept (available via manual URL editing) for now - @web.expose - def original_view( self, trans, id=None, show_deleted=False, use_panels=True ): - """View a history. If a history is importable, then it is viewable by any user.""" - # Get history to view. - if not id: - return trans.show_error_message( "You must specify a history you want to view." ) - history_to_view = self.get_history( trans, id, False) - # Integrity checks. - if not history_to_view: - return trans.show_error_message( "The specified history does not exist." ) - # Admin users can view any history - if( ( history_to_view.user != trans.user ) - and ( not trans.user_is_admin() ) - and ( not history_to_view.importable ) ): - error( "Either you are not allowed to view this history or the owner of this history has not made it accessible." ) - # View history. - show_deleted = galaxy.util.string_as_bool( show_deleted ) - datasets = self.get_history_datasets( trans, history_to_view, show_deleted=show_deleted ) - try: - use_panels = galaxy.util.string_as_bool( use_panels ) - except: - pass # already a bool - return trans.stream_template_mako( "history/original_view.mako", - history = history_to_view, - datasets = datasets, - show_deleted = show_deleted, - use_panels = use_panels ) - @web.expose def view( self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True ): """ diff -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -783,77 +783,110 @@ * }); * $( '.myElement' ).modeButton( 'callModeFn', 'bler' ); */ + /** constructor */ function ModeButton( element, options ){ this.currModeIndex = 0; - return this.init( element, options ); + return this._init( element, options ); } + /** html5 data key to store this object inside an element */ ModeButton.prototype.DATA_KEY = 'mode-button'; + /** default options */ ModeButton.prototype.defaults = { - modes : [ - { mode: 'default' } - ] + switchModesOnClick : true }; - ModeButton.prototype.init = function _init( element, options ){ + // ---- private interface + /** set up options, intial mode, and the click handler */ + ModeButton.prototype._init = function _init( element, options ){ + //console.debug( 'ModeButton._init:', element, options ); options = options || {}; this.$element = $( element ); this.options = jQuery.extend( true, {}, this.defaults, options ); + if( !options.modes ){ + throw new Error( 'ModeButton requires a "modes" array' ); + } var modeButton = this; this.$element.click( function _ModeButtonClick( event ){ - // call the curr mode fn modeButton.callModeFn(); // inc the curr mode index - modeButton._incModeIndex(); + if( modeButton.options.switchModesOnClick ){ modeButton._incModeIndex(); } // set the element html $( this ).html( modeButton.options.modes[ modeButton.currModeIndex ].html ); }); - - this.currModeIndex = 0; - if( this.options.initialMode ){ - this.currModeIndex = this._getModeIndex( this.options.initialMode ); - } - return this; + return this.reset(); }; - - - ModeButton.prototype._getModeIndex = function __getModeIndex( modeKey ){ - for( var i=0; i<this.options.modes.length; i+=1 ){ - if( this.options.modes[ i ].mode === modeKey ){ return i; } - } - throw new Error( 'mode not found: ' + modeKey ); - }; - ModeButton.prototype.getCurrMode = function _getCurrMode(){ - return this.options.modes[ this.currModeIndex ]; - }; - ModeButton.prototype.getMode = function _getMode( modeKey ){ - if( !modeKey ){ return this.getCurrMode(); } - return this.options.modes[( this._getModeIndex( modeKey ) )]; - }; - ModeButton.prototype.hasMode = function _hasMode( modeKey ){ - return !!this.getMode( modeKey ); - }; - ModeButton.prototype.currentMode = function _currentMode(){ - return this.options.modes[ this.currModeIndex ]; - }; - ModeButton.prototype.setMode = function _setMode( newModeKey ){ - var newMode = this.getMode( newModeKey ); - this.$element.html( newMode.html || null ); - return this; - }; - ModeButton.prototype._incModeIndex = function __incModeIndex(){ + /** increment the mode index to the next in the array, looping back to zero if at the last */ + ModeButton.prototype._incModeIndex = function _incModeIndex(){ this.currModeIndex += 1; if( this.currModeIndex >= this.options.modes.length ){ this.currModeIndex = 0; } return this; }; - ModeButton.prototype.callModeFn = function _callModeFn( modeKey ){ + /** get the mode index in the modes array for the given key (mode name) */ + ModeButton.prototype._getModeIndex = function _getModeIndex( modeKey ){ + for( var i=0; i<this.options.modes.length; i+=1 ){ + if( this.options.modes[ i ].mode === modeKey ){ return i; } + } + throw new Error( 'mode not found: ' + modeKey ); + }; + /** set the current mode to the one with the given index and set button html */ + ModeButton.prototype._setModeByIndex = function _setModeByIndex( index ){ + var newMode = this.options.modes[ index ]; + if( !newMode ){ + throw new Error( 'mode index not found: ' + index ); + } + this.currModeIndex = index; + if( newMode.html ){ + this.$element.html( newMode.html ); + } + return this; + }; + + // ---- public interface + /** get the current mode object (not just the mode name) */ + ModeButton.prototype.currentMode = function currentMode(){ + return this.options.modes[ this.currModeIndex ]; + }; + /** return the mode key of the current mode */ + ModeButton.prototype.current = function current(){ + // sugar for returning mode name + return this.currentMode().mode; + }; + /** get the mode with the given modeKey or the current mode if modeKey is undefined */ + ModeButton.prototype.getMode = function getMode( modeKey ){ + if( !modeKey ){ return this.currentMode(); } + return this.options.modes[( this._getModeIndex( modeKey ) )]; + }; + /** T/F if the button has the given mode */ + ModeButton.prototype.hasMode = function hasMode( modeKey ){ + try { + return !!this.getMode( modeKey ); + } catch( err ){} + return false; + }; + /** set the current mode to the mode with the given name */ + ModeButton.prototype.setMode = function setMode( modeKey ){ + return this._setModeByIndex( this._getModeIndex( modeKey ) ); + }; + /** reset to the initial mode */ + ModeButton.prototype.reset = function reset(){ + this.currModeIndex = 0; + if( this.options.initialMode ){ + this.currModeIndex = this._getModeIndex( this.options.initialMode ); + } + return this._setModeByIndex( this.currModeIndex ); + }; + /** manually call the click handler of the given mode */ + ModeButton.prototype.callModeFn = function callModeFn( modeKey ){ var modeFn = this.getMode( modeKey ).onclick; if( modeFn && jQuery.type( modeFn === 'function' ) ){ - return modeFn.call( this ); + // call with the element as context (std jquery pattern) + modeFn.call( this.$element.get(0) ); + return this; } return undefined; }; @@ -861,26 +894,32 @@ // as jq plugin jQuery.fn.extend({ modeButton : function $modeButton( options ){ - var nonOptionsArgs = jQuery.makeArray( arguments ).slice( 1 ); + if( !this.size() ){ return this; } + //TODO: does map still work with jq multi selection (i.e. $( '.class-for-many-btns' ).modeButton)? - return this.map( function(){ - var $this = $( this ), - data = $this.data( 'mode-button' ); + if( jQuery.type( options ) === 'object' ){ + return this.map( function(){ + var $this = $( this ); + $this.data( 'mode-button', new ModeButton( $this, options ) ); + return this; + }); + } - if( jQuery.type( options ) === 'object' ){ - data = new ModeButton( $this, options ); - $this.data( 'mode-button', data ); + var $first = $( this[0] ), + button = $first.data( 'mode-button' ); + console.debug( 'first, button', $first, button ); - } else if( data && jQuery.type( options ) === 'string' ){ - var fn = data[ options ]; - if( jQuery.type( fn ) === 'function' ){ - return fn.apply( data, nonOptionsArgs ); - } - } else if ( data ){ - return data; + if( !button ){ + throw new Error( 'modeButton needs an options object or string name of a function' ); + } + + if( button && jQuery.type( options ) === 'string' ){ + var fnName = options; + if( button && jQuery.type( button[ fnName ] ) === 'function' ){ + return button[ fnName ].apply( button, jQuery.makeArray( arguments ).slice( 1 ) ); } - return this; - }); + } + return button; } }); }()); diff -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$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 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n=$(this),m=n.data(e.prototype.DATA_KEY);if(jQuery.type(k)==="object"){m=new e(n,k);n.data(e.prototype.DATA_KEY,m)}if(m&&jQuery.type(k)==="string"){var l=m[k];if(jQuery.type(l)==="function"){return l.apply(m,j)}}return this})}})}());(function(){function i(o,n){this.numPages=null;this.currPage=0;return this.init(o,n)}i.prototype.DATA_KEY="pagination";i.prototype.defaults={startingPage:0,perPage:20,totalDataSize:null,currDataSize:null};i.prototype.init=function g(n,o){o=o||{};this.$element=n;this.options=jQuery.extend(true,{},this.defaults,o);this.currPage=this.options.startingPage;if(this.options.totalDataSize!==null){this.numPages=Math.ceil(this.options.totalDataSize/this.options.perPage);if(this.currPage>=this.numPages){this.currPage=this.numPages-1}}this.$element.data(i.prototype.DATA_KEY,this);this._render();return this};function m(n){return $(['<li><a href="javascript:void(0);">',n,"</a></li>"].join(""))}i.prototype._render=function e(){if(this.options.totalDataSize===0){return 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H=$(this),J=H.text().replace(/^\d+\.*/,""),F=E.columnNames[G]||J;H.attr("data-"+a,F).text((G+1)+((F)?("."+F):("")))});if(E.renameColumns){B.addClass(q).click(function x(){var G=$(this),F=G.index()+(E.includePrompts?0:1),I=G.data(a),H=prompt("New column name:",I);if(H!==null&&H!==I){G.text(F+(H?("."+H):"")).data(a,H).attr("data-",a,H);var J=jQuery.makeArray(G.parent().children("th:not(.top-left)").map(function(){return $(this).data(a)}));G.parents(".peek").trigger(t,J)}})}E.controls.forEach(function(G,F){i(G);var H=r(z,G,E.includePrompts);A.find("tbody").append(H)});return this}jQuery.fn.extend({peekControl:function d(w){return this.map(function(){return b.call(this,w)})}})}()); \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$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;if(!this.$button.size()){this.$button=$("<div/>")}this.options=a||[];var c=this;this.$button.click(function(d){$(".popmenu-wrapper").remove();c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body").css(this._getShownPosition(a)).show();this._setUpCloseBehavior()},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 c=this;function a(e){$(document).off("click.close_popup");if(window.parent!==window){try{$(window.parent.document).off("click.close_popup")}catch(d){}}else{try{$("iframe#galaxy_main").contents().off("click.close_popup")}catch(d){}}c.remove()}$("html").one("click.close_popup",a);if(window.parent!==window){try{$(window.parent.document).find("html").one("click.close_popup",a)}catch(b){}}else{try{$("iframe#galaxy_main").contents().one("click.close_popup",a)}catch(b){}}},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.create=function _create(b,a){return new PopupMenu(b,a)};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.disabled&&a.target)?(' target="'+a.target+'"'):("")),' href="',((!a.disabled&&a.href)?(a.href):("javascript:void(0);")),'">','<span class="fa ',a.faIcon,'"></span>',"</a>"].join("");var c=$(b).tooltip(a.tooltipConfig);if(_.isFunction(a.onclick)){c.click(a.onclick)}return c};function LoadingIndicator(a,c){var b=this;c=jQuery.extend({cover:false},c||{});function d(){var e=['<div class="loading-indicator">','<div class="loading-indicator-text">','<span class="fa fa-spinner fa-spin fa-lg"></span>','<span class="loading-indicator-message">loading...</span>',"</div>","</div>"].join("\n");var 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E=$(this);E.toggleClass(c);e(E,z,x);var C=E.parent().find("."+c).map(function(G,H){return $(H).data(p)});var B={},A=E.parent().attr("id"),F=jQuery.makeArray(C);B[A]=F;E.parents(".peek").trigger(s,B)})}return y}function j(y,z){var w=[];for(var x=0;x<y;x+=1){w.push(z.multiselect?m(z,x):h(z,x))}return w}function r(y,z,x){var A=$("<tr/>").attr("id",z.id).addClass(v);if(x){var w=$("<td/>").addClass(f).text(z.label+":");A.append(w)}A.append(j(y,z));return A}function b(E){E=jQuery.extend(true,{},g,E);var D=$(this).addClass(l),A=D.find("table"),z=A.find("th").size(),C=A.find("tr").size(),w=A.find("td[colspan]").map(function(H,F){var G=$(this);if(G.text()&&G.text().match(new RegExp("^"+E.commentChar))){return $(this).css("color","grey").parent().get(0)}return null});if(E.hideCommentRows){w.hide();C-=w.size()}if(E.includePrompts){var y=$("<th/>").addClass("top-left").text(E.topLeftContent).attr("rowspan",C);A.find("tr").first().prepend(y)}var B=A.find("th:not(.top-left)").each(function(G,I){var H=$(this),J=H.text().replace(/^\d+\.*/,""),F=E.columnNames[G]||J;H.attr("data-"+a,F).text((G+1)+((F)?("."+F):("")))});if(E.renameColumns){B.addClass(q).click(function x(){var G=$(this),F=G.index()+(E.includePrompts?0:1),I=G.data(a),H=prompt("New column name:",I);if(H!==null&&H!==I){G.text(F+(H?("."+H):"")).data(a,H).attr("data-",a,H);var J=jQuery.makeArray(G.parent().children("th:not(.top-left)").map(function(){return $(this).data(a)}));G.parents(".peek").trigger(t,J)}})}E.controls.forEach(function(G,F){i(G);var H=r(z,G,E.includePrompts);A.find("tbody").append(H)});return this}jQuery.fn.extend({peekControl:function d(w){return this.map(function(){return b.call(this,w)})}})}()); \ No newline at end of file diff -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 templates/webapps/galaxy/history/original_view.mako --- a/templates/webapps/galaxy/history/original_view.mako +++ /dev/null @@ -1,173 +0,0 @@ -<%namespace file="/display_common.mako" import="get_history_link, get_controller_name" /> -<%namespace file="/root/history_common.mako" import="render_dataset" /> -<%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/galaxy/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "libs/jquery/jstorage" )} - <script type="text/javascript"> - $(function() { - init_history_items( $("div.historyItemWrapper"), false, "nochanges" ); - $( '#switch-to-link' ).click( function( event ){ - var galaxy = window.Galaxy || window.parent.Galaxy; - if( galaxy ){ - galaxy.currHistoryPanel.switchToHistory( '${ trans.security.encode_id( history.id ) }' ); - } - }); - $( '#refresh' ).click( function( event ){ window.location.reload( true ); }) - }); - </script> -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "history", "autocomplete_tagging" )} - - <style type="text/css"> - - /* these don't appear to be used? */ - .page-body - { - padding: 10px; - float: left; - width: 65%; - } - .page-meta - { - float: right; - width: 27%; - padding: 0.5em; - margin: 0.25em; - vertical-align: text-top; - border: 2px solid #DDDDDD; - border-top: 4px solid #DDDDDD; - } - - - body { - padding: 0px; - margin: 0px; - } - - div.unified-panel-body { - position: absolute; - top: 0px; - width: 100%; - } - - #history-name-area { - margin: 12px 0px 0px 16px; - font-size: 120%; - } - #top-links { - margin: 4px 0px 8px 16px; - } - - .historyItemContainer { - /*padding-right: 3px;*/ - } - .historyItemBody { - display: none; - } - div.historyItemWrapper { - margin: 0px 4px 0px 4px ; - border-left: 1px solid #999999; - border-right: 1px solid #999999; - } - /* TODO: unify with other history css and into .less */ - </style> - - <noscript> - <style> - .historyItemBody { - display: block; - } - </style> - </noscript> -</%def> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.message_box_visible=False -%> -</%def> - -<%def name="body()"> - ${center_panel()} -</%def> - -<%def name="center_panel()"> - ## Get URL to other histories owned by user that owns this history. - <% - ##TODO: is there a better way to create this URL? Can't use 'f-username' as a key b/c it's not a valid identifier. - href_to_published_histories = h.url_for( controller='/history', action='list_published') - if history.user is not None: - href_to_user_histories = h.url_for( controller='/history', action='list_published', xxx=history.user.username).replace( 'xxx', 'f-username') - else: - href_to_user_histories = h.url_for( controller='/history', action='list_published' )##should this instead be be None or empty string? - %> - - <div class="unified-panel-body"> - <div style="overflow: auto; height: 100%;"> - ## Render view of history. - <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> - <div id="history-name">${history.get_display_name()}</div> - </div> - - <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> - %if not history.purged and history.user != trans.user: - ##TODO: need to remove _top - <a href="${h.url_for(controller='history', action='imp', id=trans.security.encode_id(history.id) )}" - >import and start using history</a> | - <a id="refresh" href="javascript:void(0)" >${_('refresh')}</a> | - %endif - %if not history.purged and history.user == trans.user: - <a id="switch-to-link" href="javascript:void(0)">${_('switch to this history')}</a> | - <a id="refresh" href="javascript:void(0)" >${_('refresh')}</a> | - %endif - %if show_deleted: - <a href="${h.url_for(controller='history', action='view', id=trans.security.encode_id(history.id), show_deleted=False, use_panels=use_panels )}">${_('hide deleted')}</a> | - %else: - <a href="${h.url_for(controller='history', action='view', id=trans.security.encode_id(history.id), show_deleted=True, use_panels=use_panels )}">${_('show deleted')}</a> | - %endif - <a href="#" class="toggle">collapse all</a> - </div> - - %if history.deleted: - <div class="warningmessagesmall"> - ${_('You are currently viewing a deleted history!')} - </div> - <p></p> - %endif - - %if not datasets: - <div class="infomessagesmall" id="emptyHistoryMessage"> - - %else: - ## Render requested datasets, ordered from newest to oldest - %for data in datasets: - %if data.visible: - <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} - </div> - %endif - %endfor - - <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> - %endif - ${_("Your history is empty. Click 'Get Data' on the left pane to start")} - </div> - </div> - </div> -</%def> diff -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -77,6 +77,7 @@ %endif <script type="text/javascript"> + ##TODO: remove when Galaxy is either ensured or removed from the history panel var using_panels = ${ 'false' if not use_panels else 'true' }; %if not use_panels: window.Galaxy = {}; @@ -87,113 +88,107 @@ ## ---------------------------------------------------------------------------- <%def name="center_panel()"> +<% + show_deleted = context.get( 'show_deleted', None ) + show_hidden = context.get( 'show_hidden', None ) + + user_is_owner_json = 'true' if user_is_owner else 'false' + show_deleted_json = h.to_json_string( show_deleted ) + show_hidden_json = h.to_json_string( show_hidden ) + + imp_with_deleted_url = h.url_for( controller='history', action='imp', id=history['id'], all_datasets=True ) + imp_without_deleted_url = h.url_for( controller='history', action='imp', id=history['id'] ) +%> + <div id="header" class="clear"><div id="history-view-controls" class="pull-right"> - <% - show_deleted = context.get( 'show_deleted', None ) - show_hidden = context.get( 'show_hidden', None ) - - show_deleted_js = 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) - show_hidden_js = 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) - print 'user_is_owner:', user_is_owner - %> %if not user_is_owner and not history[ 'purged' ]: - <a id="import" class="btn btn-default" style="display: none;" - href="${h.url_for( controller='history', action='imp', id=history['id'], all_datasets=show_deleted )}"> - ${_('Import and start using history')} - </a> + <button id="import" class="btn btn-default"></button> %endif - <button id="toggle-deleted" class="btn btn-default"> - ${_('Exclude deleted') if show_deleted else _('Include deleted')} - </button> - <button id="toggle-hidden" class="btn btn-default"> - ${_('Exclude hidden') if show_hidden else _('Include hidden')} - </button> + <button id="toggle-deleted" class="btn btn-default"></button> + <button id="toggle-hidden" class="btn btn-default"></button></div></div><div id="history-${ history[ 'id' ] }" class="history-panel unified-panel-body" style="overflow: auto;"></div><script type="text/javascript"> + $(function(){ + $( '#toggle-deleted' ).modeButton({ + initialMode : "${ 'showing_deleted' if show_deleted else 'not_showing_deleted' }", + modes: [ + { mode: 'showing_deleted', html: _l( 'Exclude deleted' ) }, + { mode: 'not_showing_deleted', html: _l( 'Include deleted' ) } + ] + }).click( function(){ + // allow the 'include/exclude deleted' button to control whether the 'import' button includes deleted + // datasets when importing or not; when deleted datasets are shown, they'll be imported + $( '#import' ).modeButton( 'setMode', + $( this ).modeButton( 'current' ) === 'showing_deleted'? 'with_deleted': 'without_deleted' ) + }); + + $( '#toggle-hidden' ).modeButton({ + initialMode : "${ 'showing_hidden' if show_hidden else 'not_showing_hidden' }", + modes: [ + { mode: 'showing_hidden', html: _l( 'Exclude hidden' ) }, + { mode: 'not_showing_hidden', html: _l( 'Include hidden' ) } + ] + }); + + $( '#import' ).modeButton({ + switchModesOnClick : false, + initialMode : "${ 'with_deleted' if show_deleted else 'without_deleted' }", + modes: [ + { mode: 'with_deleted', html: _l( 'Import with deleted datasets and start using history' ), + onclick: function importWithDeleted(){ + window.location = '${imp_with_deleted_url}'; + } + }, + { mode: 'without_deleted', html: _l( 'Import and start using history' ), + onclick: function importWithoutDeleted(){ + window.location = '${imp_without_deleted_url}'; + } + }, + ] + }); + }); + var debugging = JSON.parse( sessionStorage.getItem( 'debugging' ) ) || false, userIsOwner = ${'true' if user_is_owner else 'false'}, historyJSON = ${h.to_json_string( history )}, hdaJSON = ${h.to_json_string( hdas )}; - window.hdaJSON = hdaJSON; - - $( '#toggle-deleted' ).modeButton({ - initialMode : (${ show_deleted_js })?( 'exclude' ):( 'include' ), - modes: [ - { mode: 'exclude', html: _l( 'Exclude deleted' ) }, - { mode: 'include', html: _l( 'Include deleted' ) } - ] - }).click( function(){ - // allow the 'include/exclude deleted' button to control whether the 'import' button includes deleted datasets - // when importing or not; when deleted datasets are shown, they'll be imported - var $importBtn = $( '#import' ); - if( $importBtn.size() ){ - // a bit hacky - var href = $importBtn.attr( 'href' ), - includeDeleted = $( this ).modeButton()[0].getMode().mode === 'exclude'; - href = href.replace( /all_datasets=True|False/, ( includeDeleted )?( 'True' ):( 'False' ) ); - $importBtn.attr( 'href', href ); - $importBtn.text( includeDeleted ? _l( 'Import with deleted datasets and start using history' ) - : _l( 'Import and start using history' ) ); - } - }); - - $( '#toggle-hidden' ).modeButton({ - initialMode : (${ show_hidden_js })?( 'exclude' ):( 'include' ), - modes: [ - { mode: 'exclude', html: _l( 'Exclude hidden' ) }, - { mode: 'include', html: _l( 'Include hidden' ) } - ] - }); - - ##TODO: move to mako - if( Galaxy.currUser.id !== historyJSON.user_id ){ - $( '#import' ).show(); - } + panelToUse = ( userIsOwner )? + ({ location: 'mvc/history/history-panel', className: 'HistoryPanel' }): + ({ location: 'mvc/history/readonly-history-panel', className: 'ReadOnlyHistoryPanel' }); require.config({ baseUrl : "${h.url_for( '/static/scripts' )}" - })([ - %if user_is_owner: - 'mvc/history/history-panel' - %else: - 'mvc/history/readonly-history-panel' - %endif - ${ } - ], function( panelMod ){ - //require([ "mvc/history/history-panel" ], function( historyPanel ){ - // history module is already in the dpn chain from the panel. We can re-scope it here. - var historyModel = require( 'mvc/history/history-model' ), - hdaBaseView = require( 'mvc/dataset/hda-base' ), - history = new historyModel.History( historyJSON, hdaJSON, { - logger: ( debugging )?( console ):( null ) + })([ panelToUse.location ], function( panelMod ){ + $(function(){ + var panelClass = panelMod[ panelToUse.className ], + // history module is already in the dpn chain from the panel. We can re-scope it here. + historyModel = require( 'mvc/history/history-model' ), + hdaBaseView = require( 'mvc/dataset/hda-base' ), + history = new historyModel.History( historyJSON, hdaJSON, { + logger: ( debugging )?( console ):( null ) + }); + + window.historyPanel = new panelClass({ + show_deleted : ${show_deleted_json}, + show_hidden : ${show_hidden_json}, + el : $( "#history-" + historyJSON.id ), + model : history, + onready : function(){ + var panel = this; + $( '#toggle-deleted' ).on( 'click', function(){ + panel.toggleShowDeleted(); + }); + $( '#toggle-hidden' ).on( 'click', function(){ + panel.toggleShowHidden(); + }); + this.render(); + } }); - - window.panelMod = panelMod; - %if user_is_owner: - window.panelClass = panelMod.HistoryPanel; - %else: - window.panelClass = panelMod.ReadOnlyHistoryPanel; - %endif - window.historyPanel = new panelClass({ - show_deleted : ${show_deleted_js}, - show_hidden : ${show_hidden_js}, - el : $( "#history-" + historyJSON.id ), - model : history, - onready : function(){ - var panel = this; - $( '#toggle-deleted' ).on( 'click', function(){ - panel.toggleShowDeleted(); - }); - $( '#toggle-hidden' ).on( 'click', function(){ - panel.toggleShowHidden(); - }); - this.render(); - } }); }); </script> diff -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 tools/data_source/upload.xml --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -1,7 +1,6 @@ <?xml version="1.0"?><tool name="Upload File" id="upload1" version="1.1.4" workflow_compatible="false"> - <hidden>True</hidden><description> from your computer </description> 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: Add get data back to to tool panel (will be replaced by a placeholder soon)
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/742b4ffd3b99/ Changeset: 742b4ffd3b99 User: guerler Date: 2014-02-19 18:51:52 Summary: Add get data back to to tool panel (will be replaced by a placeholder soon) Affected #: 1 file diff -r 7ebec9da47844efbf37942faab3809cb0169e5c2 -r 742b4ffd3b99160cae864049f09defe710dd7ee4 tools/data_source/upload.xml --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -1,7 +1,6 @@ <?xml version="1.0"?><tool name="Upload File" id="upload1" version="1.1.4" workflow_compatible="false"> - <hidden>True</hidden><description> from your computer </description> 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: carlfeberhard: history/view: clean up, replace import link with window.location; UI mode button: several fixes, clean up, docs; Remove original_view from controllers/history (and templates)
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7ebec9da4784/ Changeset: 7ebec9da4784 User: carlfeberhard Date: 2014-02-19 18:32:06 Summary: history/view: clean up, replace import link with window.location; UI mode button: several fixes, clean up, docs; Remove original_view from controllers/history (and templates) Affected #: 5 files diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 7ebec9da47844efbf37942faab3809cb0169e5c2 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -843,35 +843,6 @@ history. <br>You can <a href="%s">continue and import this history</a> or %s. """ % ( web.url_for(controller='history', action='imp', id=id, confirm=True, referer=trans.request.referer ), referer_message ), use_panels=True ) - # Replaced with view (below) but kept (available via manual URL editing) for now - @web.expose - def original_view( self, trans, id=None, show_deleted=False, use_panels=True ): - """View a history. If a history is importable, then it is viewable by any user.""" - # Get history to view. - if not id: - return trans.show_error_message( "You must specify a history you want to view." ) - history_to_view = self.get_history( trans, id, False) - # Integrity checks. - if not history_to_view: - return trans.show_error_message( "The specified history does not exist." ) - # Admin users can view any history - if( ( history_to_view.user != trans.user ) - and ( not trans.user_is_admin() ) - and ( not history_to_view.importable ) ): - error( "Either you are not allowed to view this history or the owner of this history has not made it accessible." ) - # View history. - show_deleted = galaxy.util.string_as_bool( show_deleted ) - datasets = self.get_history_datasets( trans, history_to_view, show_deleted=show_deleted ) - try: - use_panels = galaxy.util.string_as_bool( use_panels ) - except: - pass # already a bool - return trans.stream_template_mako( "history/original_view.mako", - history = history_to_view, - datasets = datasets, - show_deleted = show_deleted, - use_panels = use_panels ) - @web.expose def view( self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True ): """ diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 7ebec9da47844efbf37942faab3809cb0169e5c2 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -783,77 +783,110 @@ * }); * $( '.myElement' ).modeButton( 'callModeFn', 'bler' ); */ + /** constructor */ function ModeButton( element, options ){ this.currModeIndex = 0; - return this.init( element, options ); + return this._init( element, options ); } + /** html5 data key to store this object inside an element */ ModeButton.prototype.DATA_KEY = 'mode-button'; + /** default options */ ModeButton.prototype.defaults = { - modes : [ - { mode: 'default' } - ] + switchModesOnClick : true }; - ModeButton.prototype.init = function _init( element, options ){ + // ---- private interface + /** set up options, intial mode, and the click handler */ + ModeButton.prototype._init = function _init( element, options ){ + //console.debug( 'ModeButton._init:', element, options ); options = options || {}; this.$element = $( element ); this.options = jQuery.extend( true, {}, this.defaults, options ); + if( !options.modes ){ + throw new Error( 'ModeButton requires a "modes" array' ); + } var modeButton = this; this.$element.click( function _ModeButtonClick( event ){ - // call the curr mode fn modeButton.callModeFn(); // inc the curr mode index - modeButton._incModeIndex(); + if( modeButton.options.switchModesOnClick ){ modeButton._incModeIndex(); } // set the element html $( this ).html( modeButton.options.modes[ modeButton.currModeIndex ].html ); }); - - this.currModeIndex = 0; - if( this.options.initialMode ){ - this.currModeIndex = this._getModeIndex( this.options.initialMode ); - } - return this; + return this.reset(); }; - - - ModeButton.prototype._getModeIndex = function __getModeIndex( modeKey ){ - for( var i=0; i<this.options.modes.length; i+=1 ){ - if( this.options.modes[ i ].mode === modeKey ){ return i; } - } - throw new Error( 'mode not found: ' + modeKey ); - }; - ModeButton.prototype.getCurrMode = function _getCurrMode(){ - return this.options.modes[ this.currModeIndex ]; - }; - ModeButton.prototype.getMode = function _getMode( modeKey ){ - if( !modeKey ){ return this.getCurrMode(); } - return this.options.modes[( this._getModeIndex( modeKey ) )]; - }; - ModeButton.prototype.hasMode = function _hasMode( modeKey ){ - return !!this.getMode( modeKey ); - }; - ModeButton.prototype.currentMode = function _currentMode(){ - return this.options.modes[ this.currModeIndex ]; - }; - ModeButton.prototype.setMode = function _setMode( newModeKey ){ - var newMode = this.getMode( newModeKey ); - this.$element.html( newMode.html || null ); - return this; - }; - ModeButton.prototype._incModeIndex = function __incModeIndex(){ + /** increment the mode index to the next in the array, looping back to zero if at the last */ + ModeButton.prototype._incModeIndex = function _incModeIndex(){ this.currModeIndex += 1; if( this.currModeIndex >= this.options.modes.length ){ this.currModeIndex = 0; } return this; }; - ModeButton.prototype.callModeFn = function _callModeFn( modeKey ){ + /** get the mode index in the modes array for the given key (mode name) */ + ModeButton.prototype._getModeIndex = function _getModeIndex( modeKey ){ + for( var i=0; i<this.options.modes.length; i+=1 ){ + if( this.options.modes[ i ].mode === modeKey ){ return i; } + } + throw new Error( 'mode not found: ' + modeKey ); + }; + /** set the current mode to the one with the given index and set button html */ + ModeButton.prototype._setModeByIndex = function _setModeByIndex( index ){ + var newMode = this.options.modes[ index ]; + if( !newMode ){ + throw new Error( 'mode index not found: ' + index ); + } + this.currModeIndex = index; + if( newMode.html ){ + this.$element.html( newMode.html ); + } + return this; + }; + + // ---- public interface + /** get the current mode object (not just the mode name) */ + ModeButton.prototype.currentMode = function currentMode(){ + return this.options.modes[ this.currModeIndex ]; + }; + /** return the mode key of the current mode */ + ModeButton.prototype.current = function current(){ + // sugar for returning mode name + return this.currentMode().mode; + }; + /** get the mode with the given modeKey or the current mode if modeKey is undefined */ + ModeButton.prototype.getMode = function getMode( modeKey ){ + if( !modeKey ){ return this.currentMode(); } + return this.options.modes[( this._getModeIndex( modeKey ) )]; + }; + /** T/F if the button has the given mode */ + ModeButton.prototype.hasMode = function hasMode( modeKey ){ + try { + return !!this.getMode( modeKey ); + } catch( err ){} + return false; + }; + /** set the current mode to the mode with the given name */ + ModeButton.prototype.setMode = function setMode( modeKey ){ + return this._setModeByIndex( this._getModeIndex( modeKey ) ); + }; + /** reset to the initial mode */ + ModeButton.prototype.reset = function reset(){ + this.currModeIndex = 0; + if( this.options.initialMode ){ + this.currModeIndex = this._getModeIndex( this.options.initialMode ); + } + return this._setModeByIndex( this.currModeIndex ); + }; + /** manually call the click handler of the given mode */ + ModeButton.prototype.callModeFn = function callModeFn( modeKey ){ var modeFn = this.getMode( modeKey ).onclick; if( modeFn && jQuery.type( modeFn === 'function' ) ){ - return modeFn.call( this ); + // call with the element as context (std jquery pattern) + modeFn.call( this.$element.get(0) ); + return this; } return undefined; }; @@ -861,26 +894,32 @@ // as jq plugin jQuery.fn.extend({ modeButton : function $modeButton( options ){ - var nonOptionsArgs = jQuery.makeArray( arguments ).slice( 1 ); + if( !this.size() ){ return this; } + //TODO: does map still work with jq multi selection (i.e. $( '.class-for-many-btns' ).modeButton)? - return this.map( function(){ - var $this = $( this ), - data = $this.data( 'mode-button' ); + if( jQuery.type( options ) === 'object' ){ + return this.map( function(){ + var $this = $( this ); + $this.data( 'mode-button', new ModeButton( $this, options ) ); + return this; + }); + } - if( jQuery.type( options ) === 'object' ){ - data = new ModeButton( $this, options ); - $this.data( 'mode-button', data ); + var $first = $( this[0] ), + button = $first.data( 'mode-button' ); + console.debug( 'first, button', $first, button ); - } else if( data && jQuery.type( options ) === 'string' ){ - var fn = data[ options ]; - if( jQuery.type( fn ) === 'function' ){ - return fn.apply( data, nonOptionsArgs ); - } - } else if ( data ){ - return data; + if( !button ){ + throw new Error( 'modeButton needs an options object or string name of a function' ); + } + + if( button && jQuery.type( options ) === 'string' ){ + var fnName = options; + if( button && jQuery.type( button[ fnName ] ) === 'function' ){ + return button[ fnName ].apply( button, jQuery.makeArray( arguments ).slice( 1 ) ); } - return this; - }); + } + return button; } }); }()); diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 7ebec9da47844efbf37942faab3809cb0169e5c2 static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$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;if(!this.$button.size()){this.$button=$("<div/>")}this.options=a||[];var c=this;this.$button.click(function(d){$(".popmenu-wrapper").remove();c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body").css(this._getShownPosition(a)).show();this._setUpCloseBehavior()},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 c=this;function a(e){$(document).off("click.close_popup");if(window.parent!==window){try{$(window.parent.document).off("click.close_popup")}catch(d){}}else{try{$("iframe#galaxy_main").contents().off("click.close_popup")}catch(d){}}c.remove()}$("html").one("click.close_popup",a);if(window.parent!==window){try{$(window.parent.document).find("html").one("click.close_popup",a)}catch(b){}}else{try{$("iframe#galaxy_main").contents().one("click.close_popup",a)}catch(b){}}},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.create=function _create(b,a){return new PopupMenu(b,a)};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.disabled&&a.target)?(' target="'+a.target+'"'):("")),' href="',((!a.disabled&&a.href)?(a.href):("javascript:void(0);")),'">','<span class="fa ',a.faIcon,'"></span>',"</a>"].join("");var c=$(b).tooltip(a.tooltipConfig);if(_.isFunction(a.onclick)){c.click(a.onclick)}return c};function LoadingIndicator(a,c){var 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j=this;if(this.currFilter.values){this.$valueSelect=dropDownSelect(this.currFilter.values,this.currFilter.values[0]).on("change.dropdown-select",function(l,k){j._triggerChange()})}else{this.$valueSelect=$("<input/>").addClass("form-control").on("change",function(k,l){j._triggerChange()})}this.$valueSelect.addClass("filter-control-value");return this.$valueSelect};e.prototype.val=function b(){var k=this.$element.find(".filter-control-key .dropdown-select-selected").text(),m=this.$element.find(".filter-control-op .dropdown-select-selected").text(),j=this.$element.find(".filter-control-value"),l=(j.hasClass("dropdown-select"))?(j.find(".dropdown-select-selected").text()):(j.val());return{key:k,op:m,value:l}};e.prototype._triggerChange=function h(){this.$element.trigger("change.filter-control",this.val())};jQuery.fn.extend({filterControl:function f(k){var j=jQuery.makeArray(arguments).slice(1);return this.map(function(){var n=$(this),m=n.data(e.prototype.DATA_KEY);if(jQuery.type(k)==="object"){m=new e(n,k);n.data(e.prototype.DATA_KEY,m)}if(m&&jQuery.type(k)==="string"){var l=m[k];if(jQuery.type(l)==="function"){return l.apply(m,j)}}return this})}})}());(function(){function i(o,n){this.numPages=null;this.currPage=0;return this.init(o,n)}i.prototype.DATA_KEY="pagination";i.prototype.defaults={startingPage:0,perPage:20,totalDataSize:null,currDataSize:null};i.prototype.init=function g(n,o){o=o||{};this.$element=n;this.options=jQuery.extend(true,{},this.defaults,o);this.currPage=this.options.startingPage;if(this.options.totalDataSize!==null){this.numPages=Math.ceil(this.options.totalDataSize/this.options.perPage);if(this.currPage>=this.numPages){this.currPage=this.numPages-1}}this.$element.data(i.prototype.DATA_KEY,this);this._render();return this};function m(n){return $(['<li><a href="javascript:void(0);">',n,"</a></li>"].join(""))}i.prototype._render=function e(){if(this.options.totalDataSize===0){return this}if(this.numPages===1){return this}if(this.numPages>0){this._renderPages();this._scrollToActivePage()}else{this._renderPrevNext()}return this};i.prototype._renderPrevNext=function b(){var o=this,p=m("Prev"),n=m("Next"),q=$("<ul/>").addClass("pagination pagination-prev-next");if(this.currPage===0){p.addClass("disabled")}else{p.click(function(){o.prevPage()})}if((this.numPages&&this.currPage===(this.numPages-1))||(this.options.currDataSize&&this.options.currDataSize<this.options.perPage)){n.addClass("disabled")}else{n.click(function(){o.nextPage()})}this.$element.html(q.append([p,n]));return this.$element};i.prototype._renderPages=function a(){var n=this,q=$("<div>").addClass("pagination-scroll-container"),s=$("<ul/>").addClass("pagination pagination-page-list"),r=function(t){n.goToPage($(this).data("page"))};for(var o=0;o<this.numPages;o+=1){var p=m(o+1).attr("data-page",o).click(r);if(o===this.currPage){p.addClass("active")}s.append(p)}return 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E=$(this);E.toggleClass(c);e(E,z,x);var C=E.parent().find("."+c).map(function(G,H){return $(H).data(p)});var B={},A=E.parent().attr("id"),F=jQuery.makeArray(C);B[A]=F;E.parents(".peek").trigger(s,B)})}return y}function j(y,z){var w=[];for(var x=0;x<y;x+=1){w.push(z.multiselect?m(z,x):h(z,x))}return w}function r(y,z,x){var A=$("<tr/>").attr("id",z.id).addClass(v);if(x){var w=$("<td/>").addClass(f).text(z.label+":");A.append(w)}A.append(j(y,z));return A}function b(E){E=jQuery.extend(true,{},g,E);var D=$(this).addClass(l),A=D.find("table"),z=A.find("th").size(),C=A.find("tr").size(),w=A.find("td[colspan]").map(function(H,F){var G=$(this);if(G.text()&&G.text().match(new RegExp("^"+E.commentChar))){return $(this).css("color","grey").parent().get(0)}return null});if(E.hideCommentRows){w.hide();C-=w.size()}if(E.includePrompts){var y=$("<th/>").addClass("top-left").text(E.topLeftContent).attr("rowspan",C);A.find("tr").first().prepend(y)}var B=A.find("th:not(.top-left)").each(function(G,I){var H=$(this),J=H.text().replace(/^\d+\.*/,""),F=E.columnNames[G]||J;H.attr("data-"+a,F).text((G+1)+((F)?("."+F):("")))});if(E.renameColumns){B.addClass(q).click(function x(){var G=$(this),F=G.index()+(E.includePrompts?0:1),I=G.data(a),H=prompt("New column name:",I);if(H!==null&&H!==I){G.text(F+(H?("."+H):"")).data(a,H).attr("data-",a,H);var J=jQuery.makeArray(G.parent().children("th:not(.top-left)").map(function(){return $(this).data(a)}));G.parents(".peek").trigger(t,J)}})}E.controls.forEach(function(G,F){i(G);var H=r(z,G,E.includePrompts);A.find("tbody").append(H)});return this}jQuery.fn.extend({peekControl:function d(w){return this.map(function(){return b.call(this,w)})}})}()); \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$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;if(!this.$button.size()){this.$button=$("<div/>")}this.options=a||[];var c=this;this.$button.click(function(d){$(".popmenu-wrapper").remove();c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body").css(this._getShownPosition(a)).show();this._setUpCloseBehavior()},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 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import="get_history_link, get_controller_name" /> -<%namespace file="/root/history_common.mako" import="render_dataset" /> -<%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/galaxy/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "libs/jquery/jstorage" )} - <script type="text/javascript"> - $(function() { - init_history_items( $("div.historyItemWrapper"), false, "nochanges" ); - $( '#switch-to-link' ).click( function( event ){ - var galaxy = window.Galaxy || window.parent.Galaxy; - if( galaxy ){ - galaxy.currHistoryPanel.switchToHistory( '${ trans.security.encode_id( history.id ) }' ); - } - }); - $( '#refresh' ).click( function( event ){ window.location.reload( true ); }) - }); - </script> -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "history", "autocomplete_tagging" )} - - <style type="text/css"> - - /* these don't appear to be used? */ - .page-body - { - padding: 10px; - float: left; - width: 65%; - } - .page-meta - { - float: right; - width: 27%; - padding: 0.5em; - margin: 0.25em; - vertical-align: text-top; - border: 2px solid #DDDDDD; - border-top: 4px solid #DDDDDD; - } - - - body { - padding: 0px; - margin: 0px; - } - - div.unified-panel-body { - position: absolute; - top: 0px; - width: 100%; - } - - #history-name-area { - margin: 12px 0px 0px 16px; - font-size: 120%; - } - #top-links { - margin: 4px 0px 8px 16px; - } - - .historyItemContainer { - /*padding-right: 3px;*/ - } - .historyItemBody { - display: none; - } - div.historyItemWrapper { - margin: 0px 4px 0px 4px ; - border-left: 1px solid #999999; - border-right: 1px solid #999999; - } - /* TODO: unify with other history css and into .less */ - </style> - - <noscript> - <style> - .historyItemBody { - display: block; - } - </style> - </noscript> -</%def> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.message_box_visible=False -%> -</%def> - -<%def name="body()"> - ${center_panel()} -</%def> - -<%def name="center_panel()"> - ## Get URL to other histories owned by user that owns this history. - <% - ##TODO: is there a better way to create this URL? Can't use 'f-username' as a key b/c it's not a valid identifier. - href_to_published_histories = h.url_for( controller='/history', action='list_published') - if history.user is not None: - href_to_user_histories = h.url_for( controller='/history', action='list_published', xxx=history.user.username).replace( 'xxx', 'f-username') - else: - href_to_user_histories = h.url_for( controller='/history', action='list_published' )##should this instead be be None or empty string? - %> - - <div class="unified-panel-body"> - <div style="overflow: auto; height: 100%;"> - ## Render view of history. - <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> - <div id="history-name">${history.get_display_name()}</div> - </div> - - <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> - %if not history.purged and history.user != trans.user: - ##TODO: need to remove _top - <a href="${h.url_for(controller='history', action='imp', id=trans.security.encode_id(history.id) )}" - >import and start using history</a> | - <a id="refresh" href="javascript:void(0)" >${_('refresh')}</a> | - %endif - %if not history.purged and history.user == trans.user: - <a id="switch-to-link" href="javascript:void(0)">${_('switch to this history')}</a> | - <a id="refresh" href="javascript:void(0)" >${_('refresh')}</a> | - %endif - %if show_deleted: - <a href="${h.url_for(controller='history', action='view', id=trans.security.encode_id(history.id), show_deleted=False, use_panels=use_panels )}">${_('hide deleted')}</a> | - %else: - <a href="${h.url_for(controller='history', action='view', id=trans.security.encode_id(history.id), show_deleted=True, use_panels=use_panels )}">${_('show deleted')}</a> | - %endif - <a href="#" class="toggle">collapse all</a> - </div> - - %if history.deleted: - <div class="warningmessagesmall"> - ${_('You are currently viewing a deleted history!')} - </div> - <p></p> - %endif - - %if not datasets: - <div class="infomessagesmall" id="emptyHistoryMessage"> - - %else: - ## Render requested datasets, ordered from newest to oldest - %for data in datasets: - %if data.visible: - <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} - </div> - %endif - %endfor - - <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> - %endif - ${_("Your history is empty. Click 'Get Data' on the left pane to start")} - </div> - </div> - </div> -</%def> diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 7ebec9da47844efbf37942faab3809cb0169e5c2 templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -77,6 +77,7 @@ %endif <script type="text/javascript"> + ##TODO: remove when Galaxy is either ensured or removed from the history panel var using_panels = ${ 'false' if not use_panels else 'true' }; %if not use_panels: window.Galaxy = {}; @@ -87,113 +88,107 @@ ## ---------------------------------------------------------------------------- <%def name="center_panel()"> +<% + show_deleted = context.get( 'show_deleted', None ) + show_hidden = context.get( 'show_hidden', None ) + + user_is_owner_json = 'true' if user_is_owner else 'false' + show_deleted_json = h.to_json_string( show_deleted ) + show_hidden_json = h.to_json_string( show_hidden ) + + imp_with_deleted_url = h.url_for( controller='history', action='imp', id=history['id'], all_datasets=True ) + imp_without_deleted_url = h.url_for( controller='history', action='imp', id=history['id'] ) +%> + <div id="header" class="clear"><div id="history-view-controls" class="pull-right"> - <% - show_deleted = context.get( 'show_deleted', None ) - show_hidden = context.get( 'show_hidden', None ) - - show_deleted_js = 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) - show_hidden_js = 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) - print 'user_is_owner:', user_is_owner - %> %if not user_is_owner and not history[ 'purged' ]: - <a id="import" class="btn btn-default" style="display: none;" - href="${h.url_for( controller='history', action='imp', id=history['id'], all_datasets=show_deleted )}"> - ${_('Import and start using history')} - </a> + <button id="import" class="btn btn-default"></button> %endif - <button id="toggle-deleted" class="btn btn-default"> - ${_('Exclude deleted') if show_deleted else _('Include deleted')} - </button> - <button id="toggle-hidden" class="btn btn-default"> - ${_('Exclude hidden') if show_hidden else _('Include hidden')} - </button> + <button id="toggle-deleted" class="btn btn-default"></button> + <button id="toggle-hidden" class="btn btn-default"></button></div></div><div id="history-${ history[ 'id' ] }" class="history-panel unified-panel-body" style="overflow: auto;"></div><script type="text/javascript"> + $(function(){ + $( '#toggle-deleted' ).modeButton({ + initialMode : "${ 'showing_deleted' if show_deleted else 'not_showing_deleted' }", + modes: [ + { mode: 'showing_deleted', html: _l( 'Exclude deleted' ) }, + { mode: 'not_showing_deleted', html: _l( 'Include deleted' ) } + ] + }).click( function(){ + // allow the 'include/exclude deleted' button to control whether the 'import' button includes deleted + // datasets when importing or not; when deleted datasets are shown, they'll be imported + $( '#import' ).modeButton( 'setMode', + $( this ).modeButton( 'current' ) === 'showing_deleted'? 'with_deleted': 'without_deleted' ) + }); + + $( '#toggle-hidden' ).modeButton({ + initialMode : "${ 'showing_hidden' if show_hidden else 'not_showing_hidden' }", + modes: [ + { mode: 'showing_hidden', html: _l( 'Exclude hidden' ) }, + { mode: 'not_showing_hidden', html: _l( 'Include hidden' ) } + ] + }); + + $( '#import' ).modeButton({ + switchModesOnClick : false, + initialMode : "${ 'with_deleted' if show_deleted else 'without_deleted' }", + modes: [ + { mode: 'with_deleted', html: _l( 'Import with deleted datasets and start using history' ), + onclick: function importWithDeleted(){ + window.location = '${imp_with_deleted_url}'; + } + }, + { mode: 'without_deleted', html: _l( 'Import and start using history' ), + onclick: function importWithoutDeleted(){ + window.location = '${imp_without_deleted_url}'; + } + }, + ] + }); + }); + var debugging = JSON.parse( sessionStorage.getItem( 'debugging' ) ) || false, userIsOwner = ${'true' if user_is_owner else 'false'}, historyJSON = ${h.to_json_string( history )}, hdaJSON = ${h.to_json_string( hdas )}; - window.hdaJSON = hdaJSON; - - $( '#toggle-deleted' ).modeButton({ - initialMode : (${ show_deleted_js })?( 'exclude' ):( 'include' ), - modes: [ - { mode: 'exclude', html: _l( 'Exclude deleted' ) }, - { mode: 'include', html: _l( 'Include deleted' ) } - ] - }).click( function(){ - // allow the 'include/exclude deleted' button to control whether the 'import' button includes deleted datasets - // when importing or not; when deleted datasets are shown, they'll be imported - var $importBtn = $( '#import' ); - if( $importBtn.size() ){ - // a bit hacky - var href = $importBtn.attr( 'href' ), - includeDeleted = $( this ).modeButton()[0].getMode().mode === 'exclude'; - href = href.replace( /all_datasets=True|False/, ( includeDeleted )?( 'True' ):( 'False' ) ); - $importBtn.attr( 'href', href ); - $importBtn.text( includeDeleted ? _l( 'Import with deleted datasets and start using history' ) - : _l( 'Import and start using history' ) ); - } - }); - - $( '#toggle-hidden' ).modeButton({ - initialMode : (${ show_hidden_js })?( 'exclude' ):( 'include' ), - modes: [ - { mode: 'exclude', html: _l( 'Exclude hidden' ) }, - { mode: 'include', html: _l( 'Include hidden' ) } - ] - }); - - ##TODO: move to mako - if( Galaxy.currUser.id !== historyJSON.user_id ){ - $( '#import' ).show(); - } + panelToUse = ( userIsOwner )? + ({ location: 'mvc/history/history-panel', className: 'HistoryPanel' }): + ({ location: 'mvc/history/readonly-history-panel', className: 'ReadOnlyHistoryPanel' }); require.config({ baseUrl : "${h.url_for( '/static/scripts' )}" - })([ - %if user_is_owner: - 'mvc/history/history-panel' - %else: - 'mvc/history/readonly-history-panel' - %endif - ${ } - ], function( panelMod ){ - //require([ "mvc/history/history-panel" ], function( historyPanel ){ - // history module is already in the dpn chain from the panel. We can re-scope it here. - var historyModel = require( 'mvc/history/history-model' ), - hdaBaseView = require( 'mvc/dataset/hda-base' ), - history = new historyModel.History( historyJSON, hdaJSON, { - logger: ( debugging )?( console ):( null ) + })([ panelToUse.location ], function( panelMod ){ + $(function(){ + var panelClass = panelMod[ panelToUse.className ], + // history module is already in the dpn chain from the panel. We can re-scope it here. + historyModel = require( 'mvc/history/history-model' ), + hdaBaseView = require( 'mvc/dataset/hda-base' ), + history = new historyModel.History( historyJSON, hdaJSON, { + logger: ( debugging )?( console ):( null ) + }); + + window.historyPanel = new panelClass({ + show_deleted : ${show_deleted_json}, + show_hidden : ${show_hidden_json}, + el : $( "#history-" + historyJSON.id ), + model : history, + onready : function(){ + var panel = this; + $( '#toggle-deleted' ).on( 'click', function(){ + panel.toggleShowDeleted(); + }); + $( '#toggle-hidden' ).on( 'click', function(){ + panel.toggleShowHidden(); + }); + this.render(); + } }); - - window.panelMod = panelMod; - %if user_is_owner: - window.panelClass = panelMod.HistoryPanel; - %else: - window.panelClass = panelMod.ReadOnlyHistoryPanel; - %endif - window.historyPanel = new panelClass({ - show_deleted : ${show_deleted_js}, - show_hidden : ${show_hidden_js}, - el : $( "#history-" + historyJSON.id ), - model : history, - onready : function(){ - var panel = this; - $( '#toggle-deleted' ).on( 'click', function(){ - panel.toggleShowDeleted(); - }); - $( '#toggle-hidden' ).on( 'click', function(){ - panel.toggleShowHidden(); - }); - this.render(); - } }); }); </script> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Fix TypeDef error in history panel by adding sanity check for tags/annotations being open (Thanks, Aysam)
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c85f8fb5d63e/ Changeset: c85f8fb5d63e User: carlfeberhard Date: 2014-02-18 22:40:23 Summary: Fix TypeDef error in history panel by adding sanity check for tags/annotations being open (Thanks, Aysam) Affected #: 2 files diff -r 82d6ee82d5d4714eefdbce041f6c983a806a58d7 -r c85f8fb5d63e667b63e10cdce518254f56002f55 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -44,6 +44,11 @@ /** selected hda ids */ this.selectedHdaIds = []; + /** editor for tags - sub-view */ + this.tagsEditor = null; + /** editor for annotations - sub-view */ + this.annotationEditor = null; + // states/modes the panel can be in /** is the panel currently showing the dataset selection controls? */ this.selecting = attributes.selecting || false; @@ -250,8 +255,8 @@ selectable : this.selecting, hasUser : this.model.ownedByCurrUser(), logger : this.logger, - tagsEditorShown : !this.tagsEditor.isHidden(), - annotationEditorShown : !this.annotationEditor.isHidden() + tagsEditorShown : ( this.tagsEditor && !this.tagsEditor.isHidden() ), + annotationEditorShown : ( this.annotationEditor && !this.annotationEditor.isHidden() ) }); this._setUpHdaListeners( hdaView ); return hdaView; diff -r 82d6ee82d5d4714eefdbce041f6c983a806a58d7 -r c85f8fb5d63e667b63e10cdce518254f56002f55 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel"],function(c,a,b){var d=b.ReadOnlyHistoryPanel.extend({HDAViewClass:a.HDAEditView,initialize:function(e){e=e||{};this.selectedHdaIds=[];this.selecting=e.selecting||false;this.annotationEditorShown=e.annotationEditorShown||false;this.tagsEditorShown=e.tagsEditorShown||false;b.ReadOnlyHistoryPanel.prototype.initialize.call(this,e)},_setUpModelEventHandlers:function(){b.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this)},renderModel:function(){var e=$("<div/>");e.append(d.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(e);this._renderAnnotation(e)}e.find(".history-secondary-actions").prepend(this._renderSelectButton());e.find(".history-dataset-actions").toggle(this.selecting);e.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(e);this.renderHdas(e);return e},_renderTags:function(e){var f=this;this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDATagEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDATagEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){var f=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDAAnnotationEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDAAnnotationEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_renderSelectButton:function(e){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(e){e=e||this.$el;e.find("[title]").tooltip({placement:"bottom"});if(!this.model){return}this._setUpDatasetActionsPopup(e);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var f=this;e.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(g){var h=f.model.get("name");if(g&&g!==h){f.$el.find(".history-name").text(g);f.model.save({name:g}).fail(function(){f.$el.find(".history-name").text(f.model.previous("name"))})}else{f.$el.find(".history-name").text(h)}}})},_setUpDatasetActionsPopup:function(e){var f=this;(new PopupMenu(e.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.hide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Unhide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.unhide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Delete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype["delete"];f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Undelete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.undelete;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var g=c.HistoryDatasetAssociation.prototype.purge;f.getSelectedHdaCollection().ajaxQueue(g)}}}]))},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},createHdaView:function(f){var e=f.get("id"),g=new this.HDAViewClass({model:f,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[e],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:!this.tagsEditor.isHidden(),annotationEditorShown:!this.annotationEditor.isHidden()});this._setUpHdaListeners(g);return g},_setUpHdaListeners:function(f){var e=this;b.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,f);f.on("selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.union(e.selectedHdaIds,[h])});f.on("de-selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.without(e.selectedHdaIds,h)})},toggleHDATagEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.tagsEditor){g.tagsEditor.toggle.apply(g.tagsEditor,f)}})},toggleHDAAnnotationEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.annotationEditor){g.annotationEditor.toggle.apply(g.annotationEditor,f)}})},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$el.find(e.emptyMsgSelector).fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},events:_.extend(_.clone(b.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":function(f){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(e){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(e);_.each(this.hdaViews,function(f){f.showSelector(e)});this.selectedHdaIds=[]},hideSelectors:function(e){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(e);_.each(this.hdaViews,function(f){f.hideSelector(e)});this.selectedHdaIds=[]},toggleSelectors:function(e){if(!this.selecting){this.showSelectors(e)}else{this.hideSelectors(e)}},selectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.select(e)})},deselectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.deselect(e)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(e){return e.selected})},getSelectedHdaCollection:function(){return new c.HDACollection(_.map(this.getSelectedHdaViews(),function(e){return e.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:d}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel"],function(c,a,b){var d=b.ReadOnlyHistoryPanel.extend({HDAViewClass:a.HDAEditView,initialize:function(e){e=e||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.selecting=e.selecting||false;this.annotationEditorShown=e.annotationEditorShown||false;this.tagsEditorShown=e.tagsEditorShown||false;b.ReadOnlyHistoryPanel.prototype.initialize.call(this,e)},_setUpModelEventHandlers:function(){b.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this)},renderModel:function(){var e=$("<div/>");e.append(d.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(e);this._renderAnnotation(e)}e.find(".history-secondary-actions").prepend(this._renderSelectButton());e.find(".history-dataset-actions").toggle(this.selecting);e.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(e);this.renderHdas(e);return e},_renderTags:function(e){var f=this;this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDATagEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDATagEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){var f=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDAAnnotationEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDAAnnotationEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_renderSelectButton:function(e){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(e){e=e||this.$el;e.find("[title]").tooltip({placement:"bottom"});if(!this.model){return}this._setUpDatasetActionsPopup(e);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var f=this;e.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(g){var h=f.model.get("name");if(g&&g!==h){f.$el.find(".history-name").text(g);f.model.save({name:g}).fail(function(){f.$el.find(".history-name").text(f.model.previous("name"))})}else{f.$el.find(".history-name").text(h)}}})},_setUpDatasetActionsPopup:function(e){var f=this;(new PopupMenu(e.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.hide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Unhide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.unhide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Delete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype["delete"];f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Undelete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.undelete;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var g=c.HistoryDatasetAssociation.prototype.purge;f.getSelectedHdaCollection().ajaxQueue(g)}}}]))},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},createHdaView:function(f){var e=f.get("id"),g=new this.HDAViewClass({model:f,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[e],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.isHidden()),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.isHidden())});this._setUpHdaListeners(g);return g},_setUpHdaListeners:function(f){var e=this;b.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,f);f.on("selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.union(e.selectedHdaIds,[h])});f.on("de-selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.without(e.selectedHdaIds,h)})},toggleHDATagEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.tagsEditor){g.tagsEditor.toggle.apply(g.tagsEditor,f)}})},toggleHDAAnnotationEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.annotationEditor){g.annotationEditor.toggle.apply(g.annotationEditor,f)}})},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$el.find(e.emptyMsgSelector).fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},events:_.extend(_.clone(b.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":function(f){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(e){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(e);_.each(this.hdaViews,function(f){f.showSelector(e)});this.selectedHdaIds=[]},hideSelectors:function(e){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(e);_.each(this.hdaViews,function(f){f.hideSelector(e)});this.selectedHdaIds=[]},toggleSelectors:function(e){if(!this.selecting){this.showSelectors(e)}else{this.hideSelectors(e)}},selectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.select(e)})},deselectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.deselect(e)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(e){return e.selected})},getSelectedHdaCollection:function(){return new c.HDACollection(_.map(this.getSelectedHdaViews(),function(e){return e.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:d}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/33812bcdc523/ Changeset: 33812bcdc523 User: carlfeberhard Date: 2014-02-18 21:11:48 Summary: History panel: begin process of breaking up panel into more focused prototypes Affected #: 11 files diff -r 26e37f6af3a8a090d9d6e923fa3e90acb0e64572 -r 33812bcdc52393bf179dd501b4334be4ec4e97a7 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -887,10 +887,13 @@ history_dictionary = {} hda_dictionaries = [] + user_is_owner = False try: history_to_view = self.get_history( trans, id, False ) if not history_to_view: return trans.show_error_message( "The specified history does not exist." ) + if history_to_view.user == trans.user: + user_is_owner = True # Admin users can view any history if( ( history_to_view.user != trans.user ) @@ -925,7 +928,7 @@ + 'Please contact a Galaxy administrator if the problem persists.' ) return trans.fill_template_mako( "history/view.mako", - history=history_dictionary, hdas=hda_dictionaries, + history=history_dictionary, hdas=hda_dictionaries, user_is_owner=user_is_owner, show_deleted=show_deleted, show_hidden=show_hidden, use_panels=use_panels ) @web.expose @@ -941,9 +944,8 @@ # Security check raises error if user cannot access history. self.security_check( trans, history, False, True) - # Get datasets. + # Get datasets and annotations datasets = self.get_history_datasets( trans, history ) - # Get annotations. history.annotation = self.get_item_annotation_str( trans.sa_session, history.user, history ) for dataset in datasets: dataset.annotation = self.get_item_annotation_str( trans.sa_session, history.user, dataset ) @@ -957,8 +959,9 @@ else: user_item_rating = 0 ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, history ) - return trans.stream_template_mako( "history/display.mako", item = history, item_data = datasets, - user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) + + return trans.stream_template_mako( "history/display.mako", item=history, item_data=datasets, + user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) @web.expose @web.require_login( "share Galaxy histories" ) diff -r 26e37f6af3a8a090d9d6e923fa3e90acb0e64572 -r 33812bcdc52393bf179dd501b4334be4ec4e97a7 static/scripts/mvc/history/current-history-panel.js --- /dev/null +++ b/static/scripts/mvc/history/current-history-panel.js @@ -0,0 +1,285 @@ +define([ + "mvc/dataset/hda-edit", + "mvc/history/history-panel" +], function( hdaEdit, hpanel ){ +// ============================================================================ +/** session storage for history panel preferences (and to maintain state) + */ +var HistoryPanelPrefs = SessionStorageModel.extend({ + defaults : { + /** is the panel currently showing the search/filter controls? */ + searching : false, + /** should the tags editor be shown or hidden initially? */ + tagsEditorShown : false, + /** should the annotation editor be shown or hidden initially? */ + annotationEditorShown : false + }, + toString : function(){ + return 'HistoryPanelPrefs(' + JSON.stringify( this.toJSON() ) + ')'; + } +}); + +/** key string to store panel prefs (made accessible on class so you can access sessionStorage directly) */ +HistoryPanelPrefs.storageKey = function storageKey(){ + return ( 'history-panel' ); +}; + +/* ============================================================================= +TODO: + +============================================================================= */ +/** @class View/Controller for the user's current history model as used in the history + * panel (current right hand panel). + * @name HistoryPanel + * + * @augments Backbone.View + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var CurrentHistoryPanel = hpanel.HistoryPanel.extend( +/** @lends HistoryPanel.prototype */{ + + ///** logger used to record this.log messages, commonly set to console */ + //// comment this out to suppress log output + //logger : console, + + /** class to use for constructing the HDA views */ + HDAViewClass : hdaEdit.HDAEditView, + + emptyMsg : _l( "This history is empty. Click 'Get Data' on the left pane to start" ), + noneFoundMsg : _l( "No matching datasets found" ), + + // ......................................................................... SET UP + /** Set up the view, set up storage, bind listeners to HDACollection events + * @param {Object} attributes + * @config {Object} urlTemplates.hda nested object containing url templates for HDAViews + * @throws 'needs urlTemplates' if urlTemplates.history or urlTemplates.hda aren't present + * @see PersistentStorage + * @see Backbone.View#initialize + */ + initialize : function( attributes ){ + attributes = attributes || {}; + + // ---- persistent preferences + /** maintain state / preferences over page loads */ + this.preferences = new HistoryPanelPrefs( _.extend({ + id : HistoryPanelPrefs.storageKey() + }, _.pick( attributes, _.keys( HistoryPanelPrefs.prototype.defaults ) ))); + + hpanel.HistoryPanel.prototype.initialize.call( this, attributes ); + if( this.model ){ + console.debug( this.model ); + this.model.checkForUpdates(); + } + }, + + // ------------------------------------------------------------------------ loading history/hda models + /** (re-)loads the user's current history & hdas w/ details */ + loadCurrentHistory : function( attributes ){ + // implemented as a 'fresh start' or for when there is no model (intial panel render) + var panel = this; + return this.loadHistoryWithHDADetails( 'current', attributes ) + .then(function( historyData, hdaData ){ + panel.trigger( 'current-history', panel ); + }); + }, + + /** loads a history & hdas w/ details and makes them the current history */ + switchToHistory : function( historyId, attributes ){ + //console.info( 'switchToHistory:', historyId, attributes ); + var panel = this, + historyFn = function(){ + // make this current and get history data with one call + return jQuery.post( galaxy_config.root + 'api/histories/' + historyId + '/set_as_current' ); + }; + return this.loadHistoryWithHDADetails( historyId, attributes, historyFn ) + .then(function( historyData, hdaData ){ + panel.trigger( 'switched-history', panel ); + }); + }, + + /** creates a new history on the server and sets it as the user's current history */ + createNewHistory : function( attributes ){ + if( !Galaxy || !Galaxy.currUser || Galaxy.currUser.isAnonymous() ){ + this.displayMessage( 'error', _l( 'You must be logged in to create histories' ) ); + return $.when(); + } + var panel = this, + historyFn = function(){ + // get history data from posting a new history (and setting it to current) + return jQuery.post( galaxy_config.root + 'api/histories', { current: true }); + }; + // id undefined bc there is no historyId yet - the server will provide + // (no need for details - nothing expanded in new history) + return this.loadHistory( undefined, attributes, historyFn ) + .then(function( historyData, hdaData ){ + panel.trigger( 'new-history', panel ); + }); + }, + + /** release/free/shutdown old models and set up panel for new models */ + setModel : function( newHistoryJSON, newHdaJSON, attributes ){ + attributes = attributes || {}; + hpanel.HistoryPanel.prototype.setModel.call( this, newHistoryJSON, newHdaJSON, attributes ); + this.model.checkForUpdates(); + return this; + }, + + // ------------------------------------------------------------------------ history/hda event listening + /** listening for history and HDA events */ + _setUpModelEventHandlers : function(){ + hpanel.HistoryPanel.prototype._setUpModelEventHandlers.call( this ); + // ---- history + // update the quota meter when current history changes size + if( Galaxy && Galaxy.quotaMeter ){ + this.listenTo( this.model, 'change:nice_size', function(){ + //console.info( '!! model size changed:', this.model.get( 'nice_size' ) ) +//TODO: global + Galaxy.quotaMeter.update(); + }); + } + + // if an a hidden hda is created (gen. by a workflow), moves thru the updater to the ready state, + // then: remove it from the collection if the panel is set to NOT show hidden datasets + this.model.hdas.on( 'state:ready', function( hda, newState, oldState ){ + if( ( !hda.get( 'visible' ) ) + && ( !this.storage.get( 'show_hidden' ) ) ){ + this.removeHdaView( this.hdaViews[ hda.id ] ); + } + }, this ); + + }, + + // ------------------------------------------------------------------------ panel rendering + /** Render urls, historyPanel body, and hdas (if any are shown) + * @fires: rendered when the panel is attached and fully visible + * @see Backbone.View#render + */ + render : function( speed, callback ){ + // send a speed of 0 to have no fade in/out performed + speed = ( speed === undefined )?( this.fxSpeed ):( speed ); + var panel = this, + $newRender; + + // handle the possibility of no model (can occur if fetching the model returns an error) + if( this.model ){ + $newRender = this.renderModel(); + } else { + $newRender = this.renderWithoutModel(); + } + + // fade out existing, swap with the new, fade in, set up behaviours + $( panel ).queue( 'fx', [ + function( next ){ + //panel.$el.fadeTo( panel.fxSpeed, 0.0001, next ); + if( speed && panel.$el.is( ':visible' ) ){ + panel.$el.fadeOut( speed, next ); + } else { + next(); + } + }, + function( next ){ + // swap over from temp div newRender + panel.$el.empty(); + if( $newRender ){ + panel.$el.append( $newRender.children() ); + panel.renderBasedOnPrefs(); + } + next(); + }, + function( next ){ + if( speed && !panel.$el.is( ':visible' ) ){ + panel.$el.fadeIn( speed, next ); + } else { + next(); + } + }, + function( next ){ + //TODO: ideally, these would be set up before the fade in (can't because of async save text) + if( callback ){ callback.call( this ); } + panel.trigger( 'rendered', this ); + next(); + } + ]); + return this; + }, + + renderBasedOnPrefs : function(){ + if( this.preferences.get( 'searching' ) ){ + this.showSearchControls( 0 ); + } + }, + + // ........................................................................ external objects/MVC + //TODO: remove quota meter from panel and remove this + /** add listeners to an external quota meter (mvc/user/user-quotameter.js) */ + connectToQuotaMeter : function( quotaMeter ){ + if( !quotaMeter ){ + return this; + } + // show/hide the 'over quota message' in the history when the meter tells it to + this.listenTo( quotaMeter, 'quota:over', this.showQuotaMessage ); + this.listenTo( quotaMeter, 'quota:under', this.hideQuotaMessage ); + + // having to add this to handle re-render of hview while overquota (the above do not fire) + this.on( 'rendered rendered:initial', function(){ + if( quotaMeter && quotaMeter.isOverQuota() ){ + this.showQuotaMessage(); + } + }); + return this; + }, + +//TODO: this seems more like a per user message than a history message; IOW, this doesn't belong here + /** Show the over quota message (which happens to be in the history panel). + */ + showQuotaMessage : function(){ + var msg = this.$el.find( '.quota-message' ); + //this.log( this + ' showing quota message:', msg, userData ); + if( msg.is( ':hidden' ) ){ msg.slideDown( this.fxSpeed ); } + }, + +//TODO: this seems more like a per user message than a history message + /** Hide the over quota message (which happens to be in the history panel). + */ + hideQuotaMessage : function(){ + var msg = this.$el.find( '.quota-message' ); + //this.log( this + ' hiding quota message:', msg, userData ); + if( !msg.is( ':hidden' ) ){ msg.slideUp( this.fxSpeed ); } + }, + +//TODO: move show_deleted/hidden into panel from opt menu and remove this + /** add listeners to an external options menu (templates/webapps/galaxy/root/index.mako) */ + connectToOptionsMenu : function( optionsMenu ){ + if( !optionsMenu ){ + return this; + } + // set a visible indication in the popupmenu for show_hidden/deleted based on the currHistoryPanel's settings + this.on( 'new-storage', function( storage, panel ){ + if( optionsMenu && storage ){ + optionsMenu.findItemByHtml( _l( 'Include Deleted Datasets' ) ).checked = storage.get( 'show_deleted' ); + optionsMenu.findItemByHtml( _l( 'Include Hidden Datasets' ) ).checked = storage.get( 'show_hidden' ); + } + }); + return this; + }, + + /** Return a string rep of the history + */ + toString : function(){ + return 'CurrentHistoryPanel(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')'; + } +}); + +//------------------------------------------------------------------------------ TEMPLATES +CurrentHistoryPanel.templates = { + historyPanel : Handlebars.templates[ 'template-history-historyPanel' ], + anonHistoryPanel : Handlebars.templates[ 'template-history-historyPanel-anon' ] +}; + +//============================================================================== + return { + CurrentHistoryPanel : CurrentHistoryPanel + }; +}); diff -r 26e37f6af3a8a090d9d6e923fa3e90acb0e64572 -r 33812bcdc52393bf179dd501b4334be4ec4e97a7 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -75,7 +75,7 @@ /** cached timeout id for the HDA updater */ this.updateTimeoutId = null; // set up update timeout if needed - this.checkForUpdates(); + //this.checkForUpdates(); }, /** set up any event listeners for this history including those to the contained HDAs diff -r 26e37f6af3a8a090d9d6e923fa3e90acb0e64572 -r 33812bcdc52393bf179dd501b4334be4ec4e97a7 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -1,157 +1,46 @@ define([ - "mvc/history/history-model", "mvc/dataset/hda-model", - "mvc/dataset/hda-base", - "mvc/dataset/hda-edit" -], function( historyModel, hdaModel, hdaBase, hdaEdit ){ + "mvc/dataset/hda-edit", + "mvc/history/readonly-history-panel" +], function( hdaModel, hdaEdit, readonlyPanel ){ +/* ============================================================================= +TODO: - -// ============================================================================ -/** session storage for history panel preferences (and to maintain state) - */ -var HistoryPanelPrefs = SessionStorageModel.extend({ - defaults : { - /** is the panel currently showing the search/filter controls? */ - searching : false, - /** should the tags editor be shown or hidden initially? */ - tagsEditorShown : false, - /** should the annotation editor be shown or hidden initially? */ - annotationEditorShown : false - }, - toString : function(){ - return 'HistoryPanelPrefs(' + JSON.stringify( this.toJSON() ) + ')'; - } -}); - -/** key string to store panel prefs (made accessible on class so you can access sessionStorage directly) */ -HistoryPanelPrefs.storageKey = function storageKey(){ - return ( 'history-panel' ); -}; - - -// ============================================================================ -/** session storage for individual history preferences - */ -var HistoryPrefs = SessionStorageModel.extend({ - defaults : { - //TODO:?? expandedHdas to array? - expandedHdas : {}, - //TODO:?? move to user? - show_deleted : false, - show_hidden : false - //TODO: add scroll position? - }, - /** add an hda id to the hash of expanded hdas */ - addExpandedHda : function( id ){ - this.save( 'expandedHdas', _.extend( this.get( 'expandedHdas' ), _.object([ id ], [ true ]) ) ); - }, - /** remove an hda id from the hash of expanded hdas */ - removeExpandedHda : function( id ){ - this.save( 'expandedHdas', _.omit( this.get( 'expandedHdas' ), id ) ); - }, - toString : function(){ - return 'HistoryPrefs(' + this.id + ')'; - } -}); - -/** key string to store each histories settings under */ -HistoryPrefs.historyStorageKey = function historyStorageKey( historyId ){ - // class lvl for access w/o instantiation - if( !historyId ){ - throw new Error( 'HistoryPrefs.historyStorageKey needs valid id: ' + historyId ); - } - // single point of change - return ( 'history:' + historyId ); -}; - - -/* ============================================================================= -Backbone.js implementation of history panel - -r.js optimizer cline: -r.js -o baseUrl=. name=./mvc/history/history-panel.js out=history-panel.min.js - -TODO: - tags & annotations -> out - use model.save instead of urls - - feature creep: - lineage - hide button - show permissions in info - show shared/sharing status on ds, history - selection, multi-select (and actions common to selected (ugh)) - searching - sorting, re-shuffling - ============================================================================= */ -/** @class View/Controller for the history model as used in the history - * panel (current right hand panel). +/** @class View/Controller for the history model. * @name HistoryPanel * + * Allows: + * (everything ReadOnlyHistoryPanel allows) + * changing the name + * displaying and editing tags and annotations + * multi-selection and operations on mulitple hdas + * Does not allow: + * changing the name + * * @augments Backbone.View * @borrows LoggableMixin#logger as #logger * @borrows LoggableMixin#log as #log * @constructs */ -var HistoryPanel = Backbone.View.extend( LoggableMixin ).extend( +var HistoryPanel = readonlyPanel.ReadOnlyHistoryPanel.extend( /** @lends HistoryPanel.prototype */{ - + ///** logger used to record this.log messages, commonly set to console */ //// comment this out to suppress log output //logger : console, - /** which class to use for constructing the HDA views */ - //defaultHDAViewClass : hdaBase.HDABaseView, - defaultHDAViewClass : hdaEdit.HDAEditView, + /** class to use for constructing the HDA views */ + HDAViewClass : hdaEdit.HDAEditView, - tagName : 'div', - className : 'history-panel', - - /** (in ms) that jquery effects will use */ - fxSpeed : 'fast', - - datasetsSelector : '.datasets-list', - emptyMsgSelector : '.empty-history-message', - msgsSelector : '.message-container', - // ......................................................................... SET UP /** Set up the view, set up storage, bind listeners to HDACollection events * @param {Object} attributes - * @config {Object} urlTemplates.hda nested object containing url templates for HDAViews - * @throws 'needs urlTemplates' if urlTemplates.history or urlTemplates.hda aren't present - * @see PersistentStorage - * @see Backbone.View#initialize */ initialize : function( attributes ){ attributes = attributes || {}; - // set the logger if requested - if( attributes.logger ){ - this.logger = attributes.logger; - } - this.log( this + '.initialize:', attributes ); // ---- set up instance vars - // control contents/behavior based on where (and in what context) the panel is being used - /** which backbone view class to use when displaying the hda list */ - this.HDAViewClass = attributes.HDAViewClass || this.defaultHDAViewClass; - /** where should pages from links be displayed? (default to new tab/window) */ - this.linkTarget = attributes.linkTarget || '_blank'; - - // ---- sub views and saved elements - /** map of hda model ids to hda views */ - this.hdaViews = {}; - /** loading indicator */ - this.indicator = new LoadingIndicator( this.$el ); - - // ---- persistent state and preferences - /** maintain state / preferences over page loads */ - this.preferences = new HistoryPanelPrefs( _.extend({ - id : HistoryPanelPrefs.storageKey() - }, _.pick( attributes, _.keys( HistoryPanelPrefs.prototype.defaults ) ))); - - /** filters for displaying hdas */ - this.filters = []; /** selected hda ids */ this.selectedHdaIds = []; @@ -161,443 +50,33 @@ this.annotationEditorShown = attributes.annotationEditorShown || false; this.tagsEditorShown = attributes.tagsEditorShown || false; - this._setUpListeners(); - - // ---- handle models passed on init - if( this.model ){ - this._setUpWebStorage( attributes.initiallyExpanded, attributes.show_deleted, attributes.show_hidden ); - this._setUpModelEventHandlers(); - } -//TODO: remove? - // ---- and any run functions - if( attributes.onready ){ - attributes.onready.call( this ); - } + readonlyPanel.ReadOnlyHistoryPanel.prototype.initialize.call( this, attributes ); }, - /** create any event listeners for the panel - * @fires: rendered:initial on the first render - * @fires: empty-history when switching to a history with no HDAs or creating a new history - */ - _setUpListeners : function(){ - // ---- event handlers for self - this.on( 'error', function( model, xhr, options, msg, details ){ - this.errorHandler( model, xhr, options, msg, details ); - }); - - this.on( 'loading-history', function(){ - // show the loading indicator when loading a new history starts... - this.showLoadingIndicator( 'loading history...', 40 ); - }); - this.on( 'loading-done', function(){ - // ...hiding it again when loading is done (or there's been an error) - this.hideLoadingIndicator( 40 ); - }); - - // throw the first render up as a diff namespace using once - // (for outside consumption) - this.once( 'rendered', function(){ - this.trigger( 'rendered:initial', this ); - return false; - }); - - // trigger an event when there are no visible hdas - // (for outside consumption) - this.on( 'switched-history current-history new-history', function(){ - if( _.isEmpty( this.hdaViews ) ){ - this.trigger( 'empty-history', this ); - } - }); - - // debugging - if( this.logger ){ - this.on( 'all', function( event ){ - this.log( this + '', arguments ); - }, this ); - } - }, - - //TODO: see base-mvc - //onFree : function(){ - // _.each( this.hdaViews, function( view, modelId ){ - // view.free(); - // }); - // this.hdaViews = null; - //}, - - // ........................................................................ error handling - /** Event listener to handle errors (from the panel, the history, or the history's HDAs) - * @param {Model or View} model the (Backbone) source of the error - * @param {XMLHTTPRequest} xhr any ajax obj. assoc. with the error - * @param {Object} options the options map commonly used with bbone ajax - * @param {String} msg optional message passed to ease error location - * @param {Object} msg optional object containing error details - */ - errorHandler : function( model, xhr, options, msg, details ){ - var parsed = this._parseErrorMessage( model, xhr, options, msg, details ); - - // interrupted ajax - if( xhr && xhr.status === 0 && xhr.readyState === 0 ){ - - // bad gateway - } else if( xhr && xhr.status === 502 ){ -//TODO: gmail style 'reconnecting in Ns' - - // otherwise, show an error message inside the panel - } else { - // it's possible to have a triggered error before the message container is rendered - wait for it to show - if( !this.$el.find( this.msgsSelector ).is( ':visible' ) ){ - this.once( 'rendered', function(){ - this.displayMessage( 'error', parsed.message, parsed.details ); - }); - } else { - this.displayMessage( 'error', parsed.message, parsed.details ); - } - } - }, - - /** Parse an error event into an Object usable by displayMessage based on the parameters - * note: see errorHandler for more info on params - */ - _parseErrorMessage : function( model, xhr, options, msg, details ){ - var user = Galaxy.currUser, - // add the args (w/ some extra info) into an obj - parsed = { - message : this._bePolite( msg ), - details : { - user : ( user instanceof User )?( user.toJSON() ):( user + '' ), - source : ( model instanceof Backbone.Model )?( model.toJSON() ):( model + '' ), - xhr : xhr, - options : ( xhr )?( _.omit( options, 'xhr' ) ):( options ) - } - }; - // add any extra details passed in - _.extend( parsed.details, details || {} ); - // fancy xhr.header parsing (--> obj) - if( xhr && _.isFunction( xhr.getAllResponseHeaders ) ){ - var responseHeaders = xhr.getAllResponseHeaders(); - responseHeaders = _.compact( responseHeaders.split( '\n' ) ); - responseHeaders = _.map( responseHeaders, function( header ){ - return header.split( ': ' ); - }); - parsed.details.xhr.responseHeaders = _.object( responseHeaders ); - } - return parsed; - }, - - /** Modify an error message to be fancy and wear a monocle. */ - _bePolite : function( msg ){ - msg = msg || _l( 'An error occurred while getting updates from the server' ); - return msg + '. ' + _l( 'Please contact a Galaxy administrator if the problem persists.' ); - }, - - // ------------------------------------------------------------------------ loading history/hda models - - //NOTE: all the following fns replace the existing history model with a new model - // (in the following 'details' refers to the full set of hda api data (urls, display_apps, misc_info, etc.) - // - hdas w/o details will have summary data only (name, hid, deleted, visible, state, etc.)) - - /** (re-)loads the user's current history & hdas w/ details */ - loadCurrentHistory : function( attributes ){ - // implemented as a 'fresh start' or for when there is no model (intial panel render) - var panel = this; - return this.loadHistoryWithHDADetails( 'current', attributes ) - .then(function( historyData, hdaData ){ - panel.trigger( 'current-history', panel ); - }); - }, - - /** loads a history & hdas w/ details and makes them the current history */ - switchToHistory : function( historyId, attributes ){ - //console.info( 'switchToHistory:', historyId, attributes ); - var panel = this, - historyFn = function(){ - // make this current and get history data with one call - return jQuery.post( galaxy_config.root + 'api/histories/' + historyId + '/set_as_current' ); - }; - return this.loadHistoryWithHDADetails( historyId, attributes, historyFn ) - .then(function( historyData, hdaData ){ - panel.trigger( 'switched-history', panel ); - }); - }, - - /** creates a new history on the server and sets it as the user's current history */ - createNewHistory : function( attributes ){ - if( !Galaxy || !Galaxy.currUser || Galaxy.currUser.isAnonymous() ){ - this.displayMessage( 'error', _l( 'You must be logged in to create histories' ) ); - return $.when(); - } - var panel = this, - historyFn = function(){ - // get history data from posting a new history (and setting it to current) - return jQuery.post( galaxy_config.root + 'api/histories', { current: true }); - }; - // id undefined bc there is no historyId yet - the server will provide - // (no need for details - nothing expanded in new history) - return this.loadHistory( undefined, attributes, historyFn ) - .then(function( historyData, hdaData ){ - panel.trigger( 'new-history', panel ); - }); - }, - - /** loads a history & hdas w/ details (but does not make them the current history) */ - loadHistoryWithHDADetails : function( historyId, attributes, historyFn, hdaFn ){ - //console.info( 'loadHistoryWithHDADetails:', historyId, attributes, historyFn, hdaFn ); - var panel = this, - // will be called to get hda ids that need details from the api - hdaDetailIds = function( historyData ){ -//TODO: non-visible HDAs are getting details loaded... either stop loading them at all or filter ids thru isVisible - return panel.getExpandedHdaIds( historyData.id ); - }; - return this.loadHistory( historyId, attributes, historyFn, hdaFn, hdaDetailIds ); - }, - - /** loads a history & hdas w/ NO details (but does not make them the current history) */ - loadHistory : function( historyId, attributes, historyFn, hdaFn, hdaDetailIds ){ - this.trigger( 'loading-history', this ); - attributes = attributes || {}; - var panel = this; - //console.info( 'loadHistory:', historyId, attributes, historyFn, hdaFn, hdaDetailIds ); - var xhr = historyModel.History.getHistoryData( historyId, { - historyFn : historyFn, - hdaFn : hdaFn, - hdaDetailIds : attributes.initiallyExpanded || hdaDetailIds - }); - return this._loadHistoryFromXHR( xhr, attributes ) - .fail( function( xhr, where, history ){ - // throw an error up for the error handler - panel.trigger( 'error', panel, xhr, attributes, _l( 'An error was encountered while ' + where ), - { historyId: historyId, history: history || {} }); - }) - .always( function(){ - // bc hideLoadingIndicator relies on this firing - panel.trigger( 'loading-done', panel ); - }); - }, - - /** given an xhr that will provide both history and hda data, pass data to set model or handle xhr errors */ - _loadHistoryFromXHR : function( xhr, attributes ){ - var panel = this; - xhr.then( function( historyJSON, hdaJSON ){ - panel.setModel( historyJSON, hdaJSON, attributes ); - }); - xhr.fail( function( xhr, where ){ - // always render - whether we get a model or not - panel.render(); - }); - return xhr; - }, - - /** release/free/shutdown old models and set up panel for new models */ - setModel : function( newHistoryJSON, newHdaJSON, attributes ){ - attributes = attributes || {}; - //console.info( 'setModel:', newHistoryJSON, newHdaJSON.length, attributes ); - - // stop/release the previous model, and clear cache to hda sub-views - if( this.model ){ - this.model.clearUpdateTimeout(); - this.stopListening( this.model ); - this.stopListening( this.model.hdas ); - //TODO: see base-mvc - //this.model.free(); - } - this.hdaViews = {}; - - // set up the new model and render - if( Galaxy && Galaxy.currUser ){ -//TODO: global - newHistoryJSON.user = Galaxy.currUser.toJSON(); - } - this.model = new historyModel.History( newHistoryJSON, newHdaJSON, attributes ); - this._setUpWebStorage( attributes.initiallyExpanded, attributes.show_deleted, attributes.show_hidden ); - this._setUpModelEventHandlers(); - this.selectedHdaIds = []; - this.trigger( 'new-model', this ); - this.render(); - return this; - }, - - // ------------------------------------------------------------------------ browser stored prefs - /** Set up client side storage. Currently PersistanStorage keyed under 'HistoryPanel.<id>' - * @param {Object} initiallyExpanded - * @param {Boolean} show_deleted whether to show deleted HDAs (overrides stored) - * @param {Boolean} show_hidden - * @see PersistentStorage - */ - _setUpWebStorage : function( initiallyExpanded, show_deleted, show_hidden ){ - //console.debug( '_setUpWebStorage', initiallyExpanded, show_deleted, show_hidden ); - this.storage = new HistoryPrefs({ - id: HistoryPrefs.historyStorageKey( this.model.get( 'id' ) ) - }); - - // expanded Hdas is a map of hda.ids -> a boolean repr'ing whether this hda's body is already expanded - // store any pre-expanded ids passed in - if( _.isObject( initiallyExpanded ) ){ - this.storage.set( 'exandedHdas', initiallyExpanded ); - } - - // get the show_deleted/hidden settings giving priority to values passed in, using web storage otherwise - // if the page has specifically requested show_deleted/hidden, these will be either true or false - // (as opposed to undefined, null) - and we give priority to that setting - if( _.isBoolean( show_deleted ) ){ - this.storage.set( 'show_deleted', show_deleted ); - } - if( _.isBoolean( show_hidden ) ){ - this.storage.set( 'show_hidden', show_hidden ); - } - - this.trigger( 'new-storage', this.storage, this ); - this.log( this + ' (init\'d) storage:', this.storage.get() ); - }, - - /** clear all stored history panel data */ - clearWebStorage : function(){ - for( var key in sessionStorage ){ - if( key.indexOf( 'history:' ) === 0 ){ - sessionStorage.removeItem( key ); - } - } - }, - - /** get all stored data as an Object for a history with the given id */ - getStoredOptions : function( historyId ){ - if( !historyId || historyId === 'current' ){ - return ( this.storage )?( this.storage.get() ):( {} ); - } - //TODO: make storage engine generic - var item = sessionStorage.getItem( HistoryPrefs.historyStorageKey( historyId ) ); - return ( item === null )?( {} ):( JSON.parse( item ) ); - }, - - /** get an array of expanded hda ids for the given history id */ - getExpandedHdaIds : function( historyId ){ - var expandedHdas = this.getStoredOptions( historyId ).expandedHdas; - return (( _.isEmpty( expandedHdas ) )?( [] ):( _.keys( expandedHdas ) )); - }, - - // ------------------------------------------------------------------------ history/hda event listening + // ------------------------------------------------------------------------ panel rendering /** listening for history and HDA events */ _setUpModelEventHandlers : function(){ - // ---- history - // on a model error - bounce it up to the panel and remove it from the model - this.model.on( 'error error:hdas', function( model, xhr, options, msg ){ - this.errorHandler( model, xhr, options, msg ); - }, this ); + readonlyPanel.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call( this ); - // don't need to re-render entire model on all changes, just render disk size when it changes this.model.on( 'change:nice_size', this.updateHistoryDiskSize, this ); - // update the quota meter when current history changes size - if( Galaxy && Galaxy.quotaMeter ){ - this.listenTo( this.model, 'change:nice_size', function(){ - //console.info( '!! model size changed:', this.model.get( 'nice_size' ) ) -//TODO: global - Galaxy.quotaMeter.update(); - }); - } - - // ---- hdas - // bind events from the model's hda collection - // note: don't listen to the hdas for errors, history will pass that to us - //this.model.hdas.on( 'reset', this.addAll, this ); - this.model.hdas.on( 'add', this.addHdaView, this ); - this.model.hdas.on( 'change:deleted', this.handleHdaDeletionChange, this ); this.model.hdas.on( 'change:visible', this.handleHdaVisibleChange, this ); - // when an hda is purged the disk size changes this.model.hdas.on( 'change:purged', function( hda ){ // hafta get the new nice-size w/o the purged hda this.model.fetch(); }, this ); - - // if an a hidden hda is created (gen. by a workflow), moves thru the updater to the ready state, - // then: remove it from the collection if the panel is set to NOT show hidden datasets - this.model.hdas.on( 'state:ready', function( hda, newState, oldState ){ - if( ( !hda.get( 'visible' ) ) - && ( !this.storage.get( 'show_hidden' ) ) ){ - this.removeHdaView( this.hdaViews[ hda.id ] ); - } - }, this ); - }, // ------------------------------------------------------------------------ panel rendering - /** Render urls, historyPanel body, and hdas (if any are shown) - * @fires: rendered when the panel is attached and fully visible - * @see Backbone.View#render - */ - render : function( speed, callback ){ - // send a speed of 0 to have no fade in/out performed - speed = ( speed === undefined )?( this.fxSpeed ):( speed ); - var panel = this, - $newRender; - - // handle the possibility of no model (can occur if fetching the model returns an error) - if( this.model ){ - $newRender = this.renderModel(); - } else { - $newRender = this.renderWithoutModel(); - } - - // fade out existing, swap with the new, fade in, set up behaviours - $( panel ).queue( 'fx', [ - function( next ){ - //panel.$el.fadeTo( panel.fxSpeed, 0.0001, next ); - if( speed && panel.$el.is( ':visible' ) ){ - panel.$el.fadeOut( speed, next ); - } else { - next(); - } - }, - function( next ){ - // swap over from temp div newRender - panel.$el.empty(); - if( $newRender ){ - panel.$el.append( $newRender.children() ); - panel.renderBasedOnPrefs(); - } - next(); - }, - function( next ){ - if( speed && !panel.$el.is( ':visible' ) ){ - panel.$el.fadeIn( speed, next ); - } else { - next(); - } - }, - function( next ){ - //TODO: ideally, these would be set up before the fade in (can't because of async save text) - if( callback ){ callback.call( this ); } - panel.trigger( 'rendered', this ); - next(); - } - ]); - return this; - }, - - /** render with no history data */ - renderWithoutModel : function( ){ - // we'll always need the message container - var $newRender = $( '<div/>' ), - $msgContainer = $( '<div/>' ).addClass( 'message-container' ) - .css({ 'margin-left': '4px', 'margin-right': '4px' }); - return $newRender.append( $msgContainer ); - }, - /** render with history data */ renderModel : function( ){ var $newRender = $( '<div/>' ); - // render based on anonymity, set up behaviors - if( !Galaxy || !Galaxy.currUser || Galaxy.currUser.isAnonymous() ){ - $newRender.append( HistoryPanel.templates.anonHistoryPanel( this.model.toJSON() ) ); - - } else { - $newRender.append( HistoryPanel.templates.historyPanel( this.model.toJSON() ) ); - if( Galaxy.currUser.id && Galaxy.currUser.id === this.model.get( 'user_id' ) ){ - this._renderTags( $newRender ); - this._renderAnnotation( $newRender ); - } + $newRender.append( HistoryPanel.templates.historyPanel( this.model.toJSON() ) ); + if( Galaxy.currUser.id && Galaxy.currUser.id === this.model.get( 'user_id' ) ){ + this._renderTags( $newRender ); + this._renderAnnotation( $newRender ); } // search and select available to both anon/logged-in users $newRender.find( '.history-secondary-actions' ).prepend( this._renderSelectButton() ); @@ -611,12 +90,6 @@ return $newRender; }, - renderBasedOnPrefs : function(){ - if( this.preferences.get( 'searching' ) ){ - this.showSearchControls( 0 ); - } - }, - _renderTags : function( $where ){ var panel = this; this.tagsEditor = new TagsEditor({ @@ -625,11 +98,9 @@ onshowFirstTime : function(){ this.render(); }, // show hide hda view tag editors when this is shown/hidden onshow : function(){ - panel.preferences.set( 'tagsEditorShown', true ); panel.toggleHDATagEditors( true, panel.fxSpeed ); }, onhide : function(){ - panel.preferences.set( 'tagsEditorShown', false ); panel.toggleHDATagEditors( false, panel.fxSpeed ); }, $activator : faIconButton({ @@ -638,9 +109,6 @@ faIcon : 'fa-tags' }).appendTo( $where.find( '.history-secondary-actions' ) ) }); - if( this.preferences.get( 'tagsEditorShown' ) ){ - this.tagsEditor.toggle( true ); - } }, _renderAnnotation : function( $where ){ var panel = this; @@ -650,11 +118,9 @@ onshowFirstTime : function(){ this.render(); }, // show hide hda view annotation editors when this is shown/hidden onshow : function(){ - panel.preferences.set( 'annotationEditorShown', true ); panel.toggleHDAAnnotationEditors( true, panel.fxSpeed ); }, onhide : function(){ - panel.preferences.set( 'annotationEditorShown', false ); panel.toggleHDAAnnotationEditors( false, panel.fxSpeed ); }, $activator : faIconButton({ @@ -663,18 +129,8 @@ faIcon : 'fa-comment' }).appendTo( $where.find( '.history-secondary-actions' ) ) }); - if( this.preferences.get( 'annotationEditorShown' ) ){ - this.annotationEditor.toggle( true ); - } }, - /** button for opening search */ - _renderSearchButton : function( $where ){ - return faIconButton({ - title : _l( 'Search datasets' ), - classes : 'history-search-btn', - faIcon : 'fa-search' - }); - }, + /** button for starting select mode */ _renderSelectButton : function( $where ){ return faIconButton({ @@ -762,45 +218,23 @@ }, // ------------------------------------------------------------------------ hda sub-views - /** alias to the model. Updates the hda list only (not the history) */ - refreshHdas : function( detailIds, options ){ - if( this.model ){ - return this.model.refresh( detailIds, options ); - } - // may have callbacks - so return an empty promise - return $.when(); + /** If this hda is deleted and we're not showing deleted hdas, remove the view + * @param {HistoryDataAssociation} the hda to check + */ + handleHdaDeletionChange : function( hda ){ + if( hda.get( 'deleted' ) && !this.storage.get( 'show_deleted' ) ){ + this.removeHdaView( this.hdaViews[ hda.id ] ); + } // otherwise, the hdaView rendering should handle it }, - /** Add an hda view to the panel for the given hda - * @param {HistoryDatasetAssociation} hda + + /** If this hda is hidden and we're not showing hidden hdas, remove the view + * @param {HistoryDataAssociation} the hda to check */ - addHdaView : function( hda ){ - this.log( 'add.' + this, hda ); - var panel = this; - - // don't add the view if it wouldn't be visible accrd. to current settings - if( !hda.isVisible( this.storage.get( 'show_deleted' ), this.storage.get( 'show_hidden' ) ) ){ - return; - } - - // create and prepend to current el, if it was empty fadeout the emptyMsg first - $({}).queue([ - function fadeOutEmptyMsg( next ){ - var $emptyMsg = panel.$el.find( panel.emptyMsgSelector ); - if( $emptyMsg.is( ':visible' ) ){ - $emptyMsg.fadeOut( panel.fxSpeed, next ); - } else { - next(); - } - }, - function createAndPrepend( next ){ - panel.scrollToTop(); - var $whereTo = panel.$el.find( panel.datasetsSelector ), - hdaView = panel.createHdaView( hda ); - panel.hdaViews[ hda.id ] = hdaView; - hdaView.render().$el.hide().prependTo( $whereTo ).slideDown( panel.fxSpeed ); - } - ]); + handleHdaVisibleChange : function( hda ){ + if( hda.hidden() && !this.storage.get( 'show_hidden' ) ){ + this.removeHdaView( this.hdaViews[ hda.id ] ); + } // otherwise, the hdaView rendering should handle it }, /** Create an HDA view for the given HDA (but leave attachment for addHdaView above) @@ -816,8 +250,8 @@ selectable : this.selecting, hasUser : this.model.ownedByCurrUser(), logger : this.logger, - tagsEditorShown : this.preferences.get( 'tagsEditorShown' ), - annotationEditorShown : this.preferences.get( 'annotationEditorShown' ) + tagsEditorShown : !this.tagsEditor.isHidden(), + annotationEditorShown : !this.annotationEditor.isHidden() }); this._setUpHdaListeners( hdaView ); return hdaView; @@ -829,13 +263,8 @@ */ _setUpHdaListeners : function( hdaView ){ var historyView = this; - // maintain a list of hdas whose bodies are expanded - hdaView.on( 'body-expanded', function( id ){ - historyView.storage.addExpandedHda( id ); - }); - hdaView.on( 'body-collapsed', function( id ){ - historyView.storage.removeExpandedHda( id ); - }); + readonlyPanel.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call( this, hdaView ); + // maintain a list of hdas that are selected hdaView.on( 'selected', function( hdaView ){ var id = hdaView.model.get( 'id' ); @@ -847,88 +276,6 @@ historyView.selectedHdaIds = _.without( historyView.selectedHdaIds, id ); //console.debug( 'de-selected', historyView.selectedHdaIds ); }); -//TODO: remove? - hdaView.on( 'error', function( model, xhr, options, msg ){ - historyView.errorHandler( model, xhr, options, msg ); - }); - }, - - /** If this hda is deleted and we're not showing deleted hdas, remove the view - * @param {HistoryDataAssociation} the hda to check - */ - handleHdaDeletionChange : function( hda ){ - if( hda.get( 'deleted' ) && !this.storage.get( 'show_deleted' ) ){ - this.removeHdaView( this.hdaViews[ hda.id ] ); - } // otherwise, the hdaView rendering should handle it - }, - - /** If this hda is hidden and we're not showing hidden hdas, remove the view - * @param {HistoryDataAssociation} the hda to check - */ - handleHdaVisibleChange : function( hda ){ - if( hda.hidden() && !this.storage.get( 'show_hidden' ) ){ - this.removeHdaView( this.hdaViews[ hda.id ] ); - } // otherwise, the hdaView rendering should handle it - }, - - /** Remove a view from the panel and if the panel is now empty, re-render - * @param {Int} the id of the hdaView to remove - */ - removeHdaView : function( hdaView ){ - if( !hdaView ){ return; } - - var panel = this; - hdaView.$el.fadeOut( panel.fxSpeed, function(){ - hdaView.off(); - hdaView.remove(); - delete panel.hdaViews[ hdaView.model.id ]; - if( _.isEmpty( panel.hdaViews ) ){ - panel.$el.find( panel.emptyMsgSelector ).fadeIn( panel.fxSpeed, function(){ - panel.trigger( 'empty-history', panel ); - }); - } - }); - }, - - /** Set up/render a view for each HDA to be shown, init with model and listeners. - * HDA views are cached to the map this.hdaViews (using the model.id as key). - * @param {jQuery} $whereTo what dom element to prepend the HDA views to - * @returns the number of visible hda views - */ - renderHdas : function( $whereTo ){ - $whereTo = $whereTo || this.$el; - var historyView = this, - newHdaViews = {}, - $datasetsList = $whereTo.find( this.datasetsSelector ), - // only render the shown hdas - //TODO: switch to more general filtered pattern - visibleHdas = this.model.hdas.getVisible( - this.storage.get( 'show_deleted' ), - this.storage.get( 'show_hidden' ), - this.filters - ); - //console.debug( 'renderHdas, visibleHdas:', visibleHdas, $whereTo ); - $datasetsList.empty(); - - if( visibleHdas.length ){ - visibleHdas.each( function( hda ){ - // render it (NOTE: reverse order, newest on top (prepend)) - var hdaId = hda.get( 'id' ), - hdaView = historyView.createHdaView( hda ); - newHdaViews[ hdaId ] = hdaView; - if( _.contains( historyView.selectedHdaIds, hdaId ) ){ - hdaView.selected = true; - } - $datasetsList.prepend( hdaView.render().$el ); - }); - $whereTo.find( this.emptyMsgSelector ).hide(); - - } else { - //console.debug( 'emptyMsg:', $whereTo.find( this.emptyMsgSelector ) ) - $whereTo.find( this.emptyMsgSelector ).show(); - } - this.hdaViews = newHdaViews; - return this.hdaViews; }, /** toggle the visibility of each hdaView's tagsEditor applying all the args sent to this function */ @@ -951,149 +298,41 @@ }); }, + /** Remove a view from the panel and if the panel is now empty, re-render + * @param {Int} the id of the hdaView to remove + */ + removeHdaView : function( hdaView ){ + if( !hdaView ){ return; } + + var panel = this; + hdaView.$el.fadeOut( panel.fxSpeed, function(){ + hdaView.off(); + hdaView.remove(); + delete panel.hdaViews[ hdaView.model.id ]; + if( _.isEmpty( panel.hdaViews ) ){ + panel.$el.find( panel.emptyMsgSelector ).fadeIn( panel.fxSpeed, function(){ + panel.trigger( 'empty-history', panel ); + }); + } + }); + }, + // ------------------------------------------------------------------------ panel events /** event map */ - events : { - // allow (error) messages to be clicked away - //TODO: switch to common close (X) idiom - 'click .message-container' : 'clearMessages', - - 'click .history-search-btn' : 'toggleSearchControls', + events : _.extend( _.clone( readonlyPanel.ReadOnlyHistoryPanel.prototype.events ), { 'click .history-select-btn' : function( e ){ this.toggleSelectors( this.fxSpeed ); }, - 'click .history-select-all-datasets-btn' : 'selectAllDatasets', 'click .history-deselect-all-datasets-btn' : 'deselectAllDatasets' - }, + }), /** Update the history size display (curr. upper right of panel). */ updateHistoryDiskSize : function(){ this.$el.find( '.history-size' ).text( this.model.get( 'nice_size' ) ); }, - - /** Collapse all hda bodies and clear expandedHdas in the storage - */ - collapseAllHdaBodies : function(){ - _.each( this.hdaViews, function( item ){ - item.toggleBodyVisibility( null, false ); - }); - this.storage.set( 'expandedHdas', {} ); - }, - - /** Handle the user toggling the deleted visibility by: - * (1) storing the new value in the persistent storage - * (2) re-rendering the history - * @returns {Boolean} new show_deleted setting - */ - toggleShowDeleted : function(){ - this.storage.set( 'show_deleted', !this.storage.get( 'show_deleted' ) ); - this.renderHdas(); - return this.storage.get( 'show_deleted' ); - }, - - /** Handle the user toggling the deleted visibility by: - * (1) storing the new value in the persistent storage - * (2) re-rendering the history - * @returns {Boolean} new show_hidden setting - */ - toggleShowHidden : function(){ - this.storage.set( 'show_hidden', !this.storage.get( 'show_hidden' ) ); - this.renderHdas(); - return this.storage.get( 'show_hidden' ); - }, - - // ........................................................................ filters - /** render a search input for filtering datasets shown - * (see the search section in the HDA model for implementation of the actual searching) - * return will start the search - * esc will clear the search - * clicking the clear button will clear the search - * uses searchInput in ui.js - */ - setUpSearchInput : function( $where ){ - var panel = this, - inputSelector = '.history-search-input'; - - function onSearch( searchFor ){ - //console.debug( 'onSearch', searchFor, panel ); - panel.searchFor = searchFor; - panel.filters = [ function( hda ){ return hda.matchesAll( panel.searchFor ); } ]; - panel.trigger( 'search:searching', searchFor, panel ); - panel.renderHdas(); - } - function onFirstSearch( searchFor ){ - //console.debug( 'onSearch', searchFor, panel ); - if( panel.model.hdas.haveDetails() ){ - onSearch( searchFor ); - return; - } - panel.$el.find( inputSelector ).searchInput( 'toggle-loading' ); - panel.model.hdas.fetchAllDetails({ silent: true }) - .always( function(){ - panel.$el.find( inputSelector ).searchInput( 'toggle-loading' ); - }) - .done( function(){ - onSearch( searchFor ); - }); - } - function onSearchClear(){ - //console.debug( 'onSearchClear', panel ); - panel.searchFor = ''; - panel.filters = []; - panel.trigger( 'search:clear', panel ); - panel.renderHdas(); - } - $where.searchInput({ - initialVal : panel.searchFor, - name : 'history-search', - placeholder : 'search datasets', - classes : 'history-search', - onfirstsearch : onFirstSearch, - onsearch : onSearch, - onclear : onSearchClear - }); - return $where; - }, -//TODO: to hidden/shown plugin - showSearchControls : function( speed ){ - speed = ( speed === undefined )?( this.fxSpeed ):( speed ); - var panel = this, - $searchControls = this.$el.find( '.history-search-controls' ), - $input = $searchControls.find( '.history-search-input' ); - // if it hasn't been rendered - do it now - if( !$input.children().size() ){ - this.setUpSearchInput( $input ); - //$searchControls.append( faIconButton({ - // title : _l( 'More search options' ), - // classes : 'history-search-advanced', - // faIcon : 'fa-ellipsis-horizontal' - //}) ); - } - // then slide open, focusing on the input, and persisting the setting when it's done - $searchControls.slideDown( speed, function(){ - $( this ).find( 'input' ).focus(); - panel.preferences.set( 'searching', true ); - }); - }, - hideSearchControls : function(){ - speed = ( speed === undefined )?( this.fxSpeed ):( speed ); - var panel = this; - this.$el.find( '.history-search-controls' ).slideUp( speed, function(){ - panel.preferences.set( 'searching', false ); - }); - }, - - /** toggle showing/hiding the search controls (rendering first on the initial show) */ - toggleSearchControls : function( eventOrSpeed ){ - speed = ( jQuery.type( eventOrSpeed ) === 'number' )?( eventOrSpeed ):( this.fxSpeed ); - if( this.$el.find( '.history-search-controls' ).is( ':visible' ) ){ - this.hideSearchControls( speed ); - } else { - this.showSearchControls( speed ); - } - }, // ........................................................................ multi-select of hdas + /** show selectors on all visible hdas and associated controls */ showSelectors : function( speed ){ this.selecting = true; this.$el.find( '.history-dataset-actions' ).slideDown( speed ); @@ -1103,6 +342,7 @@ this.selectedHdaIds = []; }, + /** hide selectors on all visible hdas and associated controls */ hideSelectors : function( speed ){ this.selecting = false; this.$el.find( '.history-dataset-actions' ).slideUp( speed ); @@ -1112,6 +352,7 @@ this.selectedHdaIds = []; }, + /** show or hide selectors on all visible hdas and associated controls */ toggleSelectors : function( speed ){ if( !this.selecting ){ this.showSelectors( speed ); @@ -1120,245 +361,36 @@ } }, + /** select all visible hdas */ selectAllDatasets : function( event ){ _.each( this.hdaViews, function( view ){ view.select( event ); }); }, + /** deselect all visible hdas */ deselectAllDatasets : function( event ){ _.each( this.hdaViews, function( view ){ view.deselect( event ); }); }, + /** return an array of all currently selected hdas */ getSelectedHdaViews : function(){ return _.filter( this.hdaViews, function( v ){ return v.selected; }); }, + /** return an HdaCollection of the models of all currenly selected hdas */ getSelectedHdaCollection : function(){ return new hdaModel.HDACollection( _.map( this.getSelectedHdaViews(), function( hdaView ){ return hdaView.model; }), { historyId: this.model.id }); }, - // ........................................................................ loading indicator - /** hide the panel and display a loading indicator (in the panel's parent) when history model's are switched */ - showLoadingIndicator : function( msg, speed, callback ){ - speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); - if( !this.indicator ){ - this.indicator = new LoadingIndicator( this.$el, this.$el.parent() ); - } - if( !this.$el.is( ':visible' ) ){ - this.indicator.show( 0, callback ); - } else { - this.$el.fadeOut( speed ); - this.indicator.show( msg, speed, callback ); - } - }, - - /** hide the loading indicator */ - hideLoadingIndicator : function( speed, callback ){ - speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); - if( this.indicator ){ - this.indicator.hide( speed, callback ); - } - }, - - // ........................................................................ (error) messages - /** Display a message in the top of the panel. - * @param {String} type type of message ('done', 'error', 'warning') - * @param {String} msg the message to display - */ - displayMessage : function( type, msg, details ){ - //precondition: msgContainer must have been rendered even if there's no model - var panel = this; - //console.debug( 'displayMessage', type, msg, details ); - - this.scrollToTop(); - var $msgContainer = this.$el.find( this.msgsSelector ), - $msg = $( '<div/>' ).addClass( type + 'message' ).html( msg ); - //console.debug( ' ', $msgContainer ); - - if( !_.isEmpty( details ) ){ - var $detailsLink = $( '<a href="javascript:void(0)">Details</a>' ) - .click( function(){ - Galaxy.modal.show( panel.messageToModalOptions( type, msg, details ) ); - return false; - }); - $msg.append( ' ', $detailsLink ); - } - return $msgContainer.html( $msg ); - }, - - /** convert msg and details into modal options usable by Galaxy.modal */ - messageToModalOptions : function( type, msg, details ){ - // only error is fleshed out here - var panel = this, - $modalBody = $( '<div/>' ), - options = { title: 'Details' }; - - //TODO: to some util library - function objToTable( obj ){ - obj = _.omit( obj, _.functions( obj ) ); - return [ - '<table>', - _.map( obj, function( val, key ){ - val = ( _.isObject( val ) )?( objToTable( val ) ):( val ); - return '<tr><td style="vertical-align: top; color: grey">' + key + '</td>' - + '<td style="padding-left: 8px">' + val + '</td></tr>'; - }).join( '' ), - '</table>' - ].join( '' ); - } - - if( _.isObject( details ) ){ - options.body = $modalBody.append( objToTable( details ) ); - - } else { - options.body = $modalBody.html( details ); - } - options.buttons = { - 'Ok': function(){ - Galaxy.modal.hide(); - panel.clearMessages(); - } - //TODO: if( type === 'error' ){ options.buttons[ 'Report this error' ] = function(){} } - }; - return options; - }, - - /** Remove all messages from the panel. - */ - clearMessages : function(){ - var $msgContainer = this.$el.find( this.msgsSelector ); - $msgContainer.empty(); - }, - - // ........................................................................ scrolling - /** get the current scroll position of the panel in its parent */ - scrollPosition : function(){ - return this.$el.parent().scrollTop(); - }, - - /** set the current scroll position of the panel in its parent */ - scrollTo : function( pos ){ - this.$el.parent().scrollTop( pos ); - }, - - /** Scrolls the panel to the top. - * @returns {HistoryPanel} the panel - */ - scrollToTop : function(){ - this.$el.parent().scrollTop( 0 ); - return this; - }, - - /** Scrolls the panel (the enclosing container - in gen., the page) so that some object - * is displayed in the vertical middle. - * NOTE: if no size is given the panel will scroll to objTop (putting it at the top). - * @param {Number} objTop the top offset of the object to view - * @param {Number} objSize the size of the object to view - * @returns {HistoryPanel} the panel - */ - scrollIntoView : function( where, size ){ - if( !size ){ - this.$el.parent().parent().scrollTop( where ); - return this; - } - // otherwise, place the object in the vertical middle - var viewport = window, - panelContainer = this.$el.parent().parent(), - containerHeight = $( viewport ).innerHeight(), - middleOffset = ( containerHeight / 2 ) - ( size / 2 ); - - $( panelContainer ).scrollTop( where - middleOffset ); - return this; - }, - - /** Scrolls the panel to show the HDA with the given id. - * @param {String} id the id of HDA to scroll into view - * @returns {HistoryPanel} the panel - */ - scrollToId : function( id ){ - // do nothing if id not found - if( ( !id ) || ( !this.hdaViews[ id ] ) ){ - return this; - } - var $viewEl = this.hdaViews[ id ].$el; - this.scrollIntoView( $viewEl.offset().top, $viewEl.outerHeight() ); - return this; - }, - - /** Scrolls the panel to show the HDA with the given hid. - * @param {Integer} hid the hid of HDA to scroll into view - * @returns {HistoryPanel} the panel - */ - scrollToHid : function( hid ){ - var hda = this.model.hdas.getByHid( hid ); - // do nothing if hid not found - if( !hda ){ return this; } - return this.scrollToId( hda.id ); - }, - - // ........................................................................ external objects/MVC - //TODO: remove quota meter from panel and remove this - /** add listeners to an external quota meter (mvc/user/user-quotameter.js) */ - connectToQuotaMeter : function( quotaMeter ){ - if( !quotaMeter ){ - return this; - } - // show/hide the 'over quota message' in the history when the meter tells it to - this.listenTo( quotaMeter, 'quota:over', this.showQuotaMessage ); - this.listenTo( quotaMeter, 'quota:under', this.hideQuotaMessage ); - - // having to add this to handle re-render of hview while overquota (the above do not fire) - this.on( 'rendered rendered:initial', function(){ - if( quotaMeter && quotaMeter.isOverQuota() ){ - this.showQuotaMessage(); - } - }); - return this; - }, - -//TODO: this seems more like a per user message than a history message; IOW, this doesn't belong here - /** Show the over quota message (which happens to be in the history panel). - */ - showQuotaMessage : function(){ - var msg = this.$el.find( '.quota-message' ); - //this.log( this + ' showing quota message:', msg, userData ); - if( msg.is( ':hidden' ) ){ msg.slideDown( this.fxSpeed ); } - }, - -//TODO: this seems more like a per user message than a history message - /** Hide the over quota message (which happens to be in the history panel). - */ - hideQuotaMessage : function(){ - var msg = this.$el.find( '.quota-message' ); - //this.log( this + ' hiding quota message:', msg, userData ); - if( !msg.is( ':hidden' ) ){ msg.slideUp( this.fxSpeed ); } - }, - -//TODO: move show_deleted/hidden into panel from opt menu and remove this - /** add listeners to an external options menu (templates/webapps/galaxy/root/index.mako) */ - connectToOptionsMenu : function( optionsMenu ){ - if( !optionsMenu ){ - return this; - } - // set a visible indication in the popupmenu for show_hidden/deleted based on the currHistoryPanel's settings - this.on( 'new-storage', function( storage, panel ){ - if( optionsMenu && storage ){ - optionsMenu.findItemByHtml( _l( 'Include Deleted Datasets' ) ).checked = storage.get( 'show_deleted' ); - optionsMenu.findItemByHtml( _l( 'Include Hidden Datasets' ) ).checked = storage.get( 'show_hidden' ); - } - }); - return this; - }, - - /** Return a string rep of the history - */ + // ........................................................................ misc + /** Return a string rep of the history */ toString : function(){ return 'HistoryPanel(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')'; } @@ -1372,6 +404,6 @@ //============================================================================== return { - HistoryPanel : HistoryPanel + HistoryPanel : HistoryPanel }; }); This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/82d6ee82d5d4/ Changeset: 82d6ee82d5d4 User: carlfeberhard Date: 2014-02-18 21:12:31 Summary: merge Affected #: 1 file diff -r 33812bcdc52393bf179dd501b4334be4ec4e97a7 -r 82d6ee82d5d4714eefdbce041f6c983a806a58d7 templates/webapps/galaxy/mobile/history/detail.mako --- a/templates/webapps/galaxy/mobile/history/detail.mako +++ b/templates/webapps/galaxy/mobile/history/detail.mako @@ -12,7 +12,7 @@ if data.state in ['no state','',None]: data_state = "queued" else: - data_state = data.state + data_state = str( data.state ) %><li id="historyItemContainer-${data.id}"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for server error caused by unicode substitution in url_for.
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e9d3248c6fc3/ Changeset: e9d3248c6fc3 User: dan Date: 2014-02-18 21:09:46 Summary: Fix for server error caused by unicode substitution in url_for. Affected #: 1 file diff -r 26e37f6af3a8a090d9d6e923fa3e90acb0e64572 -r e9d3248c6fc312f8c7671a8e1233265c4ff0a0b1 templates/webapps/galaxy/mobile/history/detail.mako --- a/templates/webapps/galaxy/mobile/history/detail.mako +++ b/templates/webapps/galaxy/mobile/history/detail.mako @@ -12,7 +12,7 @@ if data.state in ['no state','',None]: data_state = "queued" else: - data_state = data.state + data_state = str( data.state ) %><li id="historyItemContainer-${data.id}"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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